From e53deda954a3fa99a20f804a0e0a7928fc6be9a9 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Mon, 5 Mar 2018 22:50:28 +0000
Subject: update Correlation Scatterplot

---
 .../wqflask/static/new/javascript/draw_corr_scatterplot-2.js | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
index bf0a14e6..cfde6f09 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
@@ -200,23 +200,21 @@ function saveassvg_srcs() {
 drawg();
 srdrawg();
 
-
-
 $(".chartupdate").change(function () {
     chartupdate();
 });
 
 $(".chartupdatewh").change(function () {
     chartupdatewh();
+    chartupdate();
 });
 
 $(".chartupdatedata").change(function () {
     chartupdatedata();
+    chartupdate();
 });
 
 $(document).ready(function(){
-    //chartupdate();
-//chartupdatewh();
-chartupdatedata();
-//chartupdate();
-});
\ No newline at end of file
+    chartupdatedata();
+    chartupdate();
+});
-- 
cgit v1.2.3


From a3423b836a947eaa41e18077530587d2687944d4 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Mon, 5 Mar 2018 23:03:25 +0000
Subject: rename draw_corr_scatterplot-2.js to draw_corr_scatterplot.js

---
 .../new/javascript/draw_corr_scatterplot-2.js      | 220 -------------------
 .../static/new/javascript/draw_corr_scatterplot.js | 235 ++++++++++++++++++---
 2 files changed, 204 insertions(+), 251 deletions(-)
 delete mode 100644 wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js

diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
deleted file mode 100644
index cfde6f09..00000000
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js
+++ /dev/null
@@ -1,220 +0,0 @@
-var chart;
-var srchart;
-
-function drawg() {
-    //
-    chart = nv.models.scatterChart();
-    //
-    chart.showLegend(false);
-    chart.duration(300);
-    chart.color(d3.scale.category10().range());
-    chart.pointRange([0, 400]);
-    chart.pointDomain([0, 10]);
-    //
-    chart.xAxis.axisLabel(js_data.trait_1);
-    chart.xAxis.axisLabelDistance(11);
-    chart.yAxis.axisLabel(js_data.trait_2);
-    chart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.data[0]);
-    xmax = d3.max(js_data.data[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.data[1]);
-    ymax = d3.max(js_data.data[1]);
-    yrange = ymax - ymin;
-    chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
-    chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
-    chart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    chart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
-}
-
-function srdrawg() {
-    //
-    srchart = nv.models.scatterChart();
-    //
-    srchart.showLegend(false);
-    srchart.duration(300);
-    srchart.color(d3.scale.category10().range());
-    srchart.pointRange([0, 400]);
-    srchart.pointDomain([0, 10]);
-    //
-    srchart.xAxis.axisLabel(js_data.trait_1);
-    srchart.xAxis.axisLabelDistance(11);
-    srchart.yAxis.axisLabel(js_data.trait_2);
-    srchart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.rdata[0]);
-    xmax = d3.max(js_data.rdata[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.rdata[1]);
-    ymax = d3.max(js_data.rdata[1]);
-    yrange = ymax - ymin;
-    srchart.xDomain([0, xmax + xrange/10]);
-    srchart.yDomain([0, ymax + yrange/10]);
-    srchart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    srchart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    srchart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
-}
-
-function tiptext(obj) {
-    return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>';
-}
-
-function getdata(size, shape) {
-    var data = [];
-    data.push({
-            values: [],
-            slope: js_data.slope,
-            intercept: js_data.intercept
-        });
-    for (j = 0; j < js_data.data[0].length; j++) {
-        data[0].values.push({
-            x: js_data.data[0][j],
-            y: js_data.data[1][j],
-            name: js_data.indIDs[j],
-            size: size,
-            shape: shape
-        });
-    }
-    return data;
-}
-
-function srgetdata(size, shape) {
-    var data = [];
-    data.push({
-            values: [],
-            slope: js_data.srslope,
-            intercept: js_data.srintercept
-        });
-    for (j = 0; j < js_data.rdata[0].length; j++) {
-        data[0].values.push({
-            x: js_data.rdata[0][j],
-            y: js_data.rdata[1][j],
-            name: js_data.indIDs[j],
-            size: size,
-            shape: shape
-        });
-    }
-    return data;
-}
-    
-function checkformat(range) {
-    cell = range / 10.0;
-    if (cell >= 1) {
-        return ",r";
-    } else {
-        cell = -Math.log(cell);
-        n = cell.toString().split(".")[0].length;
-        return ",.0" + n + "f";
-    }
-}
-
-function chartupdate() {
-    //
-    var labelcolor = $("#labelcolor").val();
-    $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor);
-    $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor);
-    //
-    var labelfont = $("#labelfont").val();
-    $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont);
-    $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont);
-    //
-    var numbercolor = $("#numbercolor").val();
-    $("g.tick text").css("fill", numbercolor);
-    //
-    var numberfont = $("#numberfont").val();
-    $("g.tick text").css("font-size", numberfont);
-    //
-    var axiscolor = $("#axiscolor").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor);
-    $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor);
-    //
-    var axiswidth = $("#axiswidth").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth);
-    $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth);
-    //
-    var linecolor = $("#linecolor").val();
-    $("line.nv-regLine").css("stroke", linecolor);
-    //
-    var linewidth = $("#linewidth").val();
-    $("line.nv-regLine").css("stroke-width", linewidth);
-    //
-    var markcolor = $("#markcolor").val();
-    $(".nvd3 g path").css("fill", markcolor);
-}
-
-function chartupdatewh() {
-    //
-    var width = $("#width").val();
-    $("#scatterplot2 svg").css("width", width);
-    $("#srscatterplot2 svg").css("width", width);
-    //
-    var height = $("#height").val();
-    $("#scatterplot2 svg").css("height", height);
-    $("#srscatterplot2 svg").css("height", height);
-    //
-    window.dispatchEvent(new Event('resize'));
-}
-
-function chartupdatedata() {
-    //
-    var size = $("#marksize").val();
-    var shape = $("#markshape").val();
-    //
-    d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart);
-    d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
-    nv.utils.windowResize(chart.update);
-    nv.utils.windowResize(srchart.update);
-}
-
-function savesvg(svgEl, name) {
-    svgEl.setAttribute("xmlns", "http://www.w3.org/2000/svg");
-    var svgData = svgEl.outerHTML;
-    var preface = '<?xml version="1.0" standalone="no"?>\r\n';
-    preface += '<?xml-stylesheet type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css"?>\r\n';
-    var svgBlob = new Blob([preface, svgData], {type:"image/svg+xml;charset=utf-8"});
-    var svgUrl = URL.createObjectURL(svgBlob);
-    var downloadLink = document.createElement("a");
-    downloadLink.href = svgUrl;
-    downloadLink.download = name;
-    document.body.appendChild(downloadLink);
-    downloadLink.click();
-    document.body.removeChild(downloadLink);
-}
-
-function saveassvg_pcs() {
-    savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg");
-}
-
-function saveassvg_srcs() {
-    savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
-}
-
-drawg();
-srdrawg();
-
-$(".chartupdate").change(function () {
-    chartupdate();
-});
-
-$(".chartupdatewh").change(function () {
-    chartupdatewh();
-    chartupdate();
-});
-
-$(".chartupdatedata").change(function () {
-    chartupdatedata();
-    chartupdate();
-});
-
-$(document).ready(function(){
-    chartupdatedata();
-    chartupdate();
-});
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index 28534709..cfde6f09 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,47 +1,220 @@
-// Generated by CoffeeScript 1.8.0
-var data, h, halfh, halfw, indID, intercept, margin, mychart, slope, totalh, totalw, w;
+var chart;
+var srchart;
 
-h = 600;
+function drawg() {
+    //
+    chart = nv.models.scatterChart();
+    //
+    chart.showLegend(false);
+    chart.duration(300);
+    chart.color(d3.scale.category10().range());
+    chart.pointRange([0, 400]);
+    chart.pointDomain([0, 10]);
+    //
+    chart.xAxis.axisLabel(js_data.trait_1);
+    chart.xAxis.axisLabelDistance(11);
+    chart.yAxis.axisLabel(js_data.trait_2);
+    chart.yAxis.axisLabelDistance(11);
+    //
+    xmin = d3.min(js_data.data[0]);
+    xmax = d3.max(js_data.data[0]);
+    xrange = xmax - xmin;
+    ymin = d3.min(js_data.data[1]);
+    ymax = d3.max(js_data.data[1]);
+    yrange = ymax - ymin;
+    chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
+    chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
+    chart.xAxis.tickFormat(d3.format(checkformat(xrange)));
+    chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
+    //
+    chart.tooltip.contentGenerator(function (obj) {
+        return tiptext(obj);
+    });
+}
 
-w = 800;
+function srdrawg() {
+    //
+    srchart = nv.models.scatterChart();
+    //
+    srchart.showLegend(false);
+    srchart.duration(300);
+    srchart.color(d3.scale.category10().range());
+    srchart.pointRange([0, 400]);
+    srchart.pointDomain([0, 10]);
+    //
+    srchart.xAxis.axisLabel(js_data.trait_1);
+    srchart.xAxis.axisLabelDistance(11);
+    srchart.yAxis.axisLabel(js_data.trait_2);
+    srchart.yAxis.axisLabelDistance(11);
+    //
+    xmin = d3.min(js_data.rdata[0]);
+    xmax = d3.max(js_data.rdata[0]);
+    xrange = xmax - xmin;
+    ymin = d3.min(js_data.rdata[1]);
+    ymax = d3.max(js_data.rdata[1]);
+    yrange = ymax - ymin;
+    srchart.xDomain([0, xmax + xrange/10]);
+    srchart.yDomain([0, ymax + yrange/10]);
+    srchart.xAxis.tickFormat(d3.format(checkformat(xrange)));
+    srchart.yAxis.tickFormat(d3.format(checkformat(yrange)));
+    //
+    srchart.tooltip.contentGenerator(function (obj) {
+        return tiptext(obj);
+    });
+}
 
-margin = {
-  left: 80,
-  top: 60,
-  right: 40,
-  bottom: 40,
-  inner: 30
-};
+function tiptext(obj) {
+    return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>';
+}
 
-halfh = h + margin.top + margin.bottom;
+function getdata(size, shape) {
+    var data = [];
+    data.push({
+            values: [],
+            slope: js_data.slope,
+            intercept: js_data.intercept
+        });
+    for (j = 0; j < js_data.data[0].length; j++) {
+        data[0].values.push({
+            x: js_data.data[0][j],
+            y: js_data.data[1][j],
+            name: js_data.indIDs[j],
+            size: size,
+            shape: shape
+        });
+    }
+    return data;
+}
 
-totalh = halfh * 2;
+function srgetdata(size, shape) {
+    var data = [];
+    data.push({
+            values: [],
+            slope: js_data.srslope,
+            intercept: js_data.srintercept
+        });
+    for (j = 0; j < js_data.rdata[0].length; j++) {
+        data[0].values.push({
+            x: js_data.rdata[0][j],
+            y: js_data.rdata[1][j],
+            name: js_data.indIDs[j],
+            size: size,
+            shape: shape
+        });
+    }
+    return data;
+}
+    
+function checkformat(range) {
+    cell = range / 10.0;
+    if (cell >= 1) {
+        return ",r";
+    } else {
+        cell = -Math.log(cell);
+        n = cell.toString().split(".")[0].length;
+        return ",.0" + n + "f";
+    }
+}
 
-halfw = w + margin.left + margin.right;
+function chartupdate() {
+    //
+    var labelcolor = $("#labelcolor").val();
+    $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor);
+    $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor);
+    //
+    var labelfont = $("#labelfont").val();
+    $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont);
+    $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont);
+    //
+    var numbercolor = $("#numbercolor").val();
+    $("g.tick text").css("fill", numbercolor);
+    //
+    var numberfont = $("#numberfont").val();
+    $("g.tick text").css("font-size", numberfont);
+    //
+    var axiscolor = $("#axiscolor").val();
+    $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor);
+    $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor);
+    //
+    var axiswidth = $("#axiswidth").val();
+    $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth);
+    $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth);
+    //
+    var linecolor = $("#linecolor").val();
+    $("line.nv-regLine").css("stroke", linecolor);
+    //
+    var linewidth = $("#linewidth").val();
+    $("line.nv-regLine").css("stroke-width", linewidth);
+    //
+    var markcolor = $("#markcolor").val();
+    $(".nvd3 g path").css("fill", markcolor);
+}
 
-totalw = halfw * 2;
+function chartupdatewh() {
+    //
+    var width = $("#width").val();
+    $("#scatterplot2 svg").css("width", width);
+    $("#srscatterplot2 svg").css("width", width);
+    //
+    var height = $("#height").val();
+    $("#scatterplot2 svg").css("height", height);
+    $("#srscatterplot2 svg").css("height", height);
+    //
+    window.dispatchEvent(new Event('resize'));
+}
 
-mychart = scatterplot().xvar(0).yvar(1).xlab(js_data.trait_1).ylab(js_data.trait_2).height(h).width(w).margin(margin);
+function chartupdatedata() {
+    //
+    var size = $("#marksize").val();
+    var shape = $("#markshape").val();
+    //
+    d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart);
+    d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
+    nv.utils.windowResize(chart.update);
+    nv.utils.windowResize(srchart.update);
+}
 
-data = js_data.data;
+function savesvg(svgEl, name) {
+    svgEl.setAttribute("xmlns", "http://www.w3.org/2000/svg");
+    var svgData = svgEl.outerHTML;
+    var preface = '<?xml version="1.0" standalone="no"?>\r\n';
+    preface += '<?xml-stylesheet type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css"?>\r\n';
+    var svgBlob = new Blob([preface, svgData], {type:"image/svg+xml;charset=utf-8"});
+    var svgUrl = URL.createObjectURL(svgBlob);
+    var downloadLink = document.createElement("a");
+    downloadLink.href = svgUrl;
+    downloadLink.download = name;
+    document.body.appendChild(downloadLink);
+    downloadLink.click();
+    document.body.removeChild(downloadLink);
+}
 
-indID = js_data.indIDs;
+function saveassvg_pcs() {
+    savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg");
+}
 
-slope = js_data.slope;
+function saveassvg_srcs() {
+    savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
+}
 
-intercept = js_data.intercept;
+drawg();
+srdrawg();
 
-console.log("THE DATA IS:", data);
+$(".chartupdate").change(function () {
+    chartupdate();
+});
+
+$(".chartupdatewh").change(function () {
+    chartupdatewh();
+    chartupdate();
+});
 
-d3.select("div#chart1").datum({
-  data: data,
-  indID: indID,
-  slope: slope,
-  intercept: intercept
-}).call(mychart);
+$(".chartupdatedata").change(function () {
+    chartupdatedata();
+    chartupdate();
+});
 
-mychart.pointsSelect().on("mouseover", function(d) {
-  return d3.select(this).attr("r", mychart.pointsize() * 3);
-}).on("mouseout", function(d) {
-  return d3.select(this).attr("r", mychart.pointsize());
+$(document).ready(function(){
+    chartupdatedata();
+    chartupdate();
 });
-- 
cgit v1.2.3


From 178102c304e5ad1da2af5b2ab0af2484edb8a609 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 19 Mar 2018 17:08:05 +0300
Subject: * Add mapping tests. Fix link-checker tests.

* Add tests for the R/qtl and CIM mapping tools.
* Fix tests for in-page links.
---
 test/requests/link_checker.py  | 16 ++++++++++++----
 test/requests/mapping_tests.py | 35 ++++++++++++++++++++++-------------
 2 files changed, 34 insertions(+), 17 deletions(-)

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 256bf6ef..a75327f0 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -16,6 +16,10 @@ def is_internal_link(link):
     pattern = re.compile("^/.*")
     return pattern.match(link)
 
+def is_in_page_link(link):
+    pattern = re.compile("^#.*")
+    return pattern.match(link)
+
 def get_links(doc):
     return filter(
         lambda x: not (
@@ -32,17 +36,21 @@ def verify_link(link):
         else:
             print("ERROR: link `"+link+"` failed with status "
                   , result.status_code)
-    except ConnectionError as ex:
-        print("ERROR: ", link, ex)
+    except Exception as ex:
+        print("ERROR: ("+link+")", ex)
 
 def check_page(host, start_url):
     print("")
     print("Checking links in page `"+start_url+"`")
     doc = parse(start_url).getroot()
     links = get_links(doc)
+    in_page_links = filter(is_in_page_link, links)
     internal_links = filter(is_internal_link, links)
-    external_links = filter(lambda x: not is_internal_link(x), links)
-    external_links.append("http://somenon-existentsite.brr")
+    external_links = filter(lambda x: not (is_internal_link(x) or is_in_page_link(x)), links)
+
+    for link in in_page_links:
+        verify_link(start_url+link)
+
     for link in internal_links:
         verify_link(host+link)
 
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
index fd20df11..8eb19de7 100644
--- a/test/requests/mapping_tests.py
+++ b/test/requests/mapping_tests.py
@@ -1,17 +1,10 @@
 from __future__ import print_function
 import re
+import copy
 import json
 import requests
 from lxml.html import fromstring
 
-def get_data(list_item):
-    try:
-        value = list_item[1]
-    except:
-        value = None
-    #print("list_item:", list_item, "==>", value)
-    return value
-
 def load_data_from_file():
     filename = "../test/data/input/mapping/1435395_s_at_HC_M2_0606_P.json"
     file_handle = open(filename, "r")
@@ -19,6 +12,8 @@ def load_data_from_file():
     return file_data
 
 def check_pylmm_tool_selection(host, data):
+    print("")
+    print("pylmm mapping tool selection")
     data["method"] = "pylmm"
     page = requests.post(host+"/marker_regression", data=data)
     doc = fromstring(page.text)
@@ -27,10 +22,24 @@ def check_pylmm_tool_selection(host, data):
     assert form.fields["value:BXD1"] == "15.034" # Check value in the file
 
 def check_R_qtl_tool_selection(host, data):
-    pass
+    print("")
+    print("R/qtl mapping tool selection")
+    headers = {"Content-Type": "application/x-www-form-urlencoded"}
+    page = requests.post(host+"/marker_regression", data=data, headers=headers)
+    doc = fromstring(page.text)
+    form = doc.forms[1]
+    assert form.fields["dataset"] == "HC_M2_0606_P"
+    assert form.fields["value:BXD1"] == "15.034"
 
 def check_CIM_tool_selection(host, data):
-    pass
+    print("")
+    print("CIM mapping tool selection (using reaper)")
+    data["method"] = "reaper"
+    page = requests.post(host+"/marker_regression", data=data)
+    doc = fromstring(page.text)
+    form = doc.forms[1]
+    assert form.fields["dataset"] == "HC_M2_0606_P"
+    assert form.fields["value:BXD1"] == "15.034"
 
 def check_mapping(args_obj, parser):
     print("")
@@ -38,6 +47,6 @@ def check_mapping(args_obj, parser):
 
     host = args_obj.host
     data = load_data_from_file()
-    check_pylmm_tool_selection(host, data)
-    check_R_qtl_tool_selection(host, data)
-    check_CIM_tool_selection(host, data)
+    check_pylmm_tool_selection(host, copy.deepcopy(data))
+    check_R_qtl_tool_selection(host, copy.deepcopy(data)) ## Why does this fail?
+    check_CIM_tool_selection(host, copy.deepcopy(data))
-- 
cgit v1.2.3


From 883bcc257a38240de7de8888f78bac4406b5d027 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 19 Mar 2018 17:49:39 +0300
Subject: Initialise navigation tests.

* Start working on navigation tests.
---
 test/requests/navigation_tests.py | 15 +++++++++++++++
 test/requests/test-website.py     |  7 ++++---
 2 files changed, 19 insertions(+), 3 deletions(-)
 create mode 100644 test/requests/navigation_tests.py

diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py
new file mode 100644
index 00000000..eda27324
--- /dev/null
+++ b/test/requests/navigation_tests.py
@@ -0,0 +1,15 @@
+from __future__ import print_function
+import re
+import requests
+from lxml.html import parse
+
+def check_navigation(args_obj, parser):
+    print("")
+    print("Checking navigation.")
+
+    host = args_obj.host
+    url = host + "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P"
+    print("URL: ", url)
+    page = requests.get(url)
+    # Page is built by the javascript, hence using requests fails for this.
+    # Investigate use of selenium maybe?
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 2bef6eb1..dbf3b822 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -7,6 +7,7 @@ from __future__ import print_function
 import argparse
 from link_checker import check_links
 from mapping_tests import check_mapping
+from navigation_tests import check_navigation
 from main_web_functionality import check_main_web_functionality
 
 print("Mechanical Rob firing up...")
@@ -57,9 +58,9 @@ parser.add_argument("-m", "--mapping", dest="accumulate"
                     , action="store_const", const=check_mapping, default=print_help
                     , help="Checks for mapping.")
 
-# parser.add_argument("-n", "--navigation", dest="accumulate"
-#                     , action="store_const", const=check_navigation, default=print_help
-#                     , help="Checks for navigation.")
+parser.add_argument("-n", "--navigation", dest="accumulate"
+                    , action="store_const", const=check_navigation, default=print_help
+                    , help="Checks for navigation.")
 
 # parser.add_argument("-s", "--skip-broken", dest="accumulate"
 #                     , action="store_const", const=dummy, default=print_help
-- 
cgit v1.2.3


From a20004e25d0143a14763180359e8266e31f9766f Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Wed, 21 Mar 2018 11:22:48 +0300
Subject: Deactivate navigation tests

* Navigation depends on Javascript to render the elements being tested.
  That would require selenium and its ilk to run such tests, meaning
  such packages would need to be defined for Guix first.
---
 test/requests/test-website.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index dbf3b822..f03c148a 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -58,9 +58,10 @@ parser.add_argument("-m", "--mapping", dest="accumulate"
                     , action="store_const", const=check_mapping, default=print_help
                     , help="Checks for mapping.")
 
-parser.add_argument("-n", "--navigation", dest="accumulate"
-                    , action="store_const", const=check_navigation, default=print_help
-                    , help="Checks for navigation.")
+# Navigation tests deactivated since system relies on Javascript
+# parser.add_argument("-n", "--navigation", dest="accumulate"
+#                     , action="store_const", const=check_navigation, default=print_help
+#                     , help="Checks for navigation.")
 
 # parser.add_argument("-s", "--skip-broken", dest="accumulate"
 #                     , action="store_const", const=dummy, default=print_help
-- 
cgit v1.2.3


From 4c2ce5580a0891d89fc35c48da06d25fb4c8df76 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Thu, 22 Mar 2018 06:09:39 +0300
Subject: Fix 'def' statement

* End the 'def' statement with a colon (:)
* Add an empty line between lines at different indentation levels for
  clarity.
---
 wqflask/base/anon_collection.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
index 8ee73296..dd1aa27f 100644
--- a/wqflask/base/anon_collection.py
+++ b/wqflask/base/anon_collection.py
@@ -1,6 +1,6 @@
 class AnonCollection(TraitCollection):
     
-    def __init__(self, anon_id)
+    def __init__(self, anon_id):
         self.anon_id = anon_id
         self.collection_members = Redis.smembers(self.anon_id)
         print("self.collection_members is:", self.collection_members)
@@ -12,6 +12,7 @@ class AnonCollection(TraitCollection):
         print("traits_to_remove:", traits_to_remove)
         for trait in traits_to_remove:
             Redis.srem(self.anon_id, trait)
+
         members_now = self.collection_members - traits_to_remove
         print("members_now:", members_now)
         print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-- 
cgit v1.2.3


From cfce6d80be4fb38573c37d1943db2687d54cf2fc Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Thu, 22 Mar 2018 06:28:01 +0300
Subject: Change raise statement

* Change the raise statement to use an Exception object rather than
  using a string for compatibility with Python3.
---
 wqflask/utility/svg.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 512bc9e6..db13b9d1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -1029,7 +1029,7 @@ class drawing:
         try:
             xv.feed(svg)
         except:
-            raise "SVG is not well formed, see messages above"
+            raise Exception("SVG is not well formed, see messages above")
         else:
             print "SVG well formed"
 if __name__=='__main__':
-- 
cgit v1.2.3


From e246822f359938be6af7e3f5587dea635ff5f9df Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 4 Apr 2018 17:51:13 +0000
Subject: Changed bar chart y axis range to avoid situation where all variation
 is clustered at the top or bottom

---
 .../wqflask/static/new/javascript/show_trait.js    | 34 ++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 117d8f12..dfdafaf0 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -789,7 +789,41 @@
         type: 'bar'
     };
     root.bar_data = [bar_trace]
+
+    positive_error_vals = []
+    negative_error_vals = []
+    for (i = 0;i < get_sample_vals(sample_lists[0]).length; i++){
+        if (get_sample_errors(sample_lists[0])[i] != undefined) {
+            positive_error_vals.push(get_sample_vals(sample_lists[0])[i] + get_sample_errors(sample_lists[0])[i])
+            negative_error_vals.push(get_sample_vals(sample_lists[0])[i] - get_sample_errors(sample_lists[0])[i])
+        } else {
+            positive_error_vals.push(get_sample_vals(sample_lists[0])[i])
+            negative_error_vals.push(get_sample_vals(sample_lists[0])[i])
+        }
+    }
+
+    // Calculate the y axis cutoff to avoid a situation where all bar variation is clustered at the top of the chart
+    min_y_val = Math.min(...negative_error_vals)
+    max_y_val = Math.max(...positive_error_vals)
+
+    if (min_y_val == 0) {
+        range_bottom = 0;
+    } else {
+        range_top = max_y_val + Math.abs(max_y_val)*0.1
+        range_bottom = min_y_val - Math.abs(min_y_val)*0.1
+        if (min_y_val > 0) {
+            range_bottom = min_y_val - 0.1*Math.abs(min_y_val)
+        } else if (min_y_val < 0) {
+            range_bottom = min_y_val + 0.1*min_y_val
+        } else {
+            range_bottom = 0
+        }
+    }
+
     var layout = {
+        yaxis: {
+            range: [range_bottom, range_top]
+        },
         width: 1200,
         height: 500,
         margin: {
-- 
cgit v1.2.3


From 07c0daa04b2693f55dd69cae43c254ebb5c9a35b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 6 Apr 2018 15:50:29 +0000
Subject: Mapping figure output now gives more accurate information

Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
---
 wqflask/base/data_set.py                           |  147 +-
 wqflask/base/mrna_assay_tissue_data.py             |    1 -
 wqflask/base/species.py                            |   80 +-
 wqflask/base/template.py                           |  123 --
 wqflask/base/trait.py                              |  206 ---
 wqflask/wqflask/do_search.py                       |    1 -
 .../marker_regression/MarkerRegressionPage.py      | 1648 --------------------
 .../marker_regression/marker_regression_gn1.py     |   41 +-
 wqflask/wqflask/show_trait/show_trait_page.py      |  141 --
 wqflask/wqflask/templates/show_trait.html          |   10 -
 10 files changed, 33 insertions(+), 2365 deletions(-)
 delete mode 100644 wqflask/base/template.py
 delete mode 100644 wqflask/wqflask/marker_regression/MarkerRegressionPage.py
 delete mode 100644 wqflask/wqflask/show_trait/show_trait_page.py

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a4eaaa2e..9ca880d0 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -29,7 +29,6 @@ import json
 import gzip
 import cPickle as pickle
 import itertools
-from operator import itemgetter
 
 from redis import Redis
 Redis = Redis()
@@ -316,9 +315,6 @@ class DatasetGroup(object):
 
         return mapping_id, mapping_names
 
-    def get_specified_markers(self, markers = []):
-        self.markers = HumanMarkers(self.name, markers)
-
     def get_markers(self):
         logger.debug("self.species is:", self.species)
 
@@ -449,7 +445,6 @@ def datasets(group_name, this_group = None):
               group_name, webqtlConfig.PUBLICTHRESH,
               "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
 
-    #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
     for dataset_item in the_results:
         tissue_name = dataset_item[0]
         dataset = dataset_item[1]
@@ -457,14 +452,10 @@ def datasets(group_name, this_group = None):
         if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
             dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
         else:
-            dataset_sub_menu = [item[1:] for item in dataset]
-
             tissue_already_exists = False
-            tissue_position = None
             for i, tissue_dict in enumerate(dataset_menu):
                 if tissue_dict['tissue'] == tissue_name:
                     tissue_already_exists = True
-                    tissue_position = i
                     break
 
             if tissue_already_exists:
@@ -719,20 +710,6 @@ class PhenotypeDataSet(DataSet):
         # (Urgently?) Need to write this
         pass
 
-    def get_trait_list(self):
-        query = """
-            select PublishXRef.Id
-            from PublishXRef, PublishFreeze
-            where PublishFreeze.InbredSetId=PublishXRef.InbredSetId
-            and PublishFreeze.Id = {}
-            """.format(escape(str(self.id)))
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-        trait_data = {}
-        for trait in results:
-            trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
-        return trait_data
-
     def get_trait_info(self, trait_list, species = ''):
         for this_trait in trait_list:
 
@@ -746,7 +723,7 @@ class PhenotypeDataSet(DataSet):
             #of the post-publication description
             if this_trait.confidential:
                 this_trait.description_display = ""
-                continue   # for now
+                continue   # for now, because no authorization features
 
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
                         privilege=self.privilege,
@@ -770,9 +747,7 @@ class PhenotypeDataSet(DataSet):
 
             #LRS and its location
             this_trait.LRS_score_repr = "N/A"
-            this_trait.LRS_score_value = 0
             this_trait.LRS_location_repr = "N/A"
-            this_trait.LRS_location_value = 1000000
 
             if this_trait.lrs:
                 query = """
@@ -789,17 +764,7 @@ class PhenotypeDataSet(DataSet):
                         LRS_Chr = result[0]
                         LRS_Mb = result[1]
 
-                        #XZ: LRS_location_value is used for sorting
-                        try:
-                            LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
-                        except:
-                            if LRS_Chr.upper() == 'X':
-                                LRS_location_value = 20*1000 + float(LRS_Mb)
-                            else:
-                                LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
-
                         this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
-                        this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
                         this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
 
     def retrieve_sample_data(self, trait):
@@ -861,40 +826,13 @@ class GenotypeDataSet(DataSet):
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
 
-    def get_trait_list(self):
-        query = """
-            select Geno.Name
-            from Geno, GenoXRef
-            where GenoXRef.GenoId = Geno.Id
-            and GenoFreezeId = {}
-            """.format(escape(str(self.id)))
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-        trait_data = {}
-        for trait in results:
-            trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
-        return trait_data
-
     def get_trait_info(self, trait_list, species=None):
         for this_trait in trait_list:
             if not this_trait.haveinfo:
                 this_trait.retrieveInfo()
 
-            #XZ: trait_location_value is used for sorting
-            trait_location_repr = 'N/A'
-            trait_location_value = 1000000
-
             if this_trait.chr and this_trait.mb:
-                try:
-                    trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
-                except:
-                    if this_trait.chr.upper() == 'X':
-                        trait_location_value = 20*1000 + this_trait.mb
-                    else:
-                        trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
-
                 this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
-                this_trait.location_value = trait_location_value
 
     def retrieve_sample_data(self, trait):
         query = """
@@ -989,20 +927,6 @@ class MrnaAssayDataSet(DataSet):
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
 
-    def get_trait_list_1(self):
-        query = """
-            select ProbeSet.Name
-            from ProbeSet, ProbeSetXRef
-            where ProbeSetXRef.ProbeSetId = ProbeSet.Id
-            and ProbeSetFreezeId = {}
-            """.format(escape(str(self.id)))
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-        trait_data = {}
-        for trait in results:
-            trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
-        return trait_data
-
     def get_trait_info(self, trait_list=None, species=''):
 
         #  Note: setting trait_list to [] is probably not a great idea.
@@ -1034,27 +958,8 @@ class MrnaAssayDataSet(DataSet):
             # Save it for the jinja2 template
             this_trait.description_display = description_display
 
-            #XZ: trait_location_value is used for sorting
-            trait_location_repr = 'N/A'
-            trait_location_value = 1000000
-
             if this_trait.chr and this_trait.mb:
-                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                #This is so we can convert the location to a number used for sorting
-                trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb)
-                #try:
-                #    trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
-                #except ValueError:
-                #    if this_trait.chr.upper() == 'X':
-                #        trait_location_value = 20*1000 + this_trait.mb
-                #    else:
-                #        trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 +
-                #                               this_trait.mb)
-
-                #ZS: Put this in function currently called "convert_location_to_value"
-                this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr,
-                                                                float(this_trait.mb))
-                this_trait.location_value = trait_location_value
+                this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb))
 
             #Get mean expression value
             query = (
@@ -1076,9 +981,7 @@ class MrnaAssayDataSet(DataSet):
 
             #LRS and its location
             this_trait.LRS_score_repr = 'N/A'
-            this_trait.LRS_score_value = 0
             this_trait.LRS_location_repr = 'N/A'
-            this_trait.LRS_location_value = 1000000
 
             #Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
@@ -1093,40 +996,10 @@ class MrnaAssayDataSet(DataSet):
 
                 if result:
                     lrs_chr, lrs_mb = result
-                    #XZ: LRS_location_value is used for sorting
-                    lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
                     this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
-                    this_trait.LRS_score_value = this_trait.lrs
                     this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
 
-
-    def convert_location_to_value(self, chromosome, mb):
-        try:
-            location_value = int(chromosome)*1000 + float(mb)
-        except ValueError:
-            if chromosome.upper() == 'X':
-                location_value = 20*1000 + float(mb)
-            else:
-                location_value = (ord(str(chromosome).upper()[0])*1000 +
-                                  float(mb))
-
-        return location_value
-
-    def get_sequence(self):
-        query = """
-                    SELECT
-                            ProbeSet.BlatSeq
-                    FROM
-                            ProbeSet, ProbeSetFreeze, ProbeSetXRef
-                    WHERE
-                            ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-                            ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
-                            ProbeSet.Name = %s
-                            ProbeSetFreeze.Name = %s
-                """ % (escape(self.name), escape(self.dataset.name))
-        logger.sql(query)
-        results = g.db.execute(query).fetchone()
-        return results[0]
+        return trait_list
 
     def retrieve_sample_data(self, trait):
         query = """
@@ -1150,7 +1023,6 @@ class MrnaAssayDataSet(DataSet):
         #logger.debug("RETRIEVED RESULTS HERE:", results)
         return results
 
-
     def retrieve_genes(self, column_name):
         query = """
                     select ProbeSet.Name, ProbeSet.%s
@@ -1204,19 +1076,6 @@ class TempDataSet(DataSet):
         desc = self.handle_pca(desc)
         return desc
 
-    def get_group(self):
-        query = """
-                    SELECT
-                            InbredSet.Name, InbredSet.Id
-                    FROM
-                            InbredSet, Temp
-                    WHERE
-                            Temp.InbredSetId = InbredSet.Id AND
-                            Temp.Name = "%s"
-            """ % self.name
-        logger.sql(query)
-        self.group, self.group_id = g.db.execute(query).fetchone()
-
     def retrieve_sample_data(self, trait):
         query = """
                 SELECT
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index eb836e6c..53f7c16a 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -18,7 +18,6 @@ class MrnaAssayTissueData(object):
 
     def __init__(self, gene_symbols=None):
         self.gene_symbols = gene_symbols
-        self.have_data = False
         if self.gene_symbols == None:
             self.gene_symbols = []
 
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index ce763fc3..4ac2213c 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -18,19 +18,6 @@ class TheSpecies(object):
         self.dataset = dataset
         #print("self.dataset is:", pf(self.dataset.__dict__))
         self.chromosomes = Chromosomes(self.dataset)
-        self.genome_mb_length = self.chromosomes.get_genome_mb_length()
-
-    #@property
-    #def chromosomes(self):
-    #    chromosomes = [("All", -1)]
-    #
-    #    for counter, genotype in enumerate(self.dataset.group.genotype):
-    #        if len(genotype) > 1:
-    #            chromosomes.append((genotype.name, counter))
-    #
-    #    print("chromosomes is: ", pf(chromosomes))
-    #
-    #    return chromosomes
 
 class IndChromosome(object):
     def __init__(self, name, length):
@@ -42,16 +29,11 @@ class IndChromosome(object):
         """Chromosome length in megabases"""
         return self.length / 1000000
 
-    def set_cm_length(self, genofile_chr):
-        self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
-
-
 class Chromosomes(object):
     def __init__(self, dataset):
         self.dataset = dataset
         self.chromosomes = collections.OrderedDict()
 
-
         query = """
                 Select
                         Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
@@ -64,64 +46,4 @@ class Chromosomes(object):
         results = g.db.execute(query).fetchall()
 
         for item in results:
-            self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
-
-        self.set_mb_graph_interval()
-        #self.get_cm_length_list()
-
-
-    def set_mb_graph_interval(self):
-        """Empirical megabase interval"""
-
-        if self.chromosomes:
-            self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
-        else:
-            self.mb_graph_interval = 1
-
-        #if self.chromosomes:
-        #assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
-        #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
-        #else:
-            #self.mb_graph_interval = 1
-
-
-    def get_genome_mb_length(self):
-        """Gets the sum of each chromosome's length in megabases"""
-
-        return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
-
-
-    def get_genome_cm_length(self):
-        """Gets the sum of each chromosome's length in centimorgans"""
-
-        return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
-
-    def get_cm_length_list(self):
-        """Chromosome length in centimorgans
-
-        Calculates the length in centimorgans by subtracting the centimorgan position
-        of the last marker in a chromosome by the position of the first marker
-
-        """
-
-        self.dataset.group.read_genotype_file()
-
-        self.cm_length_list = []
-
-        for chromosome in self.dataset.group.genotype:
-            self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
-
-        print("self.cm_length_list:", pf(self.cm_length_list))
-
-        assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
-        for counter, chromosome in enumerate(self.chromosomes.values()):
-            chromosome.cm_length = self.cm_length_list[counter]
-            #self.chromosomes[counter].cm_length = item
-
-        for key, value in self.chromosomes.items():
-            print("bread - %s: %s" % (key, pf(vars(value))))
-
-
-# Testing
-#if __name__ == '__main__':
-#    foo = dict(bar=dict(length))
+            self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
\ No newline at end of file
diff --git a/wqflask/base/template.py b/wqflask/base/template.py
deleted file mode 100644
index aa8f90dc..00000000
--- a/wqflask/base/template.py
+++ /dev/null
@@ -1,123 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-template = """
-<?XML VERSION="1.0" ENCODING="UTF-8">
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML>
-<HEAD>
-<TITLE>%s</TITLE>
-
-<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
-<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine">
-<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." >
-<META NAME="author" CONTENT ="GeneNetwork developers" >
-<META NAME="geo.placename" CONTENT ="Memphis, TN" >
-<META NAME="geo.region" CONTENT="US-TN">
-%s
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
-<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" />
-<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
-<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' />
-<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' />
-
-<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script>
-<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
-<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT>
-<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT>
-<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT>
-<script src="/javascript/tabbed_pages.js" type="text/javascript"></script>
-<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script>
-%s
-
-<script type="text/javascript">
-  var _gaq = _gaq || [];
-  _gaq.push(['_setAccount', 'UA-3782271-1']);
-  _gaq.push(['_trackPageview']);
-  (function() {
-    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
-    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
-    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
-  })();
-</script>
-</HEAD>
-<BODY  bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s>
-%s
-<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0>
-        <TBODY>
-        <!-- Start of header -->
-        <TR>
-                %s
-        </TR>
-        <!-- End of header -->
-
-        <!-- Start of body -->
-        <TR>
-                <TD  bgColor=#eeeeee class="solidBorder">
-                <Table width= "100%%" cellSpacing=0 cellPadding=5>
-                <TR>
-                %s
-                </TR>
-                </TABLE>
-                </TD>
-        </TR>
-        <!-- End of body -->
-
-        <!-- Start of footer -->
-        <TR>
-                <TD align=center bgColor=#ddddff class="solidBorder">
-                        <TABLE width="90%%">%s</table>
-                </td>
-        </TR>
-        <!-- End of footer -->
-</TABLE>
-
-<!-- menu script itself. you should not modify this file -->
-<script language="JavaScript" src="/javascript/menu_new.js"></script>
-<!-- items structure. menu hierarchy and links are stored there -->
-<script language="JavaScript" src="/javascript/menu_items.js"></script>
-<!-- files with geometry and styles structures -->
-<script language="JavaScript" src="/javascript/menu_tpl.js"></script>
-<script language="JavaScript">
-        <!--//
-        // Note where menu initialization block is located in HTML document.
-        // Don't try to position menu locating menu initialization block in
-        // some table cell or other HTML element. Always put it before </body>
-        // each menu gets two parameters (see demo files)
-        // 1. items structure
-        // 2. geometry structure
-        new menu (MENU_ITEMS, MENU_POS);
-        // make sure files containing definitions for these variables are linked to the document
-        // if you got some javascript error like "MENU_POS is not defined", then you've made syntax
-        // error in menu_tpl.js file or that file isn't linked properly.
-
-        // also take a look at stylesheets loaded in header in order to set styles
-        //-->
-</script>
-</BODY>
-</HTML>
-"""
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index acc055d8..b71dacf6 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -25,10 +25,6 @@ logger = getLogger(__name__ )
 
 from wqflask import user_manager
 
-def print_mem(stage=""):
-    mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-    print("{}: {}".format(stage, mem/1024))
-
 class GeneralTrait(object):
     """
     Trait class defines a trait in webqtl, can be either Microarray,
@@ -63,9 +59,7 @@ class GeneralTrait(object):
         self.symbol = None
 
         self.LRS_score_repr = "N/A"
-        self.LRS_score_value = 0
         self.LRS_location_repr = "N/A"
-        self.LRS_location_value = 1000000
 
         if kw.get('fullname'):
             name2 = value.split("::")
@@ -82,90 +76,6 @@ class GeneralTrait(object):
             if get_sample_info != False:
                 self = retrieve_sample_data(self, self.dataset)
 
-
-    def get_name(self):
-        stringy = ""
-        if self.dataset and self.name:
-            stringy = "%s::%s" % (self.dataset, self.name)
-            if self.cellid:
-                stringy += "::" + self.cellid
-        else:
-            stringy = self.description
-        return stringy
-
-
-    def get_given_name(self):
-        """
-         when user enter a trait or GN generate a trait, user want show the name
-         not the name that generated by GN randomly, the two follow function are
-         used to give the real name and the database. displayName() will show the
-         database also, getGivenName() just show the name.
-         For other trait, displayName() as same as getName(), getGivenName() as
-         same as self.name
-
-         Hongqiang 11/29/07
-
-        """
-        stringy = self.name
-        if self.dataset and self.name:
-            desc = self.dataset.get_desc()
-            if desc:
-                #desc = self.handle_pca(desc)
-                stringy = desc
-        return stringy
-
-
-    def display_name(self):
-        stringy = ""
-        if self.dataset and self.name:
-            desc = self.dataset.get_desc()
-            #desc = self.handle_pca(desc)
-            if desc:
-                #desc = self.handle_pca(desc)
-                #stringy = desc
-                #if desc.__contains__('PCA'):
-                #    desc = desc[desc.rindex(':')+1:].strip()
-                #else:
-                #    desc = desc[:desc.index('entered')].strip()
-                #desc = self.handle_pca(desc)
-                stringy = "%s::%s" % (self.dataset, desc)
-            else:
-                stringy = "%s::%s" % (self.dataset, self.name)
-                if self.cellid:
-                    stringy += "::" + self.cellid
-        else:
-            stringy = self.description
-
-        return stringy
-
-
-    #def __str__(self):
-    #       #return "%s %s" % (self.getName(), self.group)
-    #       return self.getName()
-    #__str__ = getName
-    #__repr__ = __str__
-
-    def export_data(self, samplelist, the_type="val"):
-        """
-        export data according to samplelist
-        mostly used in calculating correlation
-
-        """
-        result = []
-        for sample in samplelist:
-            if self.data.has_key(sample):
-                if the_type=='val':
-                    result.append(self.data[sample].val)
-                elif the_type=='var':
-                    result.append(self.data[sample].var)
-                elif the_type=='N':
-                    result.append(self.data[sample].N)
-                else:
-                    raise KeyError, `the_type`+' the_type is incorrect.'
-            else:
-                result.append(None)
-        return result
-
     def export_informative(self, include_variance=0):
         """
         export informative sample
@@ -185,19 +95,6 @@ class GeneralTrait(object):
                     sample_aliases.append(sample_data.name2)
         return  samples, vals, the_vars, sample_aliases
 
-
-    @property
-    def name_header_fmt(self):
-        '''Return a human-readable name for use in page header'''
-        if self.dataset.type == 'ProbeSet':
-            return self.symbol
-        elif self.dataset.type == 'Geno':
-            return self.name
-        elif self.dataset.type == 'Publish':
-            return self.post_publication_abbreviation
-        else:
-            return "unnamed"
-
     @property
     def description_fmt(self):
         '''Return a text formated description'''
@@ -252,29 +149,6 @@ class GeneralTrait(object):
             fmt += (' on the minus strand ')
 
         return fmt
-
-# In ProbeSet, there are maybe several annotations match one sequence
-# so we need use sequence(BlatSeq) as the identification, when we update
-# one annotation, we update the others who match the sequence also.
-#
-# Hongqiang Li, 3/3/2008
-def getSequence(trait, dataset_name):
-    dataset = create_dataset(dataset_name)
-     
-    if dataset.type == 'ProbeSet':
-        results = g.db.execute('''
-                       SELECT
-                               ProbeSet.BlatSeq
-                       FROM
-                               ProbeSet, ProbeSetFreeze, ProbeSetXRef
-                       WHERE
-                               ProbeSet.Id=ProbeSetXRef.ProbeSetId and
-                               ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
-                               ProbeSet.Name = %s
-                               ProbeSetFreeze.Name = %s
-               ''', trait.name, dataset.name).fetchone()
-
-        return results[0]        
         
 def retrieve_sample_data(trait, dataset, samplelist=None):
     if samplelist == None:
@@ -293,18 +167,6 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
             if not samplelist or (samplelist and name in samplelist):
                 trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
     return trait
-        
-def convert_location_to_value(chromosome, mb):
-    try:
-        location_value = int(chromosome)*1000 + float(mb)
-    except ValueError:
-        if chromosome.upper() == 'X':
-            location_value = 20*1000 + float(mb)
-        else:
-            location_value = (ord(str(chromosome).upper()[0])*1000 +
-                              float(mb))
-
-    return location_value
 
 @app.route("/trait/get_sample_data")
 def get_sample_data():
@@ -542,38 +404,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             if trait.pubmed_id:
                 trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
 
-
-        trait.homologeneid = None
         if dataset.type == 'ProbeSet' and dataset.group:
-            if trait.geneid:
-                #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
-                #XZ: So I have to test if geneid is number before execute the query.
-                #XZ: The geneid values in database should be cleaned up.
-                #try:
-                #    float(self.geneid)
-                #    geneidIsNumber = True
-                #except ValueError:
-                #    geneidIsNumber = False
-                #if geneidIsNumber:
-                query = """
-                        SELECT
-                                HomologeneId
-                        FROM
-                                Homologene, Species, InbredSet
-                        WHERE
-                                Homologene.GeneId ='%s' AND
-                                InbredSet.Name = '%s' AND
-                                InbredSet.SpeciesId = Species.Id AND
-                                Species.TaxonomyId = Homologene.TaxonomyId
-                        """ % (escape(str(trait.geneid)), escape(dataset.group.name))
-                logger.sql(query)
-                result = g.db.execute(query).fetchone()
-                #else:
-                #    result = None
-
-                if result:
-                    trait.homologeneid = result[0]
-
             description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
             target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
@@ -589,46 +420,19 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             # Save it for the jinja2 template
             trait.description_display = description_display
 
-            #XZ: trait_location_value is used for sorting
             trait.location_repr = 'N/A'
-            trait.location_value = 1000000
-
             if trait.chr and trait.mb:
-                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                #This is so we can convert the location to a number used for sorting
-                trait_location_value = convert_location_to_value(trait.chr, trait.mb)
-                 #try:
-                #    trait_location_value = int(self.chr)*1000 + self.mb
-                #except ValueError:
-                #    if self.chr.upper() == 'X':
-                #        trait_location_value = 20*1000 + self.mb
-                #    else:
-                #        trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
-                #                               self.mb)
-
-                #ZS: Put this in function currently called "convert_location_to_value"
                 trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
-                trait.location_value = trait_location_value
 
         elif dataset.type == "Geno":
             trait.location_repr = 'N/A'
-            trait.location_value = 1000000
-
             if trait.chr and trait.mb:
-                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                #This is so we can convert the location to a number used for sorting
-                trait_location_value = convert_location_to_value(trait.chr, trait.mb)
-
-                #ZS: Put this in function currently called "convert_location_to_value"
                 trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
-                trait.location_value = trait_location_value
 
         if get_qtl_info:
             #LRS and its location
             trait.LRS_score_repr = "N/A"
-            trait.LRS_score_value = 0
             trait.LRS_location_repr = "N/A"
-            trait.LRS_location_value = 1000000
             if dataset.type == 'ProbeSet' and not trait.cellid:
                 query = """
                         SELECT
@@ -699,19 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                     trait.locus = trait.lrs = trait.additive = ""
 
             if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
-                #XZ: LRS_location_value is used for sorting
-                try:
-                    LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb)
-                except:
-                    if trait.locus_chr.upper() == 'X':
-                        LRS_location_value = 20*1000 + float(trait.locus_mb)
-                    else:
-                        LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb)
-
                 trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
                 if trait.lrs != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
-                    trait.LRS_score_value = LRS_score_value = trait.lrs
     else:
         raise KeyError, `trait.name`+' information is not found in the database.'
         
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 17625474..07c67384 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -948,7 +948,6 @@ if __name__ == "__main__":
 
     from base import webqtlConfig
     from base.data_set import create_dataset
-    from base.templatePage import templatePage
     from utility import webqtlUtil
     from db import webqtlDatabaseFunction
 
diff --git a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py b/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
deleted file mode 100644
index deb47ad0..00000000
--- a/wqflask/wqflask/marker_regression/MarkerRegressionPage.py
+++ /dev/null
@@ -1,1648 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import time
-import string
-import math
-from math import *
-import piddle as pid
-import sys,os
-import httplib, urllib
-
-from htmlgen import HTMLgen2 as HT
-from utility import Plot
-from intervalAnalyst import GeneUtil
-from base.webqtlTrait import webqtlTrait
-from base.templatePage import templatePage
-from utility import webqtlUtil
-from base import webqtlConfig
-from db import webqtlDatabaseFunction
-from base.GeneralObject import GeneralObject
-
-import reaper
-import cPickle
-from utility.THCell import THCell
-from utility.TDCell import TDCell
-
-class MarkerRegressionPage(templatePage):
-
-    def __init__(self, fd):
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-
-        self.initializeParameters(fd)
-
-        filename= webqtlUtil.genRandStr("Itvl_")
-        ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList= self.getChrNameOrderIdLength(RISet=fd.RISet)
-
-        if self.mappingMethodId == '4': # For PLINK
-
-            traitInfoList = string.split(string.strip(fd.identification),':')
-            probesetName = string.strip(traitInfoList[-1])
-            plinkOutputFileName= webqtlUtil.genRandStr("%s_%s_"%(fd.RISet,probesetName))
-
-            # get related values from fd.allTraitData; the format of 'allTraitValueDict'is {strainName1: value=-0.2...}
-            fd.readData()
-            allTraitValueDict = fd.allTraitData
-
-            #automatically generate pheno txt file for PLINK
-            self.genPhenoTxtFileForPlink(phenoFileName=plinkOutputFileName,RISetName=fd.RISet,probesetName=probesetName, valueDict=allTraitValueDict)
-            # os.system full path is required for input and output files; specify missing value is -9999
-            plink_command = '%splink/plink --noweb --ped %splink/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %splink/%s.map --pheno %s/%s.txt --pheno-name %s --missing-phenotype -9999 --out %s%s --assoc ' % (webqtlConfig.GENODIR, webqtlConfig.GENODIR,  fd.RISet, webqtlConfig.GENODIR, fd.RISet, webqtlConfig.TMPDIR, plinkOutputFileName, probesetName, webqtlConfig.TMPDIR, plinkOutputFileName)
-
-            os.system(plink_command)
-
-            if fd.identification:
-                heading2 = HT.Paragraph('Trait ID: %s' % fd.identification)
-                heading2.__setattr__("class","subtitle")
-                self.dict['title'] = '%s: Genome Association' % fd.identification
-            else:
-                heading2 = ""
-                self.dict['title'] = 'Genome Association'
-
-            if fd.traitInfo:
-                symbol,chromosome,MB = string.split(fd.traitInfo,'\t')
-                heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB))
-            else:
-                heading3 = ""
-
-            heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet)
-            heading.__setattr__("class","title")
-
-            # header info part:Trait Data Entered for HLC Set & Trait ID:
-            headerdiv = HT.TR(HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee'))
-
-            self.ChrList=ChrList  # get chr name from '1' to 'X'
-            self.ChrLengthMbList = ChrLengthMbList
-
-            # build plink result dict based on chr, key is chr name, value is in list type including Snpname, bp and pvalue info
-            plinkResultDict={}
-            count,minPvalue,plinkResultDict =self.getPlinkResultDict(outputFileName=plinkOutputFileName,thresholdPvalue=self.pValue,ChrOrderIdNameDict=ChrOrderIdNameDict)
-
-            # if can not find results which are matched with assigned p-value, system info will show up
-            if count >0:
-
-                #for genome association report table
-                reportTable=""
-                # sortable table object
-                resultstable,tblobj,bottomInfo = self.GenReportForPLINK(ChrNameOrderIdDict=ChrNameOrderIdDict, RISet=fd.RISet,plinkResultDict=plinkResultDict,thresholdPvalue=self.pValue,chrList=self.ChrList)
-
-                # creat object for result table for sort function
-                objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
-                cPickle.dump(tblobj, objfile)
-                objfile.close()
-
-                sortby = ("Index", "up")
-                reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable")
-
-                descriptionTable =  HT.TableLite(border=0, cellpadding=0, cellspacing=0)
-                descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3)))
-                descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR())))
-                descriptionTable.append(bottomInfo)
-
-                # get each chr's length
-                self.ChrLengthMbList = map(lambda x: x/1000000.0, self.ChrLengthMbList) # change unit from bp to mb
-                self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)# get total length of all chrs
-                if self.ChrLengthMbList:
-                    self.GraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
-                else:
-                    self.GraphInterval = 1
-
-                # for human data, there's no CM value
-                self.ChrLengthCMList = []
-                self.ChrLengthCMSum = 0
-
-                # begin: common part with human data
-                intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
-                gifmap = self.plotIntMappingForPLINK(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, plinkResultDict=plinkResultDict)
-
-                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
-                intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
-
-                TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
-                self.dict['body'] = str(headerdiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))
-
-            else:
-                heading = "Genome Association"
-                detail = ['There is no association with marker that meets this criteria. Please provide a less stringend threshold. The minimun p-value is %s.'%minPvalue]
-                self.error(heading=heading,detail=detail)
-                return
-
-        elif self.mappingMethodId == '1': # QTLreaper result
-            if not fd.genotype:
-                fd.readData()
-
-            fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
-            weightedRegression = fd.formdata.getvalue('applyVarianceSE')
-
-            if fd.parentsf14regression and fd.genotype_2:
-                _genotype = fd.genotype_2
-            else:
-                _genotype = fd.genotype_1
-
-            _strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, weightedRegression)
-
-            if fd.identification:
-                heading2 = HT.Paragraph('Trait ID: %s' % fd.identification)
-                heading2.__setattr__("class","subtitle")
-                self.dict['title'] = '%s: Genome Association' % fd.identification
-            else:
-                heading2 = ""
-                self.dict['title'] = 'Genome Association'
-
-            if fd.traitInfo:
-                symbol,chromosome,MB = string.split(fd.traitInfo,'\t')
-                heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB))
-            else:
-                heading3 = ""
-
-            if N < webqtlConfig.KMININFORMATIVE:
-                heading = "Genome Association"
-                detail = ['Fewer than %d strain data were entered for %s data set. No mapping attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)]
-                self.error(heading=heading,detail=detail)
-                return
-            else:
-                heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet)
-                heading.__setattr__("class","title")
-
-                datadiv = HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee')
-                resultstable,tblobj,bottomInfo  = self.GenReport(ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars)
-                #resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars)
-
-                # creat object for result table for sort function
-                objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
-                cPickle.dump(tblobj, objfile)
-                objfile.close()
-
-                sortby = ("Index", "up")
-                reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable")
-
-                descriptionTable =  HT.TableLite(border=0, cellpadding=0, cellspacing=0)
-                descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3)))
-                descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR())))
-                descriptionTable.append(bottomInfo)
-
-                self.traitList=_vals
-
-                ##########################plot#######################
-
-                ################################################################
-                # Generate Chr list and Retrieve Length Information
-                ################################################################
-                self.genotype= _genotype
-                self.ChrList = [("All", -1)]
-
-                for i, indChr in enumerate(self.genotype):
-                    self.ChrList.append((indChr.name, i))
-
-                self.cursor.execute("""
-                        Select
-                                Length from Chr_Length, InbredSet
-                        where
-                                Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-                                InbredSet.Name = '%s' AND
-                                Chr_Length.Name in (%s)
-                        Order by
-                                OrderId
-                        """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
-
-                self.ChrLengthMbList = self.cursor.fetchall()
-                self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
-                self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
-                if self.ChrLengthMbList:
-                    self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
-                else:
-                    self.MbGraphInterval = 1
-
-                self.ChrLengthCMList = []
-                for i, _chr in enumerate(self.genotype):
-                    self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
-                self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale
-
-                self.GraphInterval = self.MbGraphInterval #Mb
-
-                # begin: common part with human data
-                intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight))
-                gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "")
-                filename= webqtlUtil.genRandStr("Itvl_")
-                intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, filename), format='png')
-                intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap')
-
-                ################################################################
-                # footnote goes here
-                ################################################################
-                btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
-
-                if (self.additiveChecked):
-                    btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
-
-
-                TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200))
-
-                self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable)))
-
-                # end: common part with human data
-
-        else:
-            pass
-
-
-    # add by NL 10-2-2011
-    def initializeParameters(self, fd):
-        """
-        Initializes all of the MarkerRegressionPage class parameters,
-        acquiring most values from the formdata (fd)
-        """
-        ###################################
-        # manhattam plot parameters
-        ###################################
-
-        self.graphHeight = 600
-        self.graphWidth  = 1280
-        self.plotScale = 'physic'
-        self.selectedChr = -1
-        self.GRAPH_BACK_DARK_COLOR  = pid.HexColor(0xF1F1F9)
-        self.GRAPH_BACK_LIGHT_COLOR = pid.HexColor(0xFBFBFF)
-        self.LRS_COLOR  = pid.HexColor(0x0000FF)
-        self.LRS_LOD ='LRS'
-        self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0))
-        self.startMb  = fd.formdata.getvalue('startMb', "-1")
-        self.endMb  = fd.formdata.getvalue('endMb', "-1")
-        self.mappingMethodId  = fd.formdata.getvalue('mappingMethodId', "0")
-        self.permChecked=True
-        self.multipleInterval=False
-        self.SIGNIFICANT_WIDTH = 5
-        self.SUGGESTIVE_WIDTH = 5
-        self.SIGNIFICANT_COLOR   = pid.HexColor(0xEBC7C7)
-        self.SUGGESTIVE_COLOR    = pid.gainsboro
-        self.colorCollection = [self.LRS_COLOR]
-        self.additiveChecked= True
-        self.ADDITIVE_COLOR_POSITIVE = pid.green
-        self.legendChecked =False
-        self.pValue=float(fd.formdata.getvalue('pValue',-1))
-
-        # allow user to input p-value greater than 1,
-        # in this case, the value will be treated as -lgP value. so the input value needs to be transferred to power of 10 format
-        if self.pValue >1:
-            self.pValue =10**-(self.pValue)
-
-        try:
-            self.startMb = float(self.startMb)
-            self.endMb = float(self.endMb)
-            if self.startMb > self.endMb:
-                temp = self.startMb
-                self.startMb = self.endMb
-                self.endMb = temp
-            #minimal distance 10bp
-            if self.endMb - self.startMb < 0.00001:
-                self.endMb = self.startMb + 0.00001
-        except:
-            self.startMb = self.endMb = -1
-
-    def GenReportForPLINK(self, ChrNameOrderIdDict={},RISet='',plinkResultDict= {},thresholdPvalue=-1,chrList=[]):
-
-        'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.'
-        #########################################
-        #      Genome Association report
-        #########################################
-        locusFormName = webqtlUtil.genRandStr("fm_")
-        locusForm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), \
-                enctype='multipart/form-data', name=locusFormName, submit=HT.Input(type='hidden'))
-        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':RISet+"Geno",'CellID':'_', \
-                'RISet':RISet, 'incparentsf1':'on'}
-        for key in hddn.keys():
-            locusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
-        regressionHeading = HT.Paragraph('Genome Association Report')
-        regressionHeading.__setattr__("class","title")
-
-        filename= webqtlUtil.genRandStr("GenomeAsscociation_")
-        fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
-        fpText.write('The loci meet the criteria of P-Value <= %3.6f.\n'%thresholdPvalue)
-        pValueInfo =HT.Paragraph('The loci meet the criteria of P-Value <= %3.6f.\n'%thresholdPvalue)
-
-        textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
-        bottomInfo = HT.TR(HT.TD(HT.Paragraph(textUrl, ' result in tab-delimited text format.', HT.BR(), HT.BR(),Class="fs12 fwn"), colspan=3))
-
-        tblobj={}       # build dict for genTableObj function; keys include header and body
-        tblobj_header = [] # value of key 'header'
-        tblobj_body=[]          # value of key 'body'
-        reportHeaderRow=[]      # header row list for tblobj_header (html part)
-        headerList=['Index','SNP Name','Chr','Mb','-log(P)']
-        headerStyle="fs14 fwb ffl b1 cw cbrb" # style of the header
-        cellColorStyle = "fs13 b1 fwn c222" # style of the cells
-
-        if headerList:
-            for ncol, item in enumerate(headerList):
-                reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol))
-            #download file for table headers' names
-            fpText.write('SNP_Name\tChromosome\tMb\t-log(P)\n')
-
-        tblobj_header.append(reportHeaderRow)
-        tblobj['header']=tblobj_header
-
-        index=1
-        for chr in chrList:
-
-            if plinkResultDict.has_key(chr):
-                if chr in ChrNameOrderIdDict.keys():
-                    chrOrderId =ChrNameOrderIdDict[chr]
-                else:
-                    chrOrderId=chr
-
-                valueList=plinkResultDict[chr]
-
-                for value in valueList:
-                    reportBodyRow=[]        # row list for tblobj_body (html part)
-                    snpName=value[0]
-                    bp=value[1]
-                    mb=int(bp)/1000000.0
-
-                    try:
-                        pValue =float(value[2])
-                    except:
-                        pValue =1
-                    formattedPvalue = -math.log10(pValue)
-
-                    formattedPvalue = webqtlUtil.SciFloat(formattedPvalue)
-                    dbSnprs=snpName.replace('rs','')
-                    SnpHref = HT.Href(text=snpName, url="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=%s"%dbSnprs, target="_blank")
-
-                    selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
-                    reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
-                    reportBodyRow.append(TDCell(HT.TD(SnpHref, Class=cellColorStyle,nowrap='ON'),snpName, snpName))
-                    reportBodyRow.append(TDCell(HT.TD(chr, Class=cellColorStyle, align="center",nowrap='ON'),chr, chrOrderId))
-                    reportBodyRow.append(TDCell(HT.TD('%3.6f'%mb, Class=cellColorStyle, align="center",nowrap='ON'),mb, mb))
-                    reportBodyRow.append(TDCell(HT.TD(formattedPvalue, Class=cellColorStyle, align="center",nowrap='ON'),formattedPvalue, float(formattedPvalue)))
-
-                    fpText.write('%s\t%s\t%3.6f\t%s\n' % (snpName, str(chr), mb, formattedPvalue))
-                    index+=1
-
-                    tblobj_body.append(reportBodyRow)
-
-        tblobj['body']=tblobj_body
-        rv=HT.TR(HT.TD(regressionHeading,pValueInfo, locusForm, HT.P(), width='55%',valign='top', align='left',bgColor='#eeeeee'))
-
-        return rv, tblobj,bottomInfo
-
-
-    def GenReport(self, ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars= []):
-        'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.'
-        #calculate QTL for each trait
-        self.qtlresults = []
-        if webqtlUtil.ListNotNull(_vars):
-            qtlresults = _genotype.regression(strains = _strains, trait = _vals, variance = _vars)
-            LRSArray = _genotype.permutation(strains = _strains, trait = _vals, variance = _vars, nperm=fd.nperm)
-        else:
-            qtlresults = _genotype.regression(strains = _strains, trait = _vals)
-            LRSArray = _genotype.permutation(strains = _strains, trait = _vals,nperm=fd.nperm)
-
-        self.qtlresults.append(qtlresults)
-
-        filename= webqtlUtil.genRandStr("GenomeAsscociation_")
-
-        # set suggestive, significant and highly significant LRS
-        if fd.suggestive == None:
-            fd.suggestive = LRSArray[int(fd.nperm*0.37-1)]
-        else:
-            fd.suggestive = float(fd.suggestive)
-        if fd.significance == None:
-            fd.significance = LRSArray[int(fd.nperm*0.95-1)]
-        else:
-            fd.significance = float(fd.significance)
-
-        self.significance =fd.significance
-        self.suggestive = fd.suggestive
-        self.highlysignificant = LRSArray[int(fd.nperm*0.99-1)]
-        _dispAllLRS = 0
-        if fd.formdata.getvalue('displayAllLRS'):
-            _dispAllLRS = 1
-        qtlresults2 = []
-        if _dispAllLRS:
-            filtered = qtlresults[:]
-        else:
-            filtered = filter(lambda x, y=fd.suggestive: x.lrs > y, qtlresults)
-        if len(filtered) == 0:
-            qtlresults2 = qtlresults[:]
-            qtlresults2.sort()
-            filtered = qtlresults2[-10:]
-
-        #########################################
-        #      Permutation Graph
-        #########################################
-        myCanvas = pid.PILCanvas(size=(400,300))
-        #plotBar(myCanvas,10,10,390,290,LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test',identification=fd.identification)
-        Plot.plotBar(myCanvas, LRSArray,XLabel='LRS',YLabel='Frequency',title=' Histogram of Permutation Test')
-        filename= webqtlUtil.genRandStr("Reg_")
-        myCanvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
-        img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
-
-        if fd.suggestive == None:
-            fd.suggestive = LRSArray[int(fd.nperm*0.37-1)]
-        else:
-            fd.suggestive = float(fd.suggestive)
-        if fd.significance == None:
-            fd.significance = LRSArray[int(fd.nperm*0.95-1)]
-        else:
-            fd.significance = float(fd.significance)
-
-        permutationHeading = HT.Paragraph('Histogram of Permutation Test')
-        permutationHeading.__setattr__("class","title")
-
-        permutation = HT.TableLite()
-        permutation.append(HT.TR(HT.TD(img)))
-
-
-        #########################################
-        #      Genome Association report
-        #########################################
-        locusFormName = webqtlUtil.genRandStr("fm_")
-        locusForm = HT.Form(cgi = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), \
-                enctype='multipart/form-data', name=locusFormName, submit=HT.Input(type='hidden'))
-        hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', \
-                'RISet':fd.RISet, 'incparentsf1':'on'}
-        for key in hddn.keys():
-            locusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-
-        regressionHeading = HT.Paragraph('Genome Association Report')
-        regressionHeading.__setattr__("class","title")
-        # report is the info part above report table
-        if qtlresults2 != []:
-            report = HT.Blockquote(HT.Font('No association ',color="#FF0000"),HT.Font('with a likelihood ratio statistic greater than %3.1f was found. Here are the top 10 LRSs.' % fd.suggestive,color="#000000"))
-        else:
-            report = HT.Blockquote('The following loci in the %s data set have associations with the above trait data.\n' % fd.RISet, HT.P())
-        report.__setattr__("class","normalsize")
-
-        fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
-        fpText.write('Suggestive LRS =%3.2f\n'%self.suggestive)
-        fpText.write('Significant LRS =%3.2f\n'%self.significance)
-        fpText.write('Highly Significant LRS =%3.2f\n'%self.highlysignificant)
-        LRSInfo =HT.Paragraph('&nbsp;&nbsp;&nbsp;&nbsp;Suggestive LRS =%3.2f\n'%fd.suggestive, HT.BR(), '&nbsp;&nbsp;&nbsp;&nbsp;Significant LRS =%3.2f\n'%fd.significance,HT.BR(),'&nbsp;&nbsp;&nbsp;&nbsp;Highly Significant LRS =%3.2f\n' % self.highlysignificant)
-
-        textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
-
-        bottomInfo = HT.TR(HT.TD(HT.Paragraph(textUrl, ' result in tab-delimited text format.', HT.BR(), HT.BR(),'LRS values marked with',HT.Font(' * ',color="red"), 'are greater than the significance threshold (specified by you or by permutation test). ' , HT.BR(), HT.BR(), HT.Strong('Additive Effect'), ' is half the difference in the mean phenotype of all cases that are homozygous for one parental allel at this marker minus the mean of all cases that are homozygous for the other parental allele at this marker. ','In the case of %s strains, for example,' % fd.RISet,' A positive additive effect indicates that %s alleles increase trait values. Negative additive effect indicates that %s alleles increase trait values.'% (fd.ppolar,fd.mpolar),Class="fs12 fwn")))
-
-        tblobj={}       # build dict for genTableObj function; keys include header and body
-        tblobj_header = [] # value of key 'header'
-        tblobj_body=[]          # value of key 'body'
-        reportHeaderRow=[]      # header row list for tblobj_header (html part)
-        headerStyle="fs14 fwb ffl b1 cw cbrb" # style of the header
-        cellColorStyle = "fs13 b1 fwn c222" # style of the cells
-
-        headerList=['Index','LRS','Chr','Mb','Locus','Additive Effect']
-        for ncol, item in enumerate(headerList):
-            reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol))
-
-        if fd.genotype.type == 'intercross':
-            ncol =len(headerList)
-            reportHeaderRow.append(THCell(HT.TD('Dominance Effect', Class=headerStyle, valign='bottom',nowrap='ON'),text='Dominance Effect', idx=ncol))
-
-            #download file for table headers' names
-            fpText.write('LRS\tChromosome\tMb\tLocus\tAdditive Effect\tDominance Effect\n')
-
-            index=1
-            for ii in filtered:
-                #add by NL 06-20-2011: set LRS to 460 when LRS is infinite,
-                if ii.lrs==float('inf') or ii.lrs>webqtlConfig.MAXLRS:
-                    LRS=webqtlConfig.MAXLRS #maximum LRS value
-                else:
-                    LRS=ii.lrs
-
-                if LRS > fd.significance:
-                    lrs = HT.TD(HT.Font('%3.3f*' % LRS, color='#FF0000'),Class=cellColorStyle)
-                else:
-                    lrs = HT.TD('%3.3f' % LRS,Class=cellColorStyle)
-
-                if ii.locus.chr in ChrNameOrderIdDict.keys():
-                    chrOrderId =ChrNameOrderIdDict[ii.locus.chr]
-                else:
-                    chrOrderId=ii.locus.chr
-
-                reportBodyRow=[]        # row list for tblobj_body (html part)
-                selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
-                reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
-                reportBodyRow.append(TDCell(lrs,LRS, LRS))
-                reportBodyRow.append(TDCell(HT.TD(ii.locus.chr, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.chr, chrOrderId))
-                reportBodyRow.append(TDCell(HT.TD('%3.6f'%ii.locus.Mb, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.Mb, ii.locus.Mb))
-                reportBodyRow.append(TDCell(HT.TD(HT.Href(text=ii.locus.name, url = "javascript:showTrait('%s','%s');" % (locusFormName, ii.locus.name), Class='normalsize'), Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.name, ii.locus.name))
-                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.additive, Class=cellColorStyle, align="center",nowrap='ON'),ii.additive, ii.additive))
-                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.dominance, Class=cellColorStyle, align="center",nowrap='ON'),ii.dominance, ii.dominance))
-
-                fpText.write('%2.3f\t%s\t%3.6f\t%s\t%2.3f\t%2.3f\n' % (LRS, ii.locus.chr, ii.locus.Mb, ii.locus.name, ii.additive, ii.dominance))
-                index+=1
-                tblobj_body.append(reportBodyRow)
-        else:
-            #download file for table headers' names
-            fpText.write('LRS\tChromosome\tMb\tLocus\tAdditive Effect\n')
-
-            index=1
-            for ii in filtered:
-                #add by NL 06-20-2011: set LRS to 460 when LRS is infinite,
-                if ii.lrs==float('inf') or ii.lrs>webqtlConfig.MAXLRS:
-                    LRS=webqtlConfig.MAXLRS #maximum LRS value
-                else:
-                    LRS=ii.lrs
-
-                if LRS > fd.significance:
-                    lrs = HT.TD(HT.Font('%3.3f*' % LRS, color='#FF0000'),Class=cellColorStyle)
-                else:
-                    lrs = HT.TD('%3.3f' % LRS,Class=cellColorStyle)
-
-                if ii.locus.chr in ChrNameOrderIdDict.keys():
-                    chrOrderId =ChrNameOrderIdDict[ii.locus.chr]
-                else:
-                    chrOrderId=ii.locus.chr
-
-                reportBodyRow=[]        # row list for tblobj_body (html part)
-                selectCheck=HT.Input(type="checkbox", Class="checkbox", name="index",value=index, onClick="highlight(this)")
-                reportBodyRow.append(TDCell(HT.TD(str(index),selectCheck, align='right',Class=cellColorStyle,nowrap='ON'),str(index),index))
-                reportBodyRow.append(TDCell(lrs,LRS, LRS))
-                reportBodyRow.append(TDCell(HT.TD(ii.locus.chr, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.chr, chrOrderId))
-                reportBodyRow.append(TDCell(HT.TD('%3.6f'%ii.locus.Mb, Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.Mb, ii.locus.Mb))
-                reportBodyRow.append(TDCell(HT.TD(HT.Href(text=ii.locus.name, url = "javascript:showTrait('%s','%s');" % (locusFormName, ii.locus.name), Class='normalsize'), Class=cellColorStyle, align="center",nowrap='ON'),ii.locus.name, ii.locus.name))
-                reportBodyRow.append(TDCell(HT.TD('%3.3f' % ii.additive, Class=cellColorStyle, align="center",nowrap='ON'),ii.additive, ii.additive))
-
-                fpText.write('%2.3f\t%s\t%3.6f\t%s\t%2.3f\n' % (LRS, ii.locus.chr, ii.locus.Mb, ii.locus.name, ii.additive))
-                index+=1
-                tblobj_body.append(reportBodyRow)
-
-        tblobj_header.append(reportHeaderRow)
-        tblobj['header']=tblobj_header
-        tblobj['body']=tblobj_body
-
-        rv=HT.TD(regressionHeading,LRSInfo,report, locusForm, HT.P(),width='55%',valign='top', align='left', bgColor='#eeeeee')
-        if fd.genotype.type == 'intercross':
-            bottomInfo.append(HT.BR(), HT.BR(), HT.Strong('Dominance Effect'),' is the difference between the mean trait value of cases heterozygous at a marker and the average mean for the two groups homozygous at this marker: e.g.,  BD - (BB+DD)/2]. A positive dominance effect indicates that the average phenotype of BD heterozygotes exceeds the mean of BB and DD homozygotes. No dominance deviation can be computed for a set of recombinant inbred strains or for a backcross.')
-            return rv,tblobj,bottomInfo
-
-        return rv,tblobj,bottomInfo
-
-    def plotIntMappingForPLINK(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = "",plinkResultDict={}):
-        #calculating margins
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        xLeftOffset = int(xLeftOffset*fontZoom)
-        xRightOffset = int(xRightOffset*fontZoom)
-        yBottomOffset = int(yBottomOffset*fontZoom)
-
-        cWidth = canvas.size[0]
-        cHeight = canvas.size[1]
-        plotWidth = cWidth - xLeftOffset - xRightOffset
-        plotHeight = cHeight - yTopOffset - yBottomOffset
-        startPixelX = xLeftOffset
-        endPixelX   = (xLeftOffset + plotWidth)
-
-        #Drawing Area Height
-        drawAreaHeight = plotHeight
-        if self.plotScale == 'physic' and self.selectedChr > -1: # for single chr
-            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
-            if self.geneChecked:
-                drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
-        else:
-            if self.selectedChr > -1:
-                drawAreaHeight -= 20
-            else:# for all chrs
-                drawAreaHeight -= 30
-
-        #Image map
-        gifmap = HT.Map(name='WebQTLImageMap')
-
-        newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
-        # Draw the alternating-color background first and get plotXScale
-        plotXScale = self.drawGraphBackgroundForPLINK(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb,plinkResultDict=plinkResultDict)
-
-        # Draw X axis
-        self.drawXAxisForPLINK(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-        # Draw manhattam plot
-        self.drawManhattanPlotForPLINK(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb,plinkResultDict=plinkResultDict,thresholdPvalue=self.pValue)
-
-        return gifmap
-
-
-    def plotIntMapping(self, fd, canvas, offset= (80, 120, 20, 80), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
-        #calculating margins
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        xLeftOffset = int(xLeftOffset*fontZoom)
-        xRightOffset = int(xRightOffset*fontZoom)
-        yBottomOffset = int(yBottomOffset*fontZoom)
-
-        cWidth = canvas.size[0]
-        cHeight = canvas.size[1]
-        plotWidth = cWidth - xLeftOffset - xRightOffset
-        plotHeight = cHeight - yTopOffset - yBottomOffset
-        startPixelX = xLeftOffset
-        endPixelX   = (xLeftOffset + plotWidth)
-
-        #Drawing Area Height
-        drawAreaHeight = plotHeight
-        if self.plotScale == 'physic' and self.selectedChr > -1: # for single chr
-            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
-            if self.geneChecked:
-                drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
-        else:# for all chrs
-            if self.selectedChr > -1:
-                drawAreaHeight -= 20
-            else:
-                drawAreaHeight -= 30
-
-        #Image map
-        gifmap = HT.Map(name='WebQTLImageMap')
-
-        newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
-        # Draw the alternating-color background first and get plotXScale
-        plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-
-        # Draw X axis
-        self.drawXAxis(fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-        # Draw QTL curve
-        self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
-
-        #draw legend
-        if self.multipleInterval:
-            self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
-        elif self.legendChecked:
-            self.drawLegendPanel(fd, canvas, offset=newoffset)
-        else:
-            pass
-
-        #draw position, no need to use a separate function
-        if fd.genotype.Mbmap:
-            self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset)
-
-        return gifmap
-
-
-    # functions for manhattam plot of markers
-    def drawManhattanPlotForPLINK(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None,plinkResultDict={},thresholdPvalue=-1):
-
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        # INTERCROSS = (self.genotype.type=="intercross")
-        INTERCROSS ='' #??????
-
-        ChrLengthDistList = self.ChrLengthMbList
-        drawRegionDistance = self.ChrLengthMbSum
-        GraphInterval=self.GraphInterval
-        pvalueHeightThresh = drawAreaHeight - 80 #ZS: Otherwise the plot gets very close to the chromosome labels
-
-        #draw the pvalue scale
-        #We first determine whether or not we are using a sliding scale.
-        #If so, we need to compute the maximum pvalue value to determine where the max y-value should be, and call this pvalueMax.
-        #pvalueTop is then defined to be above the pvalueMax by enough to add one additional pvalueScale increment.
-        #if we are using a set-scale, then we set pvalueTop to be the user's value, and pvalueMax doesn't matter.
-
-        # for human data we use p value instead of lrs
-        pValueList=[]
-        for key in plinkResultDict:
-            valueList = plinkResultDict[key]
-            for item in valueList:
-                pValue = item[-1]
-                pValueList.append(pValue)
-
-        formattedPValueList=[]
-        for pValue in pValueList:
-            try:
-                pValue=float(pValue)
-            except:
-                pValue =1
-            formattedpValue = -math.log10(pValue)
-            formattedPValueList.append(formattedpValue)
-
-        #sliding scale
-        pvalueMax = max(formattedPValueList)
-        #pvalueMax =pvalueMax +1
-        # no permutation result for plink  func: GenReport()
-        pvalueMin = int(-math.log10(thresholdPvalue))
-
-        if pvalueMax> 100:
-            pvalueScale = 20.0
-        elif pvalueMax > 20:
-            pvalueScale = 5.0
-        elif pvalueMax > 7.5:
-            pvalueScale = 2.5
-        else:
-            pvalueScale = 1.0
-
-        # the base line for x-axis is -log(thresholdPvalue)
-        pvalueAxisList = Plot.frange(pvalueMin, pvalueMax, pvalueScale)
-        #make sure the user's value appears on the y-axis
-        #ZS: There is no way to do this without making the position of the points not directly proportional to a given distance on the y-axis
-        #tempPvalueMax=round(pvalueMax)
-        tempPvalueMax = pvalueAxisList[len(pvalueAxisList)-1] + pvalueScale
-        pvalueAxisList.append(tempPvalueMax)
-
-        #ZS: I don't understand this; the if statement will be true for any number that isn't exactly X.5.
-        #if abs(tempPvalueMax-pvalueMax) <0.5:
-        #       tempPvalueMax=tempPvalueMax+1
-        #       pvalueAxisList.append(tempPvalueMax)
-
-        #draw the "pvalue" string to the left of the axis
-        pvalueScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
-        pvalueLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
-        yZero = yTopOffset + plotHeight
-
-        #yAxis label display area
-        yAxis_label ='-log(P)'
-        canvas.drawString(yAxis_label, xLeftOffset - canvas.stringWidth("999.99", font=pvalueScaleFont) - 10*zoom, \
-                                          yZero - 150, font=pvalueLODFont, color=pid.black, angle=90)
-
-        for i,item in enumerate(pvalueAxisList):
-            ypvalue = yZero - (float(i)/float(len(pvalueAxisList) - 1)) * pvalueHeightThresh
-            canvas.drawLine(xLeftOffset, ypvalue, xLeftOffset - 4, ypvalue, color=self.LRS_COLOR, width=1*zoom)
-            scaleStr = "%2.1f" % item
-            #added by NL 6-24-2011:Y-axis scale display
-            canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=pvalueScaleFont)-5, ypvalue+3, font=pvalueScaleFont, color=self.LRS_COLOR)
-
-        ChrList=self.ChrList
-        startPosX = xLeftOffset
-
-        for i, chr in enumerate(ChrList):
-
-            if      plinkResultDict.has_key(chr):
-                plinkresultList = plinkResultDict[chr]
-
-                m = 0
-                #add by NL 06-24-2011: for mahanttam plot
-                symbolFont = pid.Font(ttf="fnt_bs", size=5,bold=0)
-                # color for point in each chr
-                chrCount=len(ChrList)
-                chrColorDict =self.getColorForMarker(chrCount=chrCount,flag=1)
-                for j, item in enumerate(plinkresultList):
-                    try :
-                        mb=float(item[1])/1000000.0
-                    except:
-                        mb=0
-
-                    try :
-                        pvalue =float(item[-1])
-                    except:
-                        pvalue =1
-
-                    try:
-                        snpName = item[0]
-                    except:
-                        snpName=''
-
-                    formattedPvalue = -math.log10(pvalue)
-
-                    Xc = startPosX + (mb-startMb)*plotXScale
-                    Yc = yZero - (formattedPvalue-pvalueMin)*pvalueHeightThresh/(tempPvalueMax - pvalueMin)
-                    canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=chrColorDict[i], font=symbolFont)
-                    m += 1
-
-            startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale
-
-        canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom)  #the blue line running up the y axis
-
-    def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
-
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        INTERCROSS = (self.genotype.type=="intercross")
-
-        ChrLengthDistList = self.ChrLengthMbList
-        GraphInterval=self.GraphInterval
-        LRSHeightThresh = drawAreaHeight
-        AdditiveHeightThresh = drawAreaHeight/2
-        DominanceHeightThresh = drawAreaHeight/2
-
-        #draw the LRS scale
-        #We first determine whether or not we are using a sliding scale.
-        #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRSMax.
-        #LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
-        #if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.
-
-        if self.LRS_LOD == 'LOD':
-            lodm = self.LODFACTOR
-        else:
-            lodm = 1.0
-
-        if self.lrsMax <= 0:  #sliding scale
-            LRSMax = max(map(max, self.qtlresults)).lrs
-            #genotype trait will give infinite LRS
-            LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
-            LRSMax = max(self.significance, LRSMax)
-        else:
-            LRSMax = self.lrsMax*lodm
-
-        if LRSMax/lodm > 100:
-            LRSScale = 20.0
-        elif LRSMax/lodm > 20:
-            LRSScale = 5.0
-        elif LRSMax/lodm > 7.5:
-            LRSScale = 2.5
-        else:
-            LRSScale = 1.0
-
-        LRSAxisList = Plot.frange(LRSScale, LRSMax/lodm, LRSScale)
-        #make sure the user's value appears on the y-axis
-        #update by NL 6-21-2011: round the LOD value to 100 when LRSMax is equal to 460
-        LRSAxisList.append(round(LRSMax/lodm))
-
-        #draw the "LRS" or "LOD" string to the left of the axis
-        LRSScaleFont=pid.Font(ttf="verdana", size=14*fontZoom, bold=0)
-        LRSLODFont=pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
-        yZero = yTopOffset + plotHeight
-
-        #yAxis label display area
-        canvas.drawString(self.LRS_LOD, xLeftOffset - canvas.stringWidth("999.99", font=LRSScaleFont) - 10*zoom, \
-                                          yZero - 150, font=LRSLODFont, color=pid.black, angle=90)
-
-        for item in LRSAxisList:
-            yLRS = yZero - (item*lodm/LRSMax) * LRSHeightThresh
-            canvas.drawLine(xLeftOffset, yLRS, xLeftOffset - 4, yLRS, color=self.LRS_COLOR, width=1*zoom)
-            scaleStr = "%2.1f" % item
-            #added by NL 6-24-2011:Y-axis scale display
-            canvas.drawString(scaleStr, xLeftOffset-4-canvas.stringWidth(scaleStr, font=LRSScaleFont)-5, yLRS+3, font=LRSScaleFont, color=self.LRS_COLOR)
-
-
-        #"Significant" and "Suggestive" Drawing Routine
-        # ======= Draw the thick lines for "Significant" and "Suggestive" =====  (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
-        if self.permChecked and not self.multipleInterval:
-            significantY = yZero - self.significance*LRSHeightThresh/LRSMax
-            suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSMax
-
-
-            startPosX = xLeftOffset
-            for i, _chr in enumerate(self.genotype):
-                rightEdge = int(startPosX + self.ChrLengthDistList[i]*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
-                #added by NL 6-24-2011:draw suggestive line (grey one)
-                canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, suggestiveY, rightEdge, suggestiveY, color=self.SUGGESTIVE_COLOR,
-                        width=self.SUGGESTIVE_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
-                #added by NL 6-24-2011:draw significant line (pink one)
-                canvas.drawLine(startPosX+self.SUGGESTIVE_WIDTH/1.5, significantY, rightEdge, significantY, color=self.SIGNIFICANT_COLOR,
-                        width=self.SIGNIFICANT_WIDTH*zoom, clipX=(xLeftOffset, xLeftOffset + plotWidth-2))
-                sugg_coords = "%d, %d, %d, %d" % (startPosX, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
-                sig_coords = "%d, %d, %d, %d" % (startPosX, significantY-2, rightEdge + 2*zoom, significantY+2)
-                if self.LRS_LOD == 'LRS':
-                    sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
-                    sig_title = "Significant LRS = %0.2f" % self.significance
-                else:
-                    sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
-                    sig_title = "Significant LOD = %0.2f" % (self.significance/4.61)
-                Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
-                Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
-                gifmap.areas.append(Areas1)
-                gifmap.areas.append(Areas2)
-
-                startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
-
-        if self.multipleInterval:
-            lrsEdgeWidth = 1
-        else:
-            additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
-            if INTERCROSS:
-                dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
-            else:
-                dominanceMax = -1
-            lrsEdgeWidth = 2
-        for i, qtlresult in enumerate(self.qtlresults):
-            m = 0
-            startPosX = xLeftOffset
-            thisLRSColor = self.colorCollection[i]
-
-            #add by NL 06-24-2011: for mahanttam plot
-            symbolFont = pid.Font(ttf="fnt_bs", size=5,bold=0)
-
-            for j, _chr in enumerate(self.genotype):
-                chrCount=len(self.genotype)
-                chrColorDict =self.getColorForMarker(chrCount=chrCount,flag=1)
-                LRSCoordXY = []
-                AdditiveCoordXY = []
-                DominanceCoordXY = []
-                for k, _locus in enumerate(_chr):
-                    if self.plotScale == 'physic':
-                        Xc = startPosX + (_locus.Mb-startMb)*plotXScale
-                    else:
-                        Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
-                    # updated by NL 06-18-2011:
-                    # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
-                    # for any lrs is over than 460(LRS max in this system), it will be reset to 460
-                    if      qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf':
-                        Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
-                    else:
-                        Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax
-
-                    LRSCoordXY.append((Xc, Yc))
-                    #add by NL 06-24-2011: for mahanttam plot
-                    #self.significance/4.61  consider chr and LOD
-                    # significantY = yZero - self.significance*LRSHeightThresh/LRSMax
-                    # if Yc >significantY:
-                        # canvas.drawString(":", Xc-canvas.stringWidth(":",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)
-                    # else:
-                        # canvas.drawString(":", Xc-canvas.stringWidth(":",font=symbolFont)/2+1,Yc+2,color=pid.black, font=symbolFont)
-
-                    # add by NL 06-27-2011: eliminate imputed value when locus name is equal to '-'
-                    if (qtlresult[m].locus.name) and (qtlresult[m].locus.name!=' - '):
-                        canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=chrColorDict[j], font=symbolFont)
-
-                    if not self.multipleInterval and self.additiveChecked:
-                        Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
-                        AdditiveCoordXY.append((Xc, Yc))
-                    if not self.multipleInterval and INTERCROSS and self.additiveChecked:
-                        Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
-                        DominanceCoordXY.append((Xc, Yc))
-                    m += 1
-
-                startPosX +=  (ChrLengthDistList[j]+GraphInterval)*plotXScale
-
-
-        ###draw additive scale
-        if not self.multipleInterval and self.additiveChecked:
-            additiveScaleFont=pid.Font(ttf="verdana",size=12*fontZoom,bold=0)
-            additiveScale = Plot.detScaleOld(0,additiveMax)
-            additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
-            additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
-            maxAdd =  additiveScale[1]
-            addPlotScale = AdditiveHeightThresh/additiveMax
-
-            additiveAxisList.append(additiveScale[1])
-            for item in additiveAxisList:
-                additiveY = yZero - item*addPlotScale
-                canvas.drawLine(xLeftOffset + plotWidth,additiveY,xLeftOffset+4+ plotWidth,additiveY,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
-                scaleStr = "%2.3f" % item
-                canvas.drawString(scaleStr,xLeftOffset + plotWidth +6,additiveY+5,font=additiveScaleFont,color=self.ADDITIVE_COLOR_POSITIVE)
-
-            canvas.drawLine(xLeftOffset+plotWidth,additiveY,xLeftOffset+plotWidth,yZero,color=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
-
-        canvas.drawLine(xLeftOffset, yZero, xLeftOffset, yTopOffset, color=self.LRS_COLOR, width=1*zoom)  #the blue line running up the y axis
-
-    def drawGraphBackgroundForPLINK(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None,plinkResultDict={} ):
-
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        #calculate plot scale
-        #XZ: all of these global variables should be passed from function signiture
-        ChrLengthDistList = self.ChrLengthMbList
-        drawRegionDistance = self.ChrLengthMbSum
-        GraphInterval=self.GraphInterval
-        ChrList =self.ChrList
-
-        #multiple chromosome view
-        plotXScale = plotWidth / ((len(ChrList)-1)*GraphInterval + drawRegionDistance)
-
-        startPosX = xLeftOffset
-        chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)
-
-        for i, _chr in enumerate(ChrList):
-
-            if (i % 2 == 0):
-                theBackColor = self.GRAPH_BACK_DARK_COLOR
-            else:
-                theBackColor = self.GRAPH_BACK_LIGHT_COLOR
-            # NL:resize chr width for drawing
-            if float(ChrLengthDistList[i])<90:
-                ChrLengthDistList[i]=90
-            #draw the shaded boxes and the sig/sug thick lines
-            canvas.drawRect(startPosX, yTopOffset, startPosX + ChrLengthDistList[i]*plotXScale, \
-                            yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)
-
-            chrNameWidth = canvas.stringWidth(_chr, font=chrLabelFont)
-            chrStartPix = startPosX + (ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
-            chrEndPix = startPosX + (ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
-
-            canvas.drawString(_chr, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
-            COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
-
-            #add by NL 09-03-2010
-            HREF = "javascript:changeView(%d,%s);" % (i,ChrLengthDistList)
-            Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
-            gifmap.areas.append(Areas)
-            startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale
-
-        return plotXScale
-
-
-    def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
-        ##conditions
-        ##multiple Chromosome view
-        ##single Chromosome Physical
-        ##single Chromosome Genetic
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        #calculate plot scale
-        if self.plotScale != 'physic':
-            self.ChrLengthDistList = self.ChrLengthCMList
-            drawRegionDistance = self.ChrLengthCMSum
-        else:
-            self.ChrLengthDistList = self.ChrLengthMbList
-            drawRegionDistance = self.ChrLengthMbSum
-
-        if self.selectedChr > -1: #single chromosome view
-            spacingAmt = plotWidth/13.5
-            i = 0
-            for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt):
-                if (i % 2 == 0):
-                    theBackColor = self.GRAPH_BACK_DARK_COLOR
-                else:
-                    theBackColor = self.GRAPH_BACK_LIGHT_COLOR
-                i += 1
-                canvas.drawRect(startPix, yTopOffset, min(startPix+spacingAmt, xLeftOffset+plotWidth), \
-                        yTopOffset+plotHeight, edgeColor=theBackColor, fillColor=theBackColor)
-
-            drawRegionDistance = self.ChrLengthDistList[self.selectedChr]
-            self.ChrLengthDistList = [drawRegionDistance]
-            if self.plotScale == 'physic':
-                plotXScale = plotWidth / (endMb-startMb)
-            else:
-                plotXScale = plotWidth / drawRegionDistance
-
-        else:   #multiple chromosome view
-            plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance)
-
-            startPosX = xLeftOffset
-            chrLabelFont=pid.Font(ttf="verdana",size=24*fontZoom,bold=0)
-
-            for i, _chr in enumerate(self.genotype):
-
-                if (i % 2 == 0):
-                    theBackColor = self.GRAPH_BACK_DARK_COLOR
-                else:
-                    theBackColor = self.GRAPH_BACK_LIGHT_COLOR
-
-                #draw the shaded boxes and the sig/sug thick lines
-                canvas.drawRect(startPosX, yTopOffset, startPosX + self.ChrLengthDistList[i]*plotXScale, \
-                                yTopOffset+plotHeight, edgeColor=pid.gainsboro,fillColor=theBackColor)
-
-                chrNameWidth = canvas.stringWidth(_chr.name, font=chrLabelFont)
-                chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
-                chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
-
-                canvas.drawString(_chr.name, chrStartPix, yTopOffset +20,font = chrLabelFont,color=pid.dimgray)
-                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
-
-                #add by NL 09-03-2010
-                HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
-                Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
-                gifmap.areas.append(Areas)
-                startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
-        return plotXScale
-
-    # XZ: The only difference of function drawXAxisForPLINK and function drawXAxis are the function name and the self.plotScale condition.
-    def drawXAxisForPLINK(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        yZero = canvas.size[1] - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        #Parameters
-        ChrLengthDistList = self.ChrLengthMbList
-        GraphInterval=self.GraphInterval
-
-        NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
-        X_MAJOR_TICK_THICKNESS = 2
-        X_MINOR_TICK_THICKNESS = 1
-        X_AXIS_THICKNESS = 1*zoom
-
-        # ======= Alex: Draw the X-axis labels (megabase location)
-        MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
-        xMajorTickHeight = 15 # How high the tick extends below the axis
-        xMinorTickHeight = 5*zoom
-        xAxisTickMarkColor = pid.black
-        xAxisLabelColor = pid.black
-        fontHeight = 12*fontZoom # How tall the font that we're using is
-        spacingFromLabelToAxis = 20
-        spacingFromLineToLabel = 3
-
-        if self.plotScale == 'physic':
-            strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
-            ###Physical single chromosome view
-            if self.selectedChr > -1:
-                graphMbWidth  = endMb - startMb
-                XScale = Plot.detScale(startMb, endMb)
-                XStart, XEnd, XStep = XScale
-                if XStep < 8:
-                    XStep *= 2
-                spacingAmtX = spacingAmt = (XEnd-XStart)/XStep
-
-                j = 0
-                while  abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
-                    j += 1
-                    spacingAmtX *= 10
-
-                formatStr = '%%2.%df' % j
-
-                for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
-                    if _Mb < startMb or _Mb > endMb:
-                        continue
-                    Xc = xLeftOffset + plotXScale*(_Mb - startMb)
-                    if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
-                        canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
-                        labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
-                        strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
-                        drawStringXc = (Xc - (strWidth / 2.0))
-                        canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
-                    else:
-                        canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
-                    # end else
-
-            ###Physical genome wide view
-            else:
-                distScale = 0
-                startPosX = xLeftOffset
-                for i, distLen in enumerate(ChrLengthDistList):
-                    if distScale == 0: #universal scale in whole genome mapping
-                        if distLen > 75:
-                            distScale = 25
-                        elif distLen > 30:
-                            distScale = 10
-                        else:
-                            distScale = 5
-                    for tickdists in range(distScale, ceil(distLen), distScale):
-                        canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
-                        canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
-                    startPosX +=  (ChrLengthDistList[i]+GraphInterval)*plotXScale
-
-            megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
-            canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
-                    strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
-            pass
-
-        canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself
-
-    def drawXAxis(self, fd, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        yZero = canvas.size[1] - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        #Parameters
-        NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
-        X_MAJOR_TICK_THICKNESS = 2
-        X_MINOR_TICK_THICKNESS = 1
-        X_AXIS_THICKNESS = 1*zoom
-
-        # ======= Alex: Draw the X-axis labels (megabase location)
-        MBLabelFont = pid.Font(ttf="verdana", size=12*fontZoom, bold=0)
-        xMajorTickHeight = 15 # How high the tick extends below the axis
-        xMinorTickHeight = 5*zoom
-        xAxisTickMarkColor = pid.black
-        xAxisLabelColor = pid.black
-        fontHeight = 12*fontZoom # How tall the font that we're using is
-        spacingFromLabelToAxis = 20
-        spacingFromLineToLabel = 3
-
-        if self.plotScale == 'physic':
-            strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
-            ###Physical single chromosome view
-            if self.selectedChr > -1:
-                graphMbWidth  = endMb - startMb
-                XScale = Plot.detScale(startMb, endMb)
-                XStart, XEnd, XStep = XScale
-                if XStep < 8:
-                    XStep *= 2
-                spacingAmtX = spacingAmt = (XEnd-XStart)/XStep
-
-                j = 0
-                while  abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
-                    j += 1
-                    spacingAmtX *= 10
-
-                formatStr = '%%2.%df' % j
-
-                for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
-                    if _Mb < startMb or _Mb > endMb:
-                        continue
-                    Xc = xLeftOffset + plotXScale*(_Mb - startMb)
-                    if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
-                        canvas.drawLine(Xc, yZero, Xc, yZero+xMajorTickHeight, color=xAxisTickMarkColor, width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
-                        labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
-                        strWidth = canvas.stringWidth(labelStr, font=MBLabelFont)
-                        drawStringXc = (Xc - (strWidth / 2.0))
-                        canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
-                    else:
-                        canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
-                    # end else
-
-            ###Physical genome wide view
-            else:
-                distScale = 0
-                startPosX = xLeftOffset
-                for i, distLen in enumerate(self.ChrLengthDistList):
-                    if distScale == 0: #universal scale in whole genome mapping
-                        if distLen > 75:
-                            distScale = 25
-                        elif distLen > 30:
-                            distScale = 10
-                        else:
-                            distScale = 5
-                    for tickdists in range(distScale, ceil(distLen), distScale):
-                        canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
-                        canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
-                    startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
-
-            megabaseLabelFont = pid.Font(ttf="verdana", size=14*zoom*1.5, bold=0)
-            canvas.drawString("Megabases", xLeftOffset + (plotWidth -canvas.stringWidth("Megabases", font=megabaseLabelFont))/2,
-                    strYLoc + canvas.fontHeight(MBLabelFont) + 5*zoom, font=megabaseLabelFont, color=pid.black)
-            pass
-        else:
-            ChrAInfo = []
-            preLpos = -1
-            distinctCount = 0.0
-            if len(self.genotype) > 1:
-                for i, _chr in enumerate(self.genotype):
-                    thisChr = []
-                    Locus0CM = _chr[0].cM
-                    nLoci = len(_chr)
-                    if  nLoci <= 8:
-                        for _locus in _chr:
-                            if _locus.name != ' - ':
-                                if _locus.cM != preLpos:
-                                    distinctCount += 1
-                                preLpos = _locus.cM
-                                thisChr.append([_locus.name, _locus.cM-Locus0CM])
-                    else:
-                        for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1):
-                            while _chr[j].name == ' - ':
-                                j += 1
-                            if _chr[j].cM != preLpos:
-                                distinctCount += 1
-                            preLpos = _chr[j].cM
-                            thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM])
-                    ChrAInfo.append(thisChr)
-            else:
-                for i, _chr in enumerate(self.genotype):
-                    thisChr = []
-                    Locus0CM = _chr[0].cM
-                    for _locus in _chr:
-                        if _locus.name != ' - ':
-                            if _locus.cM != preLpos:
-                                distinctCount += 1
-                            preLpos = _locus.cM
-                            thisChr.append([_locus.name, _locus.cM-Locus0CM])
-                    ChrAInfo.append(thisChr)
-
-            stepA =  (plotWidth+0.0)/distinctCount
-
-            LRectWidth = 10
-            LRectHeight = 3
-            offsetA = -stepA
-            lineColor = pid.lightblue
-            startPosX = xLeftOffset
-            for j, ChrInfo in enumerate(ChrAInfo):
-                preLpos = -1
-                for i, item in enumerate(ChrInfo):
-                    Lname,Lpos = item
-                    if Lpos != preLpos:
-                        offsetA += stepA
-                        differ = 1
-                    else:
-                        differ = 0
-                    preLpos = Lpos
-                    Lpos *= plotXScale
-                    if self.selectedChr > -1:
-                        Zorder = i % 5
-                    else:
-                        Zorder = 0
-                    if differ:
-                        canvas.drawLine(startPosX+Lpos,yZero,xLeftOffset+offsetA,\
-                        yZero+25, color=lineColor)
-                        canvas.drawLine(xLeftOffset+offsetA,yZero+25,xLeftOffset+offsetA,\
-                        yZero+40+Zorder*(LRectWidth+3),color=lineColor)
-                        rectColor = pid.orange
-                    else:
-                        canvas.drawLine(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3,\
-                        xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),color=lineColor)
-                        rectColor = pid.deeppink
-                    canvas.drawRect(xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3),\
-                            xLeftOffset+offsetA-LRectHeight,yZero+40+Zorder*(LRectWidth+3)+LRectWidth,\
-                            edgeColor=rectColor,fillColor=rectColor,edgeWidth = 0)
-                    COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
-                            xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
-                    HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
-                    Areas=HT.Area(shape='rect',coords=COORDS,href=HREF, title="Locus : " + Lname)
-                    gifmap.areas.append(Areas)
-                ##piddle bug
-                if j == 0:
-                    canvas.drawLine(startPosX,yZero,startPosX,yZero+40, color=lineColor)
-                startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-
-        canvas.drawLine(xLeftOffset, yZero, xLeftOffset+plotWidth, yZero, color=pid.black, width=X_AXIS_THICKNESS) # Draw the X axis itself
-
-    def getColorForMarker(self, chrCount,flag):# no change is needed
-        chrColorDict={}
-        for i in range(chrCount):
-            if flag==1: # display blue and lightblue intercross
-                chrColorDict[i]=pid.black
-            elif flag==0:
-                if (i%2==0):
-                    chrColorDict[i]=pid.blue
-                else:
-                    chrColorDict[i]=pid.lightblue
-            else:#display different color for different chr
-                if i in [0,8,16]:
-                    chrColorDict[i]=pid.black
-                elif i in [1,9,17]:
-                    chrColorDict[i]=pid.red
-                elif i in [2,10,18]:
-                    chrColorDict[i]=pid.lightgreen
-                elif i in [3,11,19]:
-                    chrColorDict[i]=pid.blue
-                elif i in [4,12]:
-                    chrColorDict[i]=pid.lightblue
-                elif i in [5,13]:
-                    chrColorDict[i]=pid.hotpink
-                elif i in [6,14]:
-                    chrColorDict[i]=pid.gold
-                elif i in [7,15]:
-                    chrColorDict[i]=pid.grey
-
-        return chrColorDict
-
-
-    def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
-        if len(self.traitList) != 1:
-            return
-
-        xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-        plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-        plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-        yZero = canvas.size[1] - yBottomOffset
-        fontZoom = zoom
-        if zoom == 2:
-            fontZoom = 1.5
-
-        try:
-            Chr = self.traitList[0].chr # self.traitListChr =self.traitList[0].chr=_vals   need to change to chrList and mbList
-            Mb = self.traitList[0].mb # self.traitListMb =self.traitList[0].mb=_vals
-        except:
-            return
-
-        if self.plotScale == 'physic':
-            if self.selectedChr > -1:
-                if self.genotype[0].name != Chr or Mb < self.startMb or Mb > self.endMb:
-                    return
-                else:
-                    locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
-            else:
-                locPixel = xLeftOffset
-                for i, _chr in enumerate(self.genotype):
-                    if _chr.name != Chr:
-                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
-                    else:
-                        locPixel += Mb*plotXScale
-                        break
-        else:
-            if self.selectedChr > -1:
-                if self.genotype[0].name != Chr:
-                    return
-                else:
-                    for i, _locus in enumerate(self.genotype[0]):
-                        #the trait's position is on the left of the first genotype
-                        if i==0 and _locus.Mb >= Mb:
-                            locPixel=-1
-                            break
-
-                        #the trait's position is between two traits
-                        if i > 0 and self.genotype[0][i-1].Mb < Mb and _locus.Mb >= Mb:
-                            locPixel = xLeftOffset + plotXScale*(self.genotype[0][i-1].cM+(_locus.cM-self.genotype[0][i-1].cM)*(Mb -self.genotype[0][i-1].Mb)/(_locus.Mb-self.genotype[0][i-1].Mb))
-                            break
-
-                        #the trait's position is on the right of the last genotype
-                        if i==len(self.genotype[0]) and Mb>=_locus.Mb:
-                            locPixel = -1
-            else:
-                locPixel = xLeftOffset
-                for i, _chr in enumerate(self.genotype):
-                    if _chr.name != Chr:
-                        locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
-                    else:
-                        locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
-                        break
-        if locPixel >= 0:
-            traitPixel = ((locPixel, yZero), (locPixel-6, yZero+12), (locPixel+6, yZero+12))
-            canvas.drawPolygon(traitPixel, edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
-
-        if self.legendChecked:
-            startPosY = 15
-            nCol = 2
-            smallLabelFont = pid.Font(ttf="trebuc", size=12, bold=1)
-            leftOffset = xLeftOffset+(nCol-1)*200
-            canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
-            canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)
-
-    # build dict based on plink result, key is chr, value is list of [snp,BP,pValue]
-    def getPlinkResultDict(self,outputFileName='',thresholdPvalue=-1,ChrOrderIdNameDict={}):
-
-        ChrList =self.ChrList
-        plinkResultDict={}
-
-        plinkResultfp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, outputFileName), "rb")
-
-        headerLine=plinkResultfp.readline()# read header line
-        line = plinkResultfp.readline()
-
-        valueList=[] # initialize value list, this list will include snp, bp and pvalue info
-        pValueList=[]
-        count=0
-
-        while line:
-            #convert line from str to list
-            lineList=self.buildLineList(line=line)
-
-            # only keep the records whose chromosome name is in db
-            if ChrOrderIdNameDict.has_key(int(lineList[0])) and lineList[-1] and lineList[-1].strip()!='NA':
-
-                chrName=ChrOrderIdNameDict[int(lineList[0])]
-                snp = lineList[1]
-                BP = lineList[2]
-                pValue = float(lineList[-1])
-                pValueList.append(pValue)
-
-                if plinkResultDict.has_key(chrName):
-                    valueList=plinkResultDict[chrName]
-
-                    # pvalue range is [0,1]
-                    if thresholdPvalue >=0 and thresholdPvalue<=1:
-                        if pValue < thresholdPvalue:
-                            valueList.append((snp,BP,pValue))
-                            count+=1
-
-                    plinkResultDict[chrName]=valueList
-                    valueList=[]
-                else:
-                    if thresholdPvalue>=0 and thresholdPvalue<=1:
-                        if pValue < thresholdPvalue:
-                            valueList.append((snp,BP,pValue))
-                            count+=1
-
-                    if valueList:
-                        plinkResultDict[chrName]=valueList
-
-                    valueList=[]
-
-
-                line =plinkResultfp.readline()
-            else:
-                line=plinkResultfp.readline()
-
-        if pValueList:
-            minPvalue= min(pValueList)
-        else:
-            minPvalue=0
-
-        return count,minPvalue,plinkResultDict
-
-
-    ######################################################
-    # input: line: str,one line read from file
-    # function: convert line from str to list;
-    # output: lineList list
-    #######################################################
-    def buildLineList(self,line=None):
-
-        lineList = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
-        lineList =[ item for item in lineList if item <>'']
-        lineList = map(string.strip, lineList)
-
-        return lineList
-
-    #added by NL: automatically generate pheno txt file for PLINK based on strainList passed from dataEditing page
-    def genPhenoTxtFileForPlink(self,phenoFileName='', RISetName='', probesetName='', valueDict={}):
-        pedFileStrainList=self.getStrainNameFromPedFile(RISetName=RISetName)
-        outputFile = open("%s%s.txt"%(webqtlConfig.TMPDIR,phenoFileName),"wb")
-        headerLine = 'FID\tIID\t%s\n'%probesetName
-        outputFile.write(headerLine)
-
-        newValueList=[]
-
-        #if valueDict does not include some strain, value will be set to -9999 as missing value
-        for item in pedFileStrainList:
-            try:
-                value=valueDict[item]
-                value=str(value).replace('value=','')
-                value=value.strip()
-            except:
-                value=-9999
-
-            newValueList.append(value)
-
-
-        newLine=''
-        for i, strain in enumerate(pedFileStrainList):
-            j=i+1
-            value=newValueList[i]
-            newLine+='%s\t%s\t%s\n'%(strain, strain, value)
-
-            if j%1000==0:
-                outputFile.write(newLine)
-                newLine=''
-
-        if newLine:
-            outputFile.write(newLine)
-
-        outputFile.close()
-
-    # get strain name from ped file in order
-    def getStrainNameFromPedFile(self, RISetName=''):
-        pedFileopen= open("%splink/%s.ped"%(webqtlConfig.GENODIR, RISetName),"r")
-        line =pedFileopen.readline()
-        strainNameList=[]
-
-        while line:
-            lineList=string.split(string.strip(line),'\t')
-            lineList=map(string.strip,lineList)
-
-            strainName=lineList[0]
-            strainNameList.append(strainName)
-
-            line =pedFileopen.readline()
-
-        return strainNameList
-
-    ################################################################
-    # Generate Chr list, Chr OrderId and Retrieve Length Information
-    ################################################################
-    def getChrNameOrderIdLength(self,RISet=''):
-
-        try:
-            query = """
-                    Select
-                            Chr_Length.Name,Chr_Length.OrderId,Length from Chr_Length, InbredSet
-                    where
-                            Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-                            InbredSet.Name = '%s'
-                    Order by OrderId
-                    """ % (RISet)
-            self.cursor.execute(query)
-
-            results =self.cursor.fetchall()
-            ChrList=[]
-            ChrLengthMbList=[]
-            ChrNameOrderIdDict={}
-            ChrOrderIdNameDict={}
-
-            for item in results:
-                ChrList.append(item[0])
-                ChrNameOrderIdDict[item[0]]=item[1] # key is chr name, value is orderId
-                ChrOrderIdNameDict[item[1]]=item[0] # key is orderId, value is chr name
-                ChrLengthMbList.append(item[2])
-
-        except:
-            ChrList=[]
-            ChrNameOrderIdDict={}
-            ChrLengthMbList=[]
-
-        return ChrList,ChrNameOrderIdDict,ChrOrderIdNameDict,ChrLengthMbList
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 66884b0c..a55b6c10 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1193,25 +1193,40 @@ class MarkerRegression(object):
             canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
             canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
 
-        labelFont=pid.Font(ttf="verdana",size=12*fontZoom)
+        labelFont = pid.Font(ttf="verdana",size=12*fontZoom)
         labelColor = pid.black
         if self.selectedChr == -1:
             string1 = 'Mapping for Dataset: %s, mapping on All Chromosomes' % self.dataset.group.name
         else:
             string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (self.dataset.group.name, self.ChrList[self.selectedChr][0])
-        if self.controlLocus and self.doControl != "false":
-            string2 = 'Using %s as control' % self.controlLocus
+
+        if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
+            if self.use_loco == "True":
+                string2 = 'Using GEMMA mapping method with LOCO and '
+            else:
+                string2 = 'Using GEMMA mapping method with '
+            if self.covariates != "":
+                string2 += 'the cofactors below:'
+                cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")])
+                string3 = cofactor_names
+            else:
+                string2 += 'no cofactors.'
+                string3 = ''
+        elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
+            string2 = 'Using R/qtl mapping method with '
+            if self.controlLocus and self.doControl != "false":
+                string2 += '%s as control' % self.controlLocus
+            else:
+                string2 += 'no control for other QTLs'
+        elif self.mapping_method == "plink":
+            string2 = 'Using PLINK mapping method with no control for other QTLs.'
         else:
-            if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
-                string2 = 'Using GEMMA mapping method with no control for other QTLs.'
-                if self.covariates != "":
-                    string3 = 'Using following traits as covariates: ' + self.covariates
-            elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
-                string2 = 'Using R/qtl mapping method with no control for other QTLs.'
-            elif self.mapping_method == "plink":
-                string2 = 'Using PLINK mapping method with no control for other QTLs.'
+            string2 = 'Using Haldane mapping function with '
+            if self.controlLocus and self.doControl != "false":
+                string2 += '%s as control' % self.controlLocus
             else:
-                string2 = 'Using Haldane mapping function with no control for other QTLs'
+                string2 += 'no control for other QTLs'
+
         if self.this_trait.name:
             identification = "Trait ID: %s : %s" % (self.dataset.fullname, self.this_trait.name)
             d = 4+ max(canvas.stringWidth(identification, font=labelFont), canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
@@ -1220,6 +1235,8 @@ class MarkerRegression(object):
             d = 4+ max(canvas.stringWidth(string1, font=labelFont), canvas.stringWidth(string2, font=labelFont))
         canvas.drawString(string1,canvas.size[0] - xRightOffset-d,35*fontZoom,font=labelFont,color=labelColor)
         canvas.drawString(string2,canvas.size[0] - xRightOffset-d,50*fontZoom,font=labelFont,color=labelColor)
+        if string3 != '':
+            canvas.drawString(string3,canvas.size[0] - xRightOffset-d,65*fontZoom,font=labelFont,color=labelColor)
 
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
diff --git a/wqflask/wqflask/show_trait/show_trait_page.py b/wqflask/wqflask/show_trait/show_trait_page.py
deleted file mode 100644
index de818a64..00000000
--- a/wqflask/wqflask/show_trait/show_trait_page.py
+++ /dev/null
@@ -1,141 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-from __future__ import division, print_function
-
-from flask import request
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
-from base.templatePage import templatePage
-from DataEditingPage import DataEditingPage
-
-
-
-class ShowTraitPage(DataEditingPage):
-
-    def __init__(self, fd, traitInfos = None):
-        self.fd = fd
-
-        # This sets self.cursor
-        assert self.openMysql(), "No database"
-
-        # When is traitInfos used?
-        if traitInfos:
-            database, ProbeSetID, CellID = traitInfos
-        else:
-            print("fd is:", fd)
-            database = fd['database']
-            ProbeSetID = fd['ProbeSetID']
-
-            CellID = fd.get('CellID')
-
-
-        thisTrait = webqtlTrait(db=database, name=ProbeSetID, cellid=CellID, cursor=self.cursor)
-
-        if thisTrait.db.type == "ProbeSet":
-
-            self.cursor.execute('''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers
-                                    FROM ProbeSetFreeze WHERE Name = "%s"''' %  database)
-
-            indId, indName, indFullName, confidential, AuthorisedUsers = self.cursor.fetchall()[0]
-
-            if confidential == 1:
-                access_to_confidential_dataset = 0
-
-                #for the dataset that confidentiality is 1
-                #1. 'admin' and 'root' can see all of the dataset
-                #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
-                if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
-                    access_to_confidential_dataset = 1
-                else:
-                    AuthorisedUsersList=AuthorisedUsers.split(',')
-                    if AuthorisedUsersList.__contains__(self.userName):
-                        access_to_confidential_dataset = 1
-
-                if not access_to_confidential_dataset:
-                    #Error, Confidential Database
-                    heading = "Show Database"
-                    detail = ["The %s database you selected is not open to the public \
-                    at this time, please go back and select other database." % indFullName]
-                    self.error(heading=heading,detail=detail,error="Confidential Database")
-                    return
-        print("environ:", request.environ)
-
-        # Becuase of proxying remote_addr is probably localhost, so we first try for
-        # HTTP_X_FORWARDED_FOR
-        user_ip = request.environ.get('HTTP_X_FORWARDED_FOR') or request.remote_addr   # in old app was fd.remote_ip
-        print("user_ip is:", user_ip)
-        query = "SELECT count(id) FROM AccessLog WHERE ip_address = %s and \
-                        UNIX_TIMESTAMP()-UNIX_TIMESTAMP(accesstime)<86400"
-        self.cursor.execute(query,user_ip)
-        daycount = self.cursor.fetchall()
-        if daycount:
-            daycount = daycount[0][0]
-            if daycount > webqtlConfig.DAILYMAXIMUM:
-                heading = "Retrieve Data"
-                detail = ['For security reasons, the maximum access to a database is \
-                %d times per day per ip address. You have reached the limit, please \
-                try it again tomorrow.' % webqtlConfig.DAILYMAXIMUM]
-                self.error(heading=heading,detail=detail)
-                return
-
-
-        if thisTrait.db.type != 'ProbeSet' and thisTrait.cellid:
-            heading = "Retrieve Data"
-            detail = ['The Record you requested doesn\'t exist!']
-            self.error(heading=heading,detail=detail)
-            return
-
-        ##identification, etc.
-        fd.identification = '%s : %s' % (thisTrait.db.shortname,ProbeSetID)
-        thisTrait.returnURL = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s\
-                &ProbeSetID=%s&RISet=%s&parentsf1=on' %(database, ProbeSetID, fd['RISet'])
-
-        if CellID:
-            fd.identification = '%s/%s'%(fd.identification, CellID)
-            thisTrait.returnURL = '%s&CellID=%s' % (thisTrait.returnURL, CellID)
-
-        thisTrait.retrieveInfo()
-        thisTrait.retrieveData()
-        self.updMysql()
-        self.cursor.execute("insert into AccessLog(accesstime,ip_address) values(Now(),%s)", user_ip)
-        self.openMysql()
-
-
-        ##read genotype file
-        fd.RISet = thisTrait.riset
-        fd.readGenotype()
-
-        #if webqtlUtil.ListNotNull(map(lambda x:x.var, thisTrait.data.values())):
-        if any([x.variance for x in thisTrait.data.values()]):
-            fd.display_variance = True
-            fd.formID = 'varianceChoice'
-
-        DataEditingPage.__init__(self, fd, thisTrait)
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 5d128b4a..4aad4242 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -16,16 +16,6 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-<!--
-    {% if dataset.type == 'Temp' %}
-	{{ header("{}".format("Temporary Trait")) }}
-    {% elif dataset.type != 'Geno' %}
-	{{ header("{}".format(this_trait.name_header_fmt),
-	    '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-    {% else %}
-	{{ header("{}".format(this_trait.name_header_fmt)) }}
-    {% endif %}
--->
     <div class="container">
         <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2>
         {% if this_trait.dataset.type != 'Publish' %}
-- 
cgit v1.2.3


From ab914075b0a83428e471ce7ffbe5700c5c0a9625 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 16:32:25 +0000
Subject: Removed some unused code in webqtlConfig; some might need to be added
 back in later when other third party links are implemented on the
 trait/collection pages

---
 wqflask/base/webqtlConfig.py                       | 28 +--------------
 .../marker_regression/marker_regression_gn1.py     | 40 ----------------------
 2 files changed, 1 insertion(+), 67 deletions(-)

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 1e66e957..4708bf0a 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -20,46 +20,20 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 #minimum number of informative strains
 KMININFORMATIVE = 5
 
-#maximum number of traits for interval mapping
-MULTIPLEMAPPINGLIMIT = 11
-
-#maximum number of traits for correlation
-MAXCORR = 100
-
 #Daily download limit from one IP
 DAILYMAXIMUM = 1000
 
 #maximum LRS value
 MAXLRS = 460.0
 
-#temporary data life span
-MAXLIFE = 86400
-
 #MINIMUM Database public value
 PUBLICTHRESH = 0
 
-#NBCI address
-NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s"
-UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
-GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
-OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
-HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
+#EXTERNAL LINK ADDRESSES
 PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
 UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
-ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
-DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
-UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
-GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
-
-# The following paths are no longer in use!
-#   HTMLPATH is replaced by GENODIR
-#   IMGDIR is replaced by GENERATED_IMAGE_DIR
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index a55b6c10..c196b58b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -406,51 +406,11 @@ class MarkerRegression(object):
         else:
             self.GraphInterval = self.cMGraphInterval #cM
 
-        ################################################################
-        # Get Trait Values and Infomation
-        ################################################################
-        ##input from search page or selection page
-        #self.searchResult = fd.formdata.getvalue('searchResult')
-        ##convert single selection into a list
-        #if type("1") == type(self.searchResult):
-        #    self.searchResult = string.split(self.searchResult,'\t')
-        #
-        #self.traitList = []
-        #if self.searchResult and len(self.searchResult) > webqtlConfig.MULTIPLEMAPPINGLIMIT:
-        #    heading = 'Multiple Interval Mapping'
-        #    detail = ['In order to get clear result, do not select more than %d traits for \
-        #            Multiple Interval Mapping analysis.' % webqtlConfig.MULTIPLEMAPPINGLIMIT]
-        #    self.error(heading=heading,detail=detail)
-        #    return
-        #elif self.searchResult:
-        #    self.dataSource = 'selectionPage'
-        #    for item in self.searchResult:
-        #        thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-        #        thisTrait.retrieveInfo()
-        #        thisTrait.retrieveData(fd.strainlist)
-        #        self.traitList.append(thisTrait)
-        #else:
-
-        #input from data editing page
-        #fd.readData()
-        #if not fd.allTraitData:
-        #    heading = "Mapping"
-        #    detail = ['No trait data was selected for %s data set. No mapping attempted.' % fd.RISet]
-        #    self.error(heading=heading,detail=detail)
-        #    return
-
         self.dataSource = 'editingPage'
         self.traitList = []
         thisTrait = start_vars['this_trait']
-        #fullname = fd.formdata.getvalue('fullname', '')
-        #if fullname:
-        #    thisTrait = webqtlTrait(fullname=fullname, data=fd.allTraitData, cursor=self.cursor)
-        #    thisTrait.retrieveInfo()
-        #else:
-        #    thisTrait = webqtlTrait(data=fd.allTraitData)
         self.traitList.append(thisTrait)
 
-
 ## BEGIN HaplotypeAnalyst
 ## count the amount of individuals to be plotted, and increase self.graphHeight
         if self.haplotypeAnalystChecked and self.selectedChr > -1:
-- 
cgit v1.2.3


From fb62420ddbbf0189c9b0fb6d227121836fc377d8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 16:40:09 +0000
Subject: Removed unused code from webqtlFormData.py

---
 wqflask/base/webqtlFormData.py | 99 +-----------------------------------------
 1 file changed, 2 insertions(+), 97 deletions(-)

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
index 10251756..1b41b2fc 100644
--- a/wqflask/base/webqtlFormData.py
+++ b/wqflask/base/webqtlFormData.py
@@ -24,8 +24,6 @@
 #
 # Last updated by GeneNetwork Core Team 2010/10/20
 
-#from mod_python import Cookie
-
 from __future__ import print_function
 from pprint import pformat as pf
 
@@ -49,20 +47,13 @@ class webqtlFormData(object):
 
     def __init__(self,
                  start_vars = None,
-                 req = None,
-                 mod_python_session=None,
-                 FieldStorage_formdata=None):
+                 req = None):
         # Todo: rework this whole thing
-        print("in webqtlFormData start_vars are:", pf(start_vars))
         for item in webqtlFormData.attrs:
             self.__dict__[item] = None
 
-        #ZS: This is only used in DataEditingPage.py (as far as I know)
-        self.varianceDispName = None
-
         for item in start_vars:
             self.__dict__[item] = start_vars[item]
-        print("  Now self.dict is:", pf(self.__dict__))
 
         #Todo: This can't be good below...rework
         try:
@@ -70,42 +61,11 @@ class webqtlFormData(object):
         except:
             self.remote_ip = '1.2.3.4'
 
-        if req and req.headers_in.has_key('referer'):
-            self.refURL = req.headers_in['referer']
-        else:
-            self.refURL = None
-
-        # For now let's just comment all this out - Sam
-
-        #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie.
-        #
-        ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable.
-        #self.input_session_data = sessionData.sessionData( mod_python_session )
-        #
-        ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data.
-        #self.formdata = cgiData( FieldStorage_formdata )
-        #
-        ##get Form ID
-        #self.formID = self.formdata.getfirst('FormID')
-        #
-        ##get rest of the attributes
-        #if self.formID:
-        #       for item in self.attrs:
-        #               value = self.formdata.getfirst(item)
-        #               if value != None:
-        #                       setattr(self,item,string.strip(value))
-
         self.ppolar = None
         self.mpolar = None
 
-        print("[yellow] self.group is:", self.group)
         if self.group:
-            #try:
-            #    # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
             _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
-            #except:
-            #    f1 = f12 = self.mpolar = self.ppolar = None
-
 
         def set_number(stringy):
             return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
@@ -113,22 +73,13 @@ class webqtlFormData(object):
         self.nperm = set_number(self.nperm)
         self.nboot = set_number(self.nboot)
 
-
-        #if self.allsamplelist:
-        #    self.allsamplelist = map(string.strip, string.split(self.allsamplelist))
-        print("self.allsamplelist is:", self.allsamplelist)
         if self.allsamplelist:
             self.allsamplelist = self.allsamplelist.split()
-        print("now self.allsamplelist is:", self.allsamplelist)
-        #self.readGenotype()
-        #self.readData()
 
         if self.group == 'BXD300':
             self.group = 'BXD'
 
-
     def __getitem__(self, key):
-        print("in __getitem__")
         return self.__dict__[key]
 
     def get(self, key, default=None):
@@ -206,8 +157,6 @@ class webqtlFormData(object):
             else:
                 samplelist = self.samplelist
 
-        #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
-
         traitfiledata = getattr(self, "traitfile", None)
         traitpastedata = getattr(self, "traitpaste", None)
         variancefiledata = getattr(self, "variancefile", None)
@@ -233,15 +182,12 @@ class webqtlFormData(object):
             print("mapping formdataasfloat")
             #values = map(self.FormDataAsFloat, samplelist)
             values = [to_float(getattr(self, key)) for key in samplelist]
-        print("rocket values is:", values)
 
 
         if len(values) < len(samplelist):
             values += [None] * (len(samplelist) - len(values))
         elif len(values) > len(samplelist):
             values = values[:len(samplelist)]
-        print("now values is:", values)
-
 
         if variancefiledata:
             tt = variancefiledata.split()
@@ -271,9 +217,6 @@ class webqtlFormData(object):
             if values[i] != None:
                 self.allTraitData[_sample] = webqtlCaseData(
                     _sample, values[i], variances[i], nsamples[i])
-        print("allTraitData is:", pf(self.allTraitData))
-
-
 
     def informativeStrains(self, samplelist=None, include_variances = None):
         '''if readData was called, use this to output informative samples (sample with values)'''
@@ -285,8 +228,6 @@ class webqtlFormData(object):
         values = []
         variances = []
 
-        #print("self.allTraitData is:", pf(self.allTraitData))
-
         for sample in samplelist:
             if sample in self.allTraitData:
                 _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
@@ -303,16 +244,6 @@ class webqtlFormData(object):
 
         return samples, values, variances, len(samples)
 
-
-
-    #def FormDataAsFloat(self, key):
-    #
-    #    #try:
-    #    #    return float(self.key)
-    #    #except:
-    #    #    return None
-
-
     def FormVarianceAsFloat(self, key):
         try:
             return float(self.formdata.getfirst('V' + key))
@@ -323,30 +254,4 @@ class webqtlFormData(object):
         try:
             return int(self.formdata.getfirst('N' + key))
         except:
-            return None
-
-    def Sample(self):
-        'Create some dummy data for testing'
-        self.group = 'BXD'
-        self.incparentsf1 = 'on'
-        #self.display = 9.2
-        #self.significance = 16.1
-        self.readGenotype()
-        self.identification = 'BXD : Coat color example by Lu Lu, et al'
-        #self.readGenotype()
-        #self.genotype.ReadMM('AXBXAforQTL')
-        #self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
-        #self.samplelist.sort()
-        self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2),
-        'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2),
-        'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4),
-        'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2),
-        'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3),
-        'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3),
-        'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2),
-        'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4),
-        'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4),
-        'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1),
-        'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4),
-        'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4),
-        'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
+            return None
\ No newline at end of file
-- 
cgit v1.2.3


From c9b0ab18457929bd7ca458f7207e50fe14099d6a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 16:51:54 +0000
Subject: Removed the basicStatistics directory/contents because nothing there
 was being used except corestats, which I moved to utility

Removed box plot code from Plot.py since we no longer use it either
---
 .../basicStatistics/BasicStatisticsFunctions.py    | 207 ---------------------
 wqflask/basicStatistics/__init__.py                |   0
 wqflask/basicStatistics/corestats.py               | 103 ----------
 wqflask/utility/Plot.py                            | 134 +------------
 wqflask/utility/corestats.py                       |  99 ++++++++++
 wqflask/wqflask/show_trait/show_trait.py           |   1 -
 6 files changed, 100 insertions(+), 444 deletions(-)
 delete mode 100644 wqflask/basicStatistics/BasicStatisticsFunctions.py
 delete mode 100644 wqflask/basicStatistics/__init__.py
 delete mode 100644 wqflask/basicStatistics/corestats.py
 create mode 100644 wqflask/utility/corestats.py

diff --git a/wqflask/basicStatistics/BasicStatisticsFunctions.py b/wqflask/basicStatistics/BasicStatisticsFunctions.py
deleted file mode 100644
index 1e5646a1..00000000
--- a/wqflask/basicStatistics/BasicStatisticsFunctions.py
+++ /dev/null
@@ -1,207 +0,0 @@
-from __future__ import print_function
-
-#import string
-from math import *
-#import piddle as pid
-#import os
-import traceback
-
-from pprint import pformat as pf
-
-from corestats import Stats
-
-import reaper
-from htmlgen import HTMLgen2 as HT
-
-#from utility import Plot
-from utility import webqtlUtil
-from base import webqtlConfig
-from db import webqtlDatabaseFunction
-
-def basicStatsTable(vals, trait_type=None, cellid=None, heritability=None):
-    print("basicStatsTable called - len of vals", len(vals))
-    st = {}  # This is the dictionary where we'll put everything for the template
-    valsOnly = []
-    dataXZ = vals[:]
-    for i in range(len(dataXZ)):
-        valsOnly.append(dataXZ[i][1])
-
-    (st['traitmean'],
-     st['traitmedian'],
-     st['traitvar'],
-     st['traitstdev'],
-     st['traitsem'],
-     st['N']) = reaper.anova(valsOnly) #ZS: Should convert this from reaper to R in the future
-
-    #tbl = HT.TableLite(cellpadding=20, cellspacing=0)
-    #dataXZ = vals[:]
-    dataXZ = sorted(vals, webqtlUtil.cmpOrder)
-
-    print("data for stats is:", pf(dataXZ))
-    for num, item in enumerate(dataXZ):
-        print(" %i - %s" % (num, item))
-    print("  length:", len(dataXZ))
-
-    st['min'] = dataXZ[0][1]
-    st['max'] = dataXZ[-1][1]
-
-    numbers = [x[1] for x in dataXZ]
-    stats = Stats(numbers)
-
-    at75 = stats.percentile(75)
-    at25 = stats.percentile(25)
-    print("should get a stack")
-    traceback.print_stack()
-    print("Interquartile:", at75 - at25)
-
-    #tbl.append(HT.TR(HT.TD("Statistic",align="left", Class="fs14 fwb ffl b1 cw cbrb", width = 180),
-    #                HT.TD("Value", align="right", Class="fs14 fwb ffl b1 cw cbrb", width = 60)))
-    #tbl.append(HT.TR(HT.TD("N of Samples",align="left", Class="fs13 b1 cbw c222"),
-    #                HT.TD(N,nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    #tbl.append(HT.TR(HT.TD("Mean",align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%2.3f" % traitmean,nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    #tbl.append(HT.TR(HT.TD("Median",align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%2.3f" % traitmedian,nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    ##tbl.append(HT.TR(HT.TD("Variance",align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    ##               HT.TD("%2.3f" % traitvar,nowrap="yes",align="left", Class="fs13 b1 cbw c222")))
-    #tbl.append(HT.TR(HT.TD("Standard Error (SE)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%2.3f" % traitsem,nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    #tbl.append(HT.TR(HT.TD("Standard Deviation (SD)", align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%2.3f" % traitstdev,nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    #tbl.append(HT.TR(HT.TD("Minimum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%s" % dataXZ[0][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-    #tbl.append(HT.TR(HT.TD("Maximum", align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-    #                HT.TD("%s" % dataXZ[-1][1],nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-
-
-
-    if (trait_type != None and trait_type == 'ProbeSet'):
-        #tbl.append(HT.TR(HT.TD("Range (log2)",align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-        #        HT.TD("%2.3f" % (dataXZ[-1][1]-dataXZ[0][1]),nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-        #tbl.append(HT.TR(HT.TD(HT.Span("Range (fold)"),align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-        #        HT.TD("%2.2f" % pow(2.0,(dataXZ[-1][1]-dataXZ[0][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-        #tbl.append(HT.TR(HT.TD(HT.Span(HT.Href(url="/glossary.html#Interquartile", target="_blank", text="Interquartile Range", Class="non_bold")), align="left", Class="fs13 b1 cbw c222",nowrap="yes"),
-        #        HT.TD("%2.2f" % pow(2.0,(dataXZ[int((N-1)*3.0/4.0)][1]-dataXZ[int((N-1)/4.0)][1])), nowrap="yes", Class="fs13 b1 cbw c222"), align="right"))
-        st['range_log2'] = dataXZ[-1][1]-dataXZ[0][1]
-        st['range_fold'] = pow(2.0, (dataXZ[-1][1]-dataXZ[0][1]))
-        st['interquartile'] = pow(2.0, (dataXZ[int((st['N']-1)*3.0/4.0)][1]-dataXZ[int((st['N']-1)/4.0)][1]))
-
-        #XZ, 04/01/2009: don't try to get H2 value for probe.
-        if not cellid:
-            if heritability:
-                # This field needs to still be put into the Jinja2 template
-                st['heritability'] = heritability
-                #tbl.append(HT.TR(HT.TD(HT.Span("Heritability"),align="center", Class="fs13 b1 cbw c222",nowrap="yes"),HT.TD("%s" % heritability, nowrap="yes",align="center", Class="fs13 b1 cbw c222")))
-
-        # Lei Yan
-        # 2008/12/19
-
-    return st
-
-def plotNormalProbability(vals=None, RISet='', title=None, showstrains=0, specialStrains=[None], size=(750,500)):
-
-    dataXZ = vals[:]
-    dataXZ.sort(webqtlUtil.cmpOrder)
-    dataLabel = []
-    dataX = map(lambda X: X[1], dataXZ)
-
-    showLabel = showstrains
-    if len(dataXZ) > 50:
-        showLabel = 0
-    for item in dataXZ:
-        strainName = webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=item[0])
-        dataLabel.append(strainName)
-
-    dataY=Plot.U(len(dataX))
-    dataZ=map(Plot.inverseCumul,dataY)
-    c = pid.PILCanvas(size=(750,500))
-    Plot.plotXY(c, dataZ, dataX, dataLabel = dataLabel, XLabel='Expected Z score', connectdot=0, YLabel='Trait value', title=title, specialCases=specialStrains, showLabel = showLabel)
-
-    filename= webqtlUtil.genRandStr("nP_")
-    c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
-
-    img=HT.Image('/image/'+filename+'.gif',border=0)
-
-    return img
-
-def plotBoxPlot(vals):
-
-    valsOnly = []
-    dataXZ = vals[:]
-    for i in range(len(dataXZ)):
-        valsOnly.append(dataXZ[i][1])
-
-    plotHeight = 320
-    plotWidth = 220
-    xLeftOffset = 60
-    xRightOffset = 40
-    yTopOffset = 40
-    yBottomOffset = 60
-
-    canvasHeight = plotHeight + yTopOffset + yBottomOffset
-    canvasWidth = plotWidth + xLeftOffset + xRightOffset
-    canvas = pid.PILCanvas(size=(canvasWidth,canvasHeight))
-    XXX = [('', valsOnly[:])]
-
-    Plot.plotBoxPlot(canvas, XXX, offset=(xLeftOffset, xRightOffset, yTopOffset, yBottomOffset), XLabel= "Trait")
-    filename= webqtlUtil.genRandStr("Box_")
-    canvas.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
-    img=HT.Image('/image/'+filename+'.gif',border=0)
-
-    plotLink = HT.Span("More about ", HT.Href(text="Box Plots", url="http://davidmlane.com/hyperstat/A37797.html", target="_blank", Class="fs13"))
-
-    return img, plotLink
-
-def plotBarGraph(identification='', RISet='', vals=None, type="name"):
-
-    this_identification = "unnamed trait"
-    if identification:
-        this_identification = identification
-
-    if type=="rank":
-        dataXZ = vals[:]
-        dataXZ.sort(webqtlUtil.cmpOrder)
-        title='%s' % this_identification
-    else:
-        dataXZ = vals[:]
-        title='%s' % this_identification
-
-    tvals = []
-    tnames = []
-    tvars = []
-    for i in range(len(dataXZ)):
-        tvals.append(dataXZ[i][1])
-        tnames.append(webqtlUtil.genShortStrainName(RISet=RISet, input_strainName=dataXZ[i][0]))
-        tvars.append(dataXZ[i][2])
-    nnStrain = len(tnames)
-
-    sLabel = 1
-
-    ###determine bar width and space width
-    if nnStrain < 20:
-        sw = 4
-    elif nnStrain < 40:
-        sw = 3
-    else:
-        sw = 2
-
-    ### 700 is the default plot width minus Xoffsets for 40 strains
-    defaultWidth = 650
-    if nnStrain > 40:
-        defaultWidth += (nnStrain-40)*10
-    defaultOffset = 100
-    bw = int(0.5+(defaultWidth - (nnStrain-1.0)*sw)/nnStrain)
-    if bw < 10:
-        bw = 10
-
-    plotWidth = (nnStrain-1)*sw + nnStrain*bw + defaultOffset
-    plotHeight = 500
-    #print [plotWidth, plotHeight, bw, sw, nnStrain]
-    c = pid.PILCanvas(size=(plotWidth,plotHeight))
-    Plot.plotBarText(c, tvals, tnames, variance=tvars, YLabel='Value', title=title, sLabel = sLabel, barSpace = sw)
-
-    filename= webqtlUtil.genRandStr("Bar_")
-    c.save(webqtlConfig.GENERATED_IMAGE_DIR+filename, format='gif')
-    img=HT.Image('/image/'+filename+'.gif',border=0)
-
-    return img
diff --git a/wqflask/basicStatistics/__init__.py b/wqflask/basicStatistics/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/wqflask/basicStatistics/corestats.py b/wqflask/basicStatistics/corestats.py
deleted file mode 100644
index eba84c52..00000000
--- a/wqflask/basicStatistics/corestats.py
+++ /dev/null
@@ -1,103 +0,0 @@
-#!/usr/bin/env python
-
-#  corestats.py (COREy STATS)
-#  Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org)
-#
-#    statistical calculation class
-#    for processing numeric sequences
-#
-#  license: GNU LGPL
-#
-#  This library is free software; you can redistribute it and/or
-#  modify it under the terms of the GNU Lesser General Public
-#  License as published by the Free Software Foundation; either
-#  version 2.1 of the License, or (at your option) any later version.
-
-
-
-import sys
-
-
-class Stats:
-
-    def __init__(self, sequence):
-        # sequence of numbers we will process
-        # convert all items to floats for numerical processing
-        self.sequence = [float(item) for item in sequence]
-
-
-    def sum(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            return sum(self.sequence)
-
-
-    def count(self):
-        return len(self.sequence)
-
-
-    def min(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            return min(self.sequence)
-
-
-    def max(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            return max(self.sequence)
-
-
-    def avg(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            return sum(self.sequence) / len(self.sequence)
-
-
-    def median(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            self.sequence.sort()
-            return self.sequence[len(self.sequence) // 2]
-
-
-    def stdev(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            avg = self.avg()
-            sdsq = sum([(i - avg) ** 2 for i in self.sequence])
-            stdev = (sdsq / (len(self.sequence) - 1)) ** .5
-            return stdev
-
-
-    def percentile(self, percentile):
-        if len(self.sequence) < 1:
-            value = None
-        elif (percentile >= 100):
-            sys.stderr.write('ERROR: percentile must be < 100.  you supplied: %s\n'% percentile)
-            value = None
-        else:
-            element_idx = int(len(self.sequence) * (percentile / 100.0))
-            self.sequence.sort()
-            value = self.sequence[element_idx]
-        return value
-
-
-
-
-# Sample script using this class:
-# -------------------------------------------
-#    #!/usr/bin/env python
-#    import corestats
-#
-#    sequence = [1, 2.5, 7, 13.4, 8.0]
-#    stats = corestats.Stats(sequence)
-#    print stats.avg()
-#    print stats.percentile(90)
-# -------------------------------------------
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d60e2bb2..3a8b8dd5 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -36,11 +36,10 @@ from numarray import linear_algebra as la
 from numarray import ones, array, dot, swapaxes
 
 import reaper
-# sys.path.append("..") Never in a running webserver
-from basicStatistics import corestats
 
 import svg
 import webqtlUtil
+import corestats
 from base import webqtlConfig
 
 import utility.logger
@@ -315,137 +314,6 @@ def find_outliers(vals):
     logger.debug(pf(locals()))
     return upper_bound, lower_bound
 
-
-def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
-    xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-    plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-    plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-    iValues = []
-    for item in data:
-        for item2 in item[1]:
-            try:
-                iValues.append(item2[1])
-            except:
-                iValues.append(item2)
-
-    #draw frame
-    max_Y = max(iValues)
-    min_Y = min(iValues)
-    scaleY = detScale(min_Y, max_Y)
-    Yll = scaleY[0]
-    Yur = scaleY[1]
-    nStep = scaleY[2]
-    stepY = (Yur - Yll)/nStep
-    stepYPixel = plotHeight/(nStep)
-    canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
-
-    ##draw Y Scale
-    YYY = Yll
-    YCoord = plotHeight + yTopOffset
-    scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-    for i in range(nStep+1):
-        strY = cformat(d=YYY, rank=0)
-        YCoord = max(YCoord, yTopOffset)
-        canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
-        canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont)
-        YYY += stepY
-        YCoord -= stepYPixel
-
-    ##draw X Scale
-    stepX = plotWidth/len(data)
-    XCoord = xLeftOffset + 0.5*stepX
-    YCoord = plotHeight + yTopOffset
-    scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
-    labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
-    for item in data:
-        itemname, itemvalue = item
-        canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
-        canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\
-        YCoord +20,font=labelFont)
-
-        nValue = len(itemvalue)
-        catValue = []
-        for item2 in itemvalue:
-            try:
-                tstrain, tvalue = item2
-            except:
-                tvalue = item2
-            if nValue <= 4:
-                canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
-            else:
-                catValue.append(tvalue)
-        if catValue != []:
-            catMean = gmean(catValue)
-            catMedian = gmedian(catValue)
-            lowHinge = gpercentile(catValue, 25)
-            upHinge = gpercentile(catValue, 75)
-            Hstep = 1.5*(upHinge - lowHinge)
-
-            outlier = []
-            extrem = []
-
-            upperAdj = None
-            for item in catValue:
-                if item >= upHinge + 2*Hstep:
-                    extrem.append(item)
-                elif item >= upHinge + Hstep:
-                    outlier.append(item)
-                elif item > upHinge and  item < upHinge + Hstep:
-                    if upperAdj == None or item > upperAdj:
-                        upperAdj = item
-                else:
-                    pass
-            lowerAdj = None
-            for item in catValue:
-                if item <= lowHinge - 2*Hstep:
-                    extrem.append(item)
-                elif item <= lowHinge - Hstep:
-                    outlier.append(item)
-                if item < lowHinge and  item > lowHinge - Hstep:
-                    if lowerAdj == None or item < lowerAdj:
-                        lowerAdj = item
-                    else:
-                        pass
-            canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-                    XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
-            canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
-                    XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
-            if upperAdj != None:
-                canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
-                XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-                canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
-                XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-            if lowerAdj != None:
-                canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-                XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-                canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
-                XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-
-            outlierFont = pid.Font(ttf="cour",size=12,bold=0)
-            if outlier != []:
-                for item in outlier:
-                    yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-                    #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-                    canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
-            if extrem != []:
-                for item in extrem:
-                    yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-                    #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-                    canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
-
-            canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
-                    color=pid.blue,size=3)
-            #print(catMean, catMedian, cat25per, cat75per)
-            pass
-
-        XCoord += stepX
-
-    labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-    canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \
-    YCoord +40, font=labelFont)
-    canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
-     font=labelFont, angle =90)
-
 def plotSecurity(canvas, text="12345"):
     if not text:
         return
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
new file mode 100644
index 00000000..c48183ed
--- /dev/null
+++ b/wqflask/utility/corestats.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+#  corestats.py (COREy STATS)
+#  Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org)
+#
+#    statistical calculation class
+#    for processing numeric sequences
+#
+#  license: GNU LGPL
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2.1 of the License, or (at your option) any later version.
+
+import sys
+
+#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+class Stats:
+
+    def __init__(self, sequence):
+        # sequence of numbers we will process
+        # convert all items to floats for numerical processing
+        self.sequence = [float(item) for item in sequence]
+
+
+    def sum(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return sum(self.sequence)
+
+
+    def count(self):
+        return len(self.sequence)
+
+
+    def min(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return min(self.sequence)
+
+
+    def max(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return max(self.sequence)
+
+
+    def avg(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return sum(self.sequence) / len(self.sequence)
+
+
+    def median(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            self.sequence.sort()
+            return self.sequence[len(self.sequence) // 2]
+
+
+    def stdev(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            avg = self.avg()
+            sdsq = sum([(i - avg) ** 2 for i in self.sequence])
+            stdev = (sdsq / (len(self.sequence) - 1)) ** .5
+            return stdev
+
+
+    def percentile(self, percentile):
+        if len(self.sequence) < 1:
+            value = None
+        elif (percentile >= 100):
+            sys.stderr.write('ERROR: percentile must be < 100.  you supplied: %s\n'% percentile)
+            value = None
+        else:
+            element_idx = int(len(self.sequence) * (percentile / 100.0))
+            self.sequence.sort()
+            value = self.sequence[element_idx]
+        return value
+
+
+# Sample script using this class:
+# -------------------------------------------
+#    #!/usr/bin/env python
+#    import corestats
+#
+#    sequence = [1, 2.5, 7, 13.4, 8.0]
+#    stats = corestats.Stats(sequence)
+#    print stats.avg()
+#    print stats.percentile(90)
+# -------------------------------------------
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 6de5cd5f..1f000564 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -24,7 +24,6 @@ from utility import webqtlUtil, Plot, Bunch, helper_functions
 from base.trait import GeneralTrait
 from base import data_set
 from db import webqtlDatabaseFunction
-from basicStatistics import BasicStatisticsFunctions
 
 from pprint import pformat as pf
 
-- 
cgit v1.2.3


From ad71cfe2828a2cc7378b83c0b0f476b53e7dd03b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 17:18:15 +0000
Subject: Removed unused code from convert_geno_to_bimbam.py and corestats.py

---
 wqflask/maintenance/convert_geno_to_bimbam.py | 77 +++++----------------------
 wqflask/utility/corestats.py                  | 16 ------
 2 files changed, 12 insertions(+), 81 deletions(-)

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 05006d5c..45522705 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -17,17 +17,12 @@ import glob
 import traceback
 import gzip
 
-#import numpy as np
-#from pyLMM import lmm
-
 import simplejson as json
 
 from pprint import pformat as pf
 
 class EmptyConfigurations(Exception): pass
 
-        
-
 class Marker(object):
     def __init__(self):
         self.name = None
@@ -39,47 +34,34 @@ class Marker(object):
 class ConvertGenoFile(object):
 
     def __init__(self, input_file, output_files):
-        
         self.input_file = input_file
         self.output_files = output_files
-        
+
         self.mb_exists = False
         self.cm_exists = False
         self.markers = []
-        
+
         self.latest_row_pos = None
         self.latest_col_pos = None
-        
+
         self.latest_row_value = None
         self.latest_col_value = None
-        
-    def convert(self):
 
+    def convert(self):
         self.haplotype_notation = {
             '@mat': "1",
             '@pat': "0",
             '@het': "0.5",
             '@unk': "NA"
             }
-        
+
         self.configurations = {}
-        #self.skipped_cols = 3
-        
-        #if self.input_file.endswith(".geno.gz"):
-        #    print("self.input_file: ", self.input_file)
-        #    self.input_fh = gzip.open(self.input_file)
-        #else:
         self.input_fh = open(self.input_file)
-        
-        with open(self.output_files[0], "w") as self.geno_fh:
-            #if self.file_type == "geno":
-            self.process_csv()
-            #elif self.file_type == "snps":
-            #    self.process_snps_file()
 
+        self.process_csv()
 
     def process_csv(self):
-        for row_count, row in enumerate(self.process_rows()):
+        for row in self.process_rows():
             row_items = row.split("\t")
 
             this_marker = Marker()
@@ -102,53 +84,30 @@ class ConvertGenoFile(object):
                     this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
                 else:
                     this_marker.genotypes.append("NA")
-                
-            #print("this_marker is:", pf(this_marker.__dict__))   
-            #if this_marker.chr == "14":
+
             self.markers.append(this_marker.__dict__)
 
         self.write_to_bimbam()    
-            
-        # with open(self.output_file, 'w') as fh:
-            # json.dump(self.markers, fh, indent="   ", sort_keys=True)
-                
-                # print('configurations:', str(configurations))
-                #self.latest_col_pos = item_count + self.skipped_cols
-                #self.latest_col_value = item
-                
-                #if item_count != 0:
-                #    self.output_fh.write(" ")
-                #self.output_fh.write(self.configurations[item.upper()])
-                    
-            #self.output_fh.write("\n")
 
     def write_to_bimbam(self):
         with open(self.output_files[0], "w") as geno_fh:
-            # geno_fh.write(str(len(self.sample_list)) + "\n")
-            # geno_fh.write("2\n")
-            # geno_fh.write("IND")
-            # for sample in self.sample_list:
-                # geno_fh.write(" " + sample)
-            # geno_fh.write("\n")
             for marker in self.markers:
                 geno_fh.write(marker['name'])
                 geno_fh.write(", X, Y")
                 geno_fh.write(", " + ", ".join(marker['genotypes']))
                 geno_fh.write("\n")
-                
-        #pheno_fh = open(self.output_files[1], 'w')
+
         with open(self.output_files[1], "w") as pheno_fh:
             for sample in self.sample_list:
                 pheno_fh.write("1\n")
-        
+
         with open(self.output_files[2], "w") as snp_fh:
             for marker in self.markers:
                 if self.mb_exists:
                     snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
                 else:
                     snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
-        
-            
+
     def get_sample_list(self, row_contents):
         self.sample_list = []
         if self.mb_exists:
@@ -164,8 +123,6 @@ class ConvertGenoFile(object):
     
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
-            #if self.input_file.endswith(".geno.gz"):
-            #    print("row: ", row)
             self.latest_row_value = row
             # Take care of headers
             if not row.strip():
@@ -208,10 +165,8 @@ class ConvertGenoFile(object):
                 convertob.convert()
             except EmptyConfigurations as why:
                 print("  No config info? Continuing...")
-                #excepted = True
                 continue
             except Exception as why:
-
                 print("  Exception:", why)
                 print(traceback.print_exc())
                 print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
@@ -219,12 +174,6 @@ class ConvertGenoFile(object):
                 print("    Column is:", convertob.latest_col_value)
                 print("    Row is:", convertob.latest_row_value)
                 break
-            
-    #def process_snps_file(cls, snps_file, new_directory):
-    #    output_file = os.path.join(new_directory, "mouse_families.json")
-    #    print("%s -> %s" % (snps_file, output_file))
-    #    convertob = ConvertGenoFile(input_file, output_file)
-
 
 if __name__=="__main__":
     Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
@@ -234,6 +183,4 @@ if __name__=="__main__":
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
     #convertob.convert()
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    #ConvertGenoFiles(Geno_Directory)
-    
-    #process_csv(Input_File, Output_File)
\ No newline at end of file
+    #ConvertGenoFiles(Geno_Directory)
\ No newline at end of file
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index c48183ed..67ca3ad3 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -23,47 +23,33 @@ class Stats:
         # convert all items to floats for numerical processing
         self.sequence = [float(item) for item in sequence]
 
-
     def sum(self):
         if len(self.sequence) < 1:
             return None
         else:
             return sum(self.sequence)
 
-
     def count(self):
         return len(self.sequence)
 
-
     def min(self):
         if len(self.sequence) < 1:
             return None
         else:
             return min(self.sequence)
 
-
     def max(self):
         if len(self.sequence) < 1:
             return None
         else:
             return max(self.sequence)
 
-
     def avg(self):
         if len(self.sequence) < 1:
             return None
         else:
             return sum(self.sequence) / len(self.sequence)
 
-
-    def median(self):
-        if len(self.sequence) < 1:
-            return None
-        else:
-            self.sequence.sort()
-            return self.sequence[len(self.sequence) // 2]
-
-
     def stdev(self):
         if len(self.sequence) < 1:
             return None
@@ -73,7 +59,6 @@ class Stats:
             stdev = (sdsq / (len(self.sequence) - 1)) ** .5
             return stdev
 
-
     def percentile(self, percentile):
         if len(self.sequence) < 1:
             value = None
@@ -86,7 +71,6 @@ class Stats:
             value = self.sequence[element_idx]
         return value
 
-
 # Sample script using this class:
 # -------------------------------------------
 #    #!/usr/bin/env python
-- 
cgit v1.2.3


From 1cf4b598dd986760627eef4144c0445679c97866 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 17:25:15 +0000
Subject: Removed unused code from get_select_dataset.py and
 get_group_samplelists.py scripts

---
 wqflask/maintenance/gen_select_dataset.py    |  9 ++++-----
 wqflask/maintenance/get_group_samplelists.py | 10 ----------
 2 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f62d0cc1..16dcebc5 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -66,7 +66,7 @@ from pprint import pformat as pf
 print('WARNING: This conversion is now OBSOLETE as the menu gets built from the database in Javascript using GN_SERVER instead!')
 
 
-def parse_db_uri(db_uri):
+def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
     parsed_uri = urlparse.urlparse(SQL_URI)
@@ -81,7 +81,6 @@ def parse_db_uri(db_uri):
     return db_conn_info
 
 
-
 def get_species():
     """Build species list"""
     Cursor.execute("select Name, MenuName from Species where Species.Name != 'macaque monkey' order by OrderId")
@@ -268,7 +267,7 @@ def build_datasets(species, group, type_name):
 def main():
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
 
-    parse_db_uri(SQL_URI)
+    parse_db_uri()
 
     species = get_species()
     groups = get_groups(species)
@@ -307,6 +306,6 @@ def _test_it():
     #print("build_datasets:", pf(datasets))
 
 if __name__ == '__main__':
-    Conn = MySQLdb.Connect(**parse_db_uri(SQL_URI))
+    Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
-    main()
+    main()
\ No newline at end of file
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 04e94886..1dc6c46c 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -6,16 +6,6 @@ import gzip
 
 from base import webqtlConfig
 
-def process_genofiles(geno_dir=webqtlConfig.GENODIR):
-    print("Yabba")
-    #sys.exit("Dabba")
-    os.chdir(geno_dir)
-    for geno_file in glob.glob("*"):
-        if geno_file.lower().endswith(('.geno', '.geno.gz')):
-            #group_name = genofilename.split('.')[0]
-            sample_list = get_samplelist(geno_file)
-
-
 def get_samplelist(file_type, geno_file):
     if file_type == "geno":
         return get_samplelist_from_geno(geno_file)
-- 
cgit v1.2.3


From bd6d36ddb366a3ee427a0c237ebf8f672606ff19 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 18:13:59 +0000
Subject: Fixed issue that caused and error for certain types of mapping due to
 variable not being initialized

Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them.

Also removed unused file AJAX_table.py and other unused code from several other files
---
 wqflask/utility/AJAX_table.py                      | 155 ----
 wqflask/utility/Plot.py                            | 854 +--------------------
 wqflask/utility/after.py                           |   8 +-
 wqflask/utility/benchmark.py                       |   2 +-
 wqflask/utility/genofile_parser.py                 |   2 +-
 wqflask/utility/logger.py                          |   2 +-
 wqflask/utility/webqtlUtil.py                      | 132 +---
 .../marker_regression/marker_regression_gn1.py     |   5 +-
 8 files changed, 10 insertions(+), 1150 deletions(-)
 delete mode 100644 wqflask/utility/AJAX_table.py

diff --git a/wqflask/utility/AJAX_table.py b/wqflask/utility/AJAX_table.py
deleted file mode 100644
index d70acfcd..00000000
--- a/wqflask/utility/AJAX_table.py
+++ /dev/null
@@ -1,155 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-import cPickle
-import os
-import MySQLdb
-import time
-import pyXLWriter as xl
-
-from htmlgen import HTMLgen2 as HT
-
-from base import webqtlConfig
-from THCell import THCell
-from TDCell import TDCell
-import webqtlUtil
-
-
-class AJAX_table:
-    def __init__(self, fd):
-        file = fd.formdata.getfirst("file", "")
-        sort = fd.formdata.getfirst("sort", "")
-        order = fd.formdata.getfirst("order", "up")
-        cmd = fd.formdata.getfirst("cmd", "")
-        tableID = fd.formdata.getfirst("tableID", "")
-        addIndex = fd.formdata.getfirst("addIndex", "1")
-        hiddenColumnsString = fd.formdata.getfirst("hiddenColumns", "")
-        hiddenColumns = hiddenColumnsString.split(',')
-
-        try:
-            fp = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'rb')
-            tblobj = cPickle.load(fp)
-            fp.close()
-
-            if cmd == 'addCorr':
-                dbId = int(fd.formdata.getfirst("db"))
-                dbFullName = fd.formdata.getfirst("dbname")
-                trait = fd.formdata.getfirst("trait")
-                form = fd.formdata.getfirst("form")
-                ids = fd.formdata.getfirst("ids")
-                vals = fd.formdata.getfirst("vals")
-                ids = eval(ids)
-                nnCorr = len(ids)
-                vals = eval(vals)
-
-                workbook = xl.Writer('%s.xls' % (webqtlConfig.TMPDIR+file))
-                worksheet = workbook.add_worksheet()
-
-                logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
-
-                con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
-                cursor = con.cursor()
-
-                cursor.execute("Select name, ShortName from ProbeSetFreeze where Id = %s", dbId)
-                dbName, dbShortName = cursor.fetchone()
-
-                tblobj['header'][0].append(
-                        THCell(HT.TD(dbShortName, Class="fs11 ffl b1 cw cbrb"),
-                        text="%s" % dbShortName, idx=tblobj['header'][0][-1].idx + 1),
-                )
-
-                headingStyle = workbook.add_format(align = 'center', bold = 1, border = 1, size=13, fg_color = 0x1E, color="white")
-                for i, item in enumerate(tblobj['header'][0]):
-                    if (i > 0):
-                        worksheet.write([8, i-1], item.text, headingStyle)
-                        worksheet.set_column([i-1, i-1], 2*len(item.text))
-
-                for i, row in enumerate(tblobj['body']):
-                    ProbeSetId = row[1].text
-                    #XZ, 03/02/2009: Xiaodong changed Data to ProbeSetData
-                    cursor.execute("""
-                            Select ProbeSetData.StrainId, ProbeSetData.Value
-                            From ProbeSetData, ProbeSetXRef, ProbeSet
-                            where ProbeSetXRef.ProbeSetFreezeId = %d AND
-                                    ProbeSetXRef.DataId = ProbeSetData.Id AND
-                                    ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                                    ProbeSet.Name = '%s'
-                    """ % (dbId, ProbeSetId))
-                    results = cursor.fetchall()
-                    vdict = {}
-                    for item in results:
-                        vdict[item[0]] = item[1]
-                    newvals = []
-                    for id in ids:
-                        if vdict.has_key(id):
-                            newvals.append(vdict[id])
-                        else:
-                            newvals.append(None)
-                    corr,nOverlap= webqtlUtil.calCorrelation(newvals,vals,nnCorr)
-                    repr = '%0.4f' % corr
-                    row.append(
-                            TDCell(HT.TD(HT.Href(text=repr, url="javascript:showCorrPlotThird('%s', '%s', '%s')" % (form, dbName, ProbeSetId), Class="fs11 fwn ffl"), " / ", nOverlap, Class="fs11 fwn ffl b1 c222", align="middle"),repr,abs(corr))
-                    )
-
-                    last_row=0
-                    for j, item in enumerate(tblobj['body'][i]):
-                        if (j > 0):
-                            worksheet.write([9+i, j-1], item.text)
-                            last_row = 9+i
-                    last_row += 1
-
-                titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
-                ##Write title Info
-                # Modified by Hongqiang Li
-                worksheet.write([0, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
-                worksheet.write([1, 0], "Trait : %s" % trait, titleStyle)
-                worksheet.write([2, 0], "Database : %s" % dbFullName, titleStyle)
-                worksheet.write([3, 0], "Date : %s" % time.strftime("%B %d, %Y", time.gmtime()), titleStyle)
-                worksheet.write([4, 0], "Time : %s GMT" % time.strftime("%H:%M ", time.gmtime()), titleStyle)
-                worksheet.write([5, 0], "Status of data ownership: Possibly unpublished data; please see %s/statusandContact.html for details on sources, ownership, and usage of these data." % webqtlConfig.PORTADDR, titleStyle)
-                #Write footer info
-                worksheet.write([1 + last_row, 0], "Funding for The GeneNetwork: NIAAA (U01AA13499, U24AA13513), NIDA, NIMH, and NIAAA (P20-DA21131), NCI MMHCC (U01CA105417), and NCRR (U01NR 105417)", titleStyle)
-                worksheet.write([2 + last_row, 0], "PLEASE RETAIN DATA SOURCE INFORMATION WHENEVER POSSIBLE", titleStyle)
-
-                cursor.close()
-                workbook.close()
-
-                objfile = open(os.path.join(webqtlConfig.TMPDIR, file + '.obj'), 'wb')
-                cPickle.dump(tblobj, objfile)
-                objfile.close()
-            else:
-                pass
-
-            self.value = str(webqtlUtil.genTableObj(tblobj=tblobj, file=file, sortby=(sort, order), tableID = tableID, addIndex = addIndex, hiddenColumns = hiddenColumns))
-
-        except:
-            self.value = "<span class='fs16 fwb cr ffl'>The table is no longer available on this server</span>"
-
-    def __str__(self):
-        return self.value
-
-    def write(self):
-        return str(self)
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 3a8b8dd5..dbcee331 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -82,202 +82,6 @@ def frange(start, end=None, inc=1.0):
         L[i] = start + i * inc
     return L
 
-
-def gammln(xx):
-    cof=[76.18009173,-86.50532033,24.01409822,-1.231739516,0.120858003e-2,-0.536382e-5]
-    x=xx-1.0
-    tmp=x+5.5
-    tmp -=(x+0.5)*log(tmp)
-    ser=1.0
-    for item in cof:
-        x+=1.0
-        ser+=item/x
-
-    return -tmp+log(2.50662827465*ser)
-
-
-def gser(a,x):
-    gln=gammln(a)
-    ITMAX=100
-    EPS=3.0e-7
-
-    if x<=0.0:
-        gamser=0.0
-        return [gamser,gln]
-    else:
-        ap=a
-        sum=1.0/a
-        dele=sum
-        for i in range(1,ITMAX+1):
-            ap+=1.0
-            dele*=x/ap
-            sum+=dele
-            if abs(dele)<abs(sum)*EPS:
-                gamser=sum*exp(-x+a*log(x)-gln)
-                return [gamser,gln]
-    return None
-
-def gcf(a,x):
-    ITMAX=100
-    EPS=3.0e-7
-    gold=0.0
-    fac=1
-    b1=1.0
-    b0=0.0
-    a0=1.0
-    gln=gammln(a)
-
-    a1=x
-    for n in range(1,ITMAX+1):
-        an=n+0.0
-        ana=an-a
-        a0=(a1+a0*ana)*fac
-        b0=(b1+b0*ana)*fac
-        anf=an*fac
-        a1=x*a0+anf*a1
-        b1=x*b0+anf*b1
-        if (a1):
-            fac=1.0/a1
-            g=b1*fac
-            if abs((g-gold)/g)<EPS:
-                gammcf=exp(-x+a*log(x)-gln)*g
-                return [gammcf,gln]
-            gold=g
-    return None
-
-def gammp(a,x):
-    if x<0.0 or a<=0.0:
-        return None
-    if x<(a+1.0):
-        a=gser(a,x)[0]
-        return a
-    else:
-        a=gcf(a,x)[0]
-        return 1.0-a
-def U(n):
-    x=pow(0.5,1.0/n)
-    m=[1-x]
-    for i in range(2,n):
-        a=(i-0.3175)/(n+0.365)
-        m.append(a)
-    m.append(x)
-    return m
-
-def erf(x):
-    if x<0.0:
-        return -gammp(0.5,x*x)
-    else:
-        return gammp(0.5,x*x)
-
-def erfcc(x):
-    z=abs(x)
-    t=1.0/(1.0+0.5*z)
-    ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
-    if x>=0.0:
-        return ans
-    else:
-        return 2.0-ans
-
-def calMeanVar(data):
-    n=len(data)
-    if n<2:
-        return None
-    else:
-        sum=reduce(lambda x,y:x+y,data,0.0)
-        mean=sum/n
-        z=data[:]
-        for i in range(n):
-            z[i]=z[i]-mean
-        variance=reduce(lambda x,y:x+y*y,z,0.0)
-        variance /= n-1
-        variance =sqrt(variance)
-        for i in range(n):
-            z[i]=z[i]/variance
-        return z
-
-def inverseCumul(p):
-    #Coefficients in rational approximations.
-    a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
-
-    b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
-
-    c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
-
-    d =  [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
-    #Define break-points.
-
-    p_low  = 0.02425
-    p_high = 1 - p_low
-
-    #Rational approximation for lower region.
-
-    if p > 0 and p < p_low:
-        q = sqrt(-2*log(p))
-        x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-
-    #Rational approximation for central region.
-
-    elif p>= p_low and p <= p_high:
-        q = p - 0.5
-        r = q*q
-        x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
-
-    #Rational approximation for upper region.
-
-    elif p>p_high and  p < 1:
-        q = sqrt(-2*log(1-p))
-        x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-    else:
-        return None
-
-    if p>0 and p < 1:
-        e = 0.5 * erfcc(-x/sqrt(2)) - p
-        u = e * sqrt(2*pi) * exp(x*x/2)
-        x = x - u/(1 + x*u/2)
-        return x
-    else:
-        return None
-
-def gmean(lst):
-    N = len(lst)
-    if N == 0:
-        return 0
-    else:
-        return (reduce(lambda x,y: x+y, lst, 0.0))/N
-
-def gmedian(lst2):
-    lst = lst2[:]
-    N = len(lst)
-    if N == 0:
-        return 0
-    else:
-        lst.sort()
-        if N % 2 == 0:
-            return (lst[N/2]+lst[(N-2)/2])/2.0
-        else:
-            return lst[(N-1)/2]
-
-def gpercentile(lst2, np):
-    """Obsolete - use percentile in corestats instead"""
-    lst = lst2[:]
-    N = len(lst)
-    if N == 0 or np > 100 or np < 0:
-        return None
-    else:
-        lst.sort()
-        pNadd1 = (np/100.0)*N
-        k = int(pNadd1)
-        d = pNadd1 - k
-        if k == 0:
-            return lst[0]
-        elif k >= N-1:
-            return lst[N-1]
-        else:
-            return lst[k-1] + d*(lst[k] - lst[k-1])
-
 def find_outliers(vals):
     """Calculates the upper and lower bounds of a set of sample/case values
 
@@ -314,34 +118,6 @@ def find_outliers(vals):
     logger.debug(pf(locals()))
     return upper_bound, lower_bound
 
-def plotSecurity(canvas, text="12345"):
-    if not text:
-        return
-
-    plotWidth = canvas.size[0]
-    plotHeight = canvas.size[1]
-    if plotHeight<=0 or plotWidth<=0:
-        return
-
-    bgColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-    canvas.drawRect(0,0,plotWidth,plotHeight, edgeColor=bgColor, fillColor=bgColor)
-
-    for i in range(30):
-        randomColor = pid.Color(0.6+0.4*random.random(), 0.6+0.4*random.random(), 0.6+0.4*random.random())
-        scaleFont=pid.Font(ttf="cour",size=random.choice(range(20, 50)))
-        canvas.drawString(random.choice('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'),
-                int(random.random()*plotWidth), int(random.random()*plotHeight), font=scaleFont,
-                color=randomColor, angle=random.choice(range(-45, 50)))
-
-    step = (plotWidth-20)/len(text)
-    startX = 20
-    for item in text:
-        randomColor = pid.Color(0.6*random.random(),0.6*random.random(), 0.6*random.random())
-        scaleFont=pid.Font(ttf="verdana",size=random.choice(range(50, 60)),bold=1)
-        canvas.drawString(item, startX, plotHeight/2-10, font=scaleFont,
-                color=randomColor, angle=random.choice(range(-45, 50)))
-        startX += step
-
 # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
 # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
 def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
@@ -429,542 +205,6 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
        canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
                20,font=labelFont,color=labelColor)
 
-def plotBarText(canvas, data, label, variance=None, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, sLabel = None, offset= (80, 20, 40, 100), barSpace = 2, zoom = 1):
-    xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-    plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-    plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-    if plotHeight<=0 or plotWidth<=0:
-       return
-
-    NNN = len(data)
-    if NNN < 2 or NNN != len(label):
-       return
-    if variance and len(variance)!=NNN:
-       variance = []
-
-    Y2 = data[:]
-    if variance:
-       for i in range(NNN):
-           if variance[i]:
-               Y2 += [data[i]-variance[i]]
-
-    #Y axis
-    YLow, YTop, stepY = detScale(min(Y2), max(Y2))
-    YScale = plotHeight/(YTop - YLow)
-
-    if YLow < 0  and  YTop > 0:
-       drawZero = 1
-    else:
-       drawZero = 0
-
-    #X axis
-    X = range(NNN)
-    Xll= 0
-    Xur= NNN-1
-
-
-    if drawZero:
-       YZero = yTopOffset+plotHeight-YScale*(0-YLow)
-       canvas.drawLine(xLeftOffset, YZero, xLeftOffset+plotWidth, YZero)
-    else:
-       YZero = yTopOffset+plotHeight
-    #draw data
-    spaceWidth = barSpace
-    if spaceWidth < 1:
-       spaceWidth = 1
-    barWidth = int((plotWidth - (NNN-1.0)*spaceWidth)/NNN)
-
-    xc= xLeftOffset
-    scaleFont=pid.Font(ttf="verdana",size=11,bold=0)
-    for i in range(NNN):
-       yc = yTopOffset+plotHeight-(data[i]-YLow)*YScale
-       canvas.drawRect(xc,YZero,xc+barWidth-1, yc, edgeColor=barColor,fillColor=barColor)
-       if variance and variance[i]:
-           varlen = variance[i]*YScale
-           if yc-varlen < yTopOffset:
-               topYd = yTopOffset
-           else:
-               topYd = yc-varlen
-               canvas.drawLine(xc+barWidth/2-2,yc-varlen,xc+barWidth/2+2,yc-varlen,color=pid.red)
-           canvas.drawLine(xc+barWidth/2,yc+varlen,xc+barWidth/2,topYd,color=pid.red)
-           canvas.drawLine(xc+barWidth/2-2,yc+varlen,xc+barWidth/2+2,yc+varlen,color=pid.red)
-       strX = label[i]
-       canvas.drawString(strX,xc+barWidth/2.0+2,yTopOffset+plotHeight+2+canvas.stringWidth(strX,font=scaleFont),font=scaleFont,angle=90)
-       xc += barWidth + spaceWidth
-
-    #draw drawing region
-    canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
-
-    #draw Y scale
-    scaleFont=pid.Font(ttf="cour",size=16,bold=1)
-    y=YLow
-    for i in range(stepY+1):
-       yc=yTopOffset+plotHeight-(y-YLow)*YScale
-       canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
-       strY = cformat(d=y, rank=0)
-       canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
-       y+= (YTop - YLow)/stepY
-
-    #draw label
-    labelFont=pid.Font(ttf="verdana",size=17,bold=0)
-    if XLabel:
-       canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,yTopOffset+plotHeight+65,font=labelFont,color=labelColor)
-
-    if YLabel:
-       canvas.drawString(YLabel,xLeftOffset-50, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,font=labelFont,color=labelColor,angle=90)
-
-    labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-    if title:
-       canvas.drawString(title,xLeftOffset,yTopOffset-15,font=labelFont,color=labelColor)
-
-    return
-
-#def plotXY(canvas, dataX, dataY, rank=0, dataLabel=[], plotColor = pid.black, axesColor=pid.black, labelColor=pid.black, lineSize="thin", lineColor=pid.grey, idFont="arial", idColor=pid.blue, idSize="14", symbolColor=pid.black, symbolType="circle", filled="yes", symbolSize="tiny", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1, bufferSpace = 15):
-#    'displayR : correlation scatter plot, loadings : loading plot'
-#
-#    dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-#
-#    #get ID font size
-#    idFontSize = int(idSize)
-#
-#    #If filled is yes, set fill color
-#    if filled == "yes":
-#        fillColor = symbolColor
-#    else:
-#        fillColor = None
-#
-#    if symbolSize == "large":
-#        sizeModifier = 7
-#        fontModifier = 12
-#    elif symbolSize == "medium":
-#        sizeModifier = 5
-#        fontModifier = 8
-#    elif symbolSize == "small":
-#        sizeModifier = 3
-#        fontModifier = 3
-#    else:
-#        sizeModifier = 1
-#        fontModifier = -1
-#
-#    if rank == 0:    # Pearson correlation
-#        bufferSpace = 0
-#        dataXPrimary = dataX
-#        dataYPrimary = dataY
-#        dataXAlt = dataXRanked    #Values used just for printing the other corr type to the graph image
-#        dataYAlt = dataYRanked    #Values used just for printing the other corr type to the graph image
-#    else:    # Spearman correlation: Switching Ranked and Unranked X and Y values
-#        dataXPrimary = dataXRanked
-#        dataYPrimary = dataYRanked
-#        dataXAlt = dataX    #Values used just for printing the other corr type to the graph image
-#        dataYAlt = dataY    #Values used just for printing the other corr type to the graph image
-#
-#    xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-#    plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-#    plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-#    if plotHeight<=0 or plotWidth<=0:
-#        return
-#    if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-#        return
-#
-#    max_X=max(dataXPrimary)
-#    min_X=min(dataXPrimary)
-#    max_Y=max(dataYPrimary)
-#    min_Y=min(dataYPrimary)
-#
-#    #for some reason I forgot why I need to do this
-#    if loadingPlot:
-#        min_X = min(-0.1,min_X)
-#        max_X = max(0.1,max_X)
-#        min_Y = min(-0.1,min_Y)
-#        max_Y = max(0.1,max_Y)
-#
-#    xLow, xTop, stepX=detScale(min_X,max_X)
-#    yLow, yTop, stepY=detScale(min_Y,max_Y)
-#    xScale = plotWidth/(xTop-xLow)
-#    yScale = plotHeight/(yTop-yLow)
-#
-#    #draw drawing region
-#    canvas.drawRect(xLeftOffset-bufferSpace, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace)
-#    canvas.drawRect(xLeftOffset-bufferSpace+1, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight+bufferSpace-1)
-#
-#    #calculate data points
-#    data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-#    xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-#
-#    labelFont=pid.Font(ttf=idFont,size=idFontSize,bold=0)
-#
-#    if loadingPlot:
-#        xZero = -xLow*xScale+xLeftOffset
-#        yZero = yTopOffset+plotHeight+yLow*yScale
-#        for point in xCoord:
-#            canvas.drawLine(xZero,yZero,point[0],point[1],color=pid.red)
-#    else:
-#        if connectdot:
-#            canvas.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-#        else:
-#            pass
-#
-#    symbolFont = pid.Font(ttf="fnt_bs", size=12+fontModifier,bold=0)
-#
-#    for i, item in enumerate(xCoord):
-#        if dataLabel and dataLabel[i] in specialCases:
-#            canvas.drawRect(item[0]-3, item[1]-3, item[0]+3, item[1]+3, edgeColor=pid.green)
-#            #canvas.drawCross(item[0],item[1],color=pid.blue,size=5)
-#        else:
-#            if symbolType == "vertRect":
-#                canvas.drawRect(x1=item[0]-sizeModifier+2,y1=item[1]-sizeModifier-2, x2=item[0]+sizeModifier-1,y2=item[1]+sizeModifier+2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-#            elif (symbolType == "circle" and filled != "yes"):
-#                canvas.drawString(":", item[0]-canvas.stringWidth(":",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-#            elif (symbolType == "circle" and filled == "yes"):
-#                canvas.drawString("5", item[0]-canvas.stringWidth("5",font=symbolFont)/2+1,item[1]+2,color=symbolColor, font=symbolFont)
-#            elif symbolType == "horiRect":
-#                canvas.drawRect(x1=item[0]-sizeModifier-1,y1=item[1]-sizeModifier+3, x2=item[0]+sizeModifier+3,y2=item[1]+sizeModifier-2, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-#            elif (symbolType == "square"):
-#                canvas.drawRect(x1=item[0]-sizeModifier+1,y1=item[1]-sizeModifier-4, x2=item[0]+sizeModifier+2,y2=item[1]+sizeModifier-3, edgeColor=symbolColor, edgeWidth=1, fillColor=fillColor)
-#            elif (symbolType == "diamond" and filled != "yes"):
-#                canvas.drawString(",", item[0]-canvas.stringWidth(",",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
-#            elif (symbolType == "diamond" and filled == "yes"):
-#                canvas.drawString("D", item[0]-canvas.stringWidth("D",font=symbolFont)/2+2, item[1]+6, font=symbolFont, color=symbolColor)
-#            elif symbolType == "4-star":
-#                canvas.drawString("l", item[0]-canvas.stringWidth("l",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
-#            elif symbolType == "3-star":
-#                canvas.drawString("k", item[0]-canvas.stringWidth("k",font=symbolFont)/2+1, item[1]+3, font=symbolFont, color=symbolColor)
-#            else:
-#                canvas.drawCross(item[0],item[1]-2,color=symbolColor, size=sizeModifier+2)
-#
-#        if showLabel and dataLabel:
-#            if (symbolType == "vertRect" or symbolType == "diamond"):
-#                labelGap = 15
-#            elif (symbolType == "4-star" or symbolType == "3-star"):
-#                labelGap = 12
-#            else:
-#                labelGap = 11
-#            canvas.drawString(dataLabel[i], item[0]- canvas.stringWidth(dataLabel[i],
-#                    font=labelFont)/2 + 1, item[1]+(labelGap+sizeModifier+(idFontSize-12)), font=labelFont, color=idColor)
-#
-#    #draw scale
-#    scaleFont=pid.Font(ttf="cour",size=16,bold=1)
-#
-#
-#    x=xLow
-#    for i in range(stepX+1):
-#        xc=xLeftOffset+(x-xLow)*xScale
-#        if ((x == 0) & (rank == 1)):
-#            pass
-#        else:
-#            canvas.drawLine(xc,yTopOffset+plotHeight + bufferSpace,xc,yTopOffset+plotHeight+5 + bufferSpace, color=axesColor)
-#        strX = cformat(d=x, rank=rank)
-#        if ((strX == "0") & (rank == 1)):
-#            pass
-#        else:
-#            canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+20 + bufferSpace,font=scaleFont)
-#        x+= (xTop - xLow)/stepX
-#
-#    y=yLow
-#    for i in range(stepY+1):
-#        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-#        if ((y == 0) & (rank == 1)):
-#            pass
-#        else:
-#            canvas.drawLine(xLeftOffset - bufferSpace,yc,xLeftOffset-5 - bufferSpace,yc, color=axesColor)
-#        strY = cformat(d=y, rank=rank)
-#        if ((strY == "0") & (rank == 1)):
-#            pass
-#        else:
-#            canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)- 10 - bufferSpace,yc+4,font=scaleFont)
-#        y+= (yTop - yLow)/stepY
-#
-#    #draw label
-#
-#    labelFont=pid.Font(ttf="verdana",size=canvas.size[0]/45,bold=0)
-#    titleFont=pid.Font(ttf="verdana",size=canvas.size[0]/40,bold=0)
-#
-#    if (rank == 1 and not title):
-#        canvas.drawString("Spearman Rank Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Spearman Rank Correlation",font=titleFont))/2.0,
-#                                          25,font=titleFont,color=labelColor)
-#    elif (rank == 0 and not title):
-#        canvas.drawString("Pearson Correlation", xLeftOffset-canvas.size[0]*.025+(plotWidth-canvas.stringWidth("Pearson Correlation",font=titleFont))/2.0,
-#                                          25,font=titleFont,color=labelColor)
-#
-#    if XLabel:
-#        canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-#                yTopOffset+plotHeight+yBottomOffset-25,font=labelFont,color=labelColor)
-#
-#    if YLabel:
-#        canvas.drawString(YLabel, xLeftOffset-65, yTopOffset+plotHeight- (plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-#                font=labelFont,color=labelColor,angle=90)
-#
-#    labelFont=pid.Font(ttf="verdana",size=20,bold=0)
-#    if title:
-#        canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-#                20,font=labelFont,color=labelColor)
-#
-#    if fitcurve:
-#        import sys
-#        sys.argv = [ "mod_python" ]
-#        #from numarray import linear_algebra as la
-#        #from numarray import ones, array, dot, swapaxes
-#        fitYY = array(dataYPrimary)
-#        fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-#        AA = dot(fitXX,swapaxes(fitXX,0,1))
-#        BB = dot(fitXX,fitYY)
-#        bb = la.linear_least_squares(AA,BB)[0]
-#
-#        xc1 = xLeftOffset
-#        yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
-#        if yc1 > yTopOffset+plotHeight:
-#            yc1 = yTopOffset+plotHeight
-#            xc1 = (yLow-bb[0])/bb[1]
-#            xc1=(xc1-xLow)*xScale+xLeftOffset
-#        elif yc1 < yTopOffset:
-#            yc1 = yTopOffset
-#            xc1 = (yTop-bb[0])/bb[1]
-#            xc1=(xc1-xLow)*xScale+xLeftOffset
-#        else:
-#            pass
-#
-#        xc2 = xLeftOffset + plotWidth
-#        yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-#        if yc2 > yTopOffset+plotHeight:
-#            yc2 = yTopOffset+plotHeight
-#            xc2 = (yLow-bb[0])/bb[1]
-#            xc2=(xc2-xLow)*xScale+xLeftOffset
-#        elif yc2 < yTopOffset:
-#            yc2 = yTopOffset
-#            xc2 = (yTop-bb[0])/bb[1]
-#            xc2=(xc2-xLow)*xScale+xLeftOffset
-#        else:
-#            pass
-#
-#        canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace,xc2,yc2,color=lineColor)
-#        if lineSize == "medium":
-#            canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-#        if lineSize == "thick":
-#            canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace+1,xc2,yc2+1,color=lineColor)
-#            canvas.drawLine(xc1 - bufferSpace,yc1 + bufferSpace-1,xc2,yc2-1,color=lineColor)
-#
-#
-#    if displayR:
-#        labelFont=pid.Font(ttf="trebuc",size=canvas.size[0]/60,bold=0)
-#        NNN = len(dataX)
-#        corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-#
-#        if NNN < 3:
-#            corrPValue = 1.0
-#        else:
-#            if abs(corr) >= 1.0:
-#                corrPValue = 0.0
-#            else:
-#                ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-#                ZValue = ZValue*sqrt(NNN-3)
-#                corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-#
-#        NStr = "N = %d" % NNN
-#        strLenN = canvas.stringWidth(NStr,font=labelFont)
-#
-#        if rank == 1:
-#            if corrPValue < 0.0000000000000001:
-#                corrStr = "Rho = %1.3f P < 1.00 E-16" % (corr)
-#            else:
-#                corrStr = "Rho = %1.3f P = %3.2E" % (corr, corrPValue)
-#        else:
-#            if corrPValue < 0.0000000000000001:
-#                corrStr = "r = %1.3f P < 1.00 E-16" % (corr)
-#            else:
-#                corrStr = "r = %1.3f P = %3.2E" % (corr, corrPValue)
-#        strLen = canvas.stringWidth(corrStr,font=labelFont)
-#
-#        canvas.drawString(NStr,xLeftOffset,yTopOffset-10,font=labelFont,color=labelColor)
-#        canvas.drawString(corrStr,xLeftOffset+plotWidth-strLen,yTopOffset-10,font=labelFont,color=labelColor)
-#
-#    return xCoord
-
-def plotXYSVG(drawSpace, dataX, dataY, rank=0, dataLabel=[], plotColor = "black", axesColor="black", labelColor="black", symbolColor="red", XLabel=None, YLabel=None, title=None, fitcurve=None, connectdot=1, displayR=None, loadingPlot = 0, offset= (80, 20, 40, 60), zoom = 1, specialCases=[], showLabel = 1):
-    'displayR : correlation scatter plot, loadings : loading plot'
-
-    dataXRanked, dataYRanked = webqtlUtil.calRank(dataX, dataY, len(dataX))
-
-    # Switching Ranked and Unranked X and Y values if a Spearman Rank Correlation
-    if rank == 0:
-        dataXPrimary = dataX
-        dataYPrimary = dataY
-        dataXAlt = dataXRanked
-        dataYAlt = dataYRanked
-
-    else:
-        dataXPrimary = dataXRanked
-        dataYPrimary = dataYRanked
-        dataXAlt = dataX
-        dataYAlt = dataY
-
-
-
-    xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-    plotWidth = drawSpace.attributes['width'] - xLeftOffset - xRightOffset
-    plotHeight = drawSpace.attributes['height'] - yTopOffset - yBottomOffset
-    if plotHeight<=0 or plotWidth<=0:
-        return
-    if len(dataXPrimary) < 1 or  len(dataXPrimary) != len(dataYPrimary) or (dataLabel and len(dataXPrimary) != len(dataLabel)):
-        return
-
-    max_X=max(dataXPrimary)
-    min_X=min(dataXPrimary)
-    max_Y=max(dataYPrimary)
-    min_Y=min(dataYPrimary)
-
-    #for some reason I forgot why I need to do this
-    if loadingPlot:
-        min_X = min(-0.1,min_X)
-        max_X = max(0.1,max_X)
-        min_Y = min(-0.1,min_Y)
-        max_Y = max(0.1,max_Y)
-
-    xLow, xTop, stepX=detScale(min_X,max_X)
-    yLow, yTop, stepY=detScale(min_Y,max_Y)
-    xScale = plotWidth/(xTop-xLow)
-    yScale = plotHeight/(yTop-yLow)
-
-    #draw drawing region
-    r = svg.rect(xLeftOffset, yTopOffset, plotWidth,  plotHeight, 'none', axesColor, 1)
-    drawSpace.addElement(r)
-
-    #calculate data points
-    data = map(lambda X, Y: (X, Y), dataXPrimary, dataYPrimary)
-    xCoord = map(lambda X, Y: ((X-xLow)*xScale + xLeftOffset, yTopOffset+plotHeight-(Y-yLow)*yScale), dataXPrimary, dataYPrimary)
-    labelFontF = "verdana"
-    labelFontS = 11
-
-    if loadingPlot:
-        xZero = -xLow*xScale+xLeftOffset
-        yZero = yTopOffset+plotHeight+yLow*yScale
-        for point in xCoord:
-            drawSpace.addElement(svg.line(xZero,yZero,point[0],point[1], "red", 1))
-    else:
-        if connectdot:
-            pass
-            #drawSpace.drawPolygon(xCoord,edgeColor=plotColor,closed=0)
-        else:
-            pass
-
-    for i, item in enumerate(xCoord):
-        if dataLabel and dataLabel[i] in specialCases:
-            drawSpace.addElement(svg.rect(item[0]-3, item[1]-3, 6, 6, "none", "green", 0.5))
-            #drawSpace.drawCross(item[0],item[1],color=pid.blue,size=5)
-        else:
-            drawSpace.addElement(svg.line(item[0],item[1]+5,item[0],item[1]-5,symbolColor,1))
-            drawSpace.addElement(svg.line(item[0]+5,item[1],item[0]-5,item[1],symbolColor,1))
-        if showLabel and dataLabel:
-            pass
-            drawSpace.addElement(svg.text(item[0], item[1]+14, dataLabel[i], labelFontS,
-                    labelFontF, text_anchor="middle", style="stroke:blue;stroke-width:0.5;"))
-            #canvas.drawString(, item[0]- canvas.stringWidth(dataLabel[i],
-            #       font=labelFont)/2, item[1]+14, font=labelFont, color=pid.blue)
-
-    #draw scale
-    #scaleFont=pid.Font(ttf="cour",size=14,bold=1)
-    x=xLow
-    for i in range(stepX+1):
-        xc=xLeftOffset+(x-xLow)*xScale
-        drawSpace.addElement(svg.line(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, axesColor, 1))
-        strX = cformat(d=x, rank=rank)
-        drawSpace.addElement(svg.text(xc,yTopOffset+plotHeight+20,strX,13, "courier", text_anchor="middle"))
-        x+= (xTop - xLow)/stepX
-
-    y=yLow
-    for i in range(stepY+1):
-        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-        drawSpace.addElement(svg.line(xLeftOffset,yc,xLeftOffset-5,yc, axesColor, 1))
-        strY = cformat(d=y, rank=rank)
-        drawSpace.addElement(svg.text(xLeftOffset-10,yc+5,strY,13, "courier", text_anchor="end"))
-        y+= (yTop - yLow)/stepY
-
-    #draw label
-    labelFontF = "verdana"
-    labelFontS = 17
-    if XLabel:
-        drawSpace.addElement(svg.text(xLeftOffset+plotWidth/2.0,
-                yTopOffset+plotHeight+yBottomOffset-10,XLabel,
-                labelFontS, labelFontF, text_anchor="middle"))
-
-    if YLabel:
-        drawSpace.addElement(svg.text(xLeftOffset-50,
-                 yTopOffset+plotHeight/2,YLabel,
-                labelFontS, labelFontF, text_anchor="middle", style="writing-mode:tb-rl", transform="rotate(270 %d %d)" % (xLeftOffset-50,  yTopOffset+plotHeight/2)))
-        #drawSpace.drawString(YLabel, xLeftOffset-50, yTopOffset+plotHeight- (plotHeight-drawSpace.stringWidth(YLabel,font=labelFont))/2.0,
-        #       font=labelFont,color=labelColor,angle=90)
-
-
-    if fitcurve:
-        sys.argv = [ "mod_python" ]
-        #from numarray import linear_algebra as la
-        #from numarray import ones, array, dot, swapaxes
-        fitYY = array(dataYPrimary)
-        fitXX = array([ones(len(dataXPrimary)),dataXPrimary])
-        AA = dot(fitXX,swapaxes(fitXX,0,1))
-        BB = dot(fitXX,fitYY)
-        bb = la.linear_least_squares(AA,BB)[0]
-
-        xc1 = xLeftOffset
-        yc1 = yTopOffset+plotHeight-(bb[0]+bb[1]*xLow-yLow)*yScale
-        if yc1 > yTopOffset+plotHeight:
-            yc1 = yTopOffset+plotHeight
-            xc1 = (yLow-bb[0])/bb[1]
-            xc1=(xc1-xLow)*xScale+xLeftOffset
-        elif yc1 < yTopOffset:
-            yc1 = yTopOffset
-            xc1 = (yTop-bb[0])/bb[1]
-            xc1=(xc1-xLow)*xScale+xLeftOffset
-        else:
-            pass
-
-        xc2 = xLeftOffset + plotWidth
-        yc2 = yTopOffset+plotHeight-(bb[0]+bb[1]*xTop-yLow)*yScale
-        if yc2 > yTopOffset+plotHeight:
-            yc2 = yTopOffset+plotHeight
-            xc2 = (yLow-bb[0])/bb[1]
-            xc2=(xc2-xLow)*xScale+xLeftOffset
-        elif yc2 < yTopOffset:
-            yc2 = yTopOffset
-            xc2 = (yTop-bb[0])/bb[1]
-            xc2=(xc2-xLow)*xScale+xLeftOffset
-        else:
-            pass
-
-        drawSpace.addElement(svg.line(xc1,yc1,xc2,yc2,"green", 1))
-
-    if displayR:
-        labelFontF = "trebuc"
-        labelFontS = 14
-        NNN = len(dataX)
-
-        corr = webqtlUtil.calCorrelation(dataXPrimary,dataYPrimary,NNN)[0]
-
-        if NNN < 3:
-            corrPValue = 1.0
-        else:
-            if abs(corr) >= 1.0:
-                corrPValue = 0.0
-            else:
-                ZValue = 0.5*log((1.0+corr)/(1.0-corr))
-                ZValue = ZValue*sqrt(NNN-3)
-                corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
-        NStr = "N of Cases=%d" % NNN
-
-        if rank == 1:
-            corrStr = "Spearman's r=%1.3f P=%3.2E" % (corr, corrPValue)
-        else:
-            corrStr = "Pearson's r=%1.3f P=%3.2E" % (corr, corrPValue)
-
-        drawSpace.addElement(svg.text(xLeftOffset,yTopOffset-10,NStr,
-                labelFontS, labelFontF, text_anchor="start"))
-        drawSpace.addElement(svg.text(xLeftOffset+plotWidth,yTopOffset-25,corrStr,
-                labelFontS, labelFontF, text_anchor="end"))
-    """
-    """
-    return
-
-
 # This function determines the scale of the plot
 def detScaleOld(min,max):
     if min>=max:
@@ -982,7 +222,7 @@ def detScaleOld(min,max):
         high=c*ceil(max/c)
         return [low,high,round((high-low)/c)]
 
-def detScale(min=0,max=0,bufferSpace=3):
+def detScale(min=0,max=0):
 
     if min>=max:
         return None
@@ -1019,57 +259,9 @@ def detScale(min=0,max=0,bufferSpace=3):
 
         return [low,high,n]
 
-
-
-def colorSpectrumOld(n):
-    if n == 1:
-        return [pid.Color(1,0,0)]
-    elif n == 2:
-        return [pid.Color(1,0,0),pid.Color(0,0,1)]
-    elif n == 3:
-        return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
-    else:
-        step = 2.0/(n-1)
-        red = 1.0
-        green = 0.0
-        blue = 0.0
-        colors = [pid.Color(red,green,blue)]
-        i = 1
-        greenpeak = 0
-        while i < n:
-            if red >= step:
-                red -= step
-                green += step
-                if green >= 1.0:
-                    greenpeak = 1
-                    blue += green -1.0
-                    green = 1.0
-            else:
-                red = 0.0
-                if greenpeak:
-                    green -= step
-                    blue += step
-                else:
-                    green += step
-                if green >= 1.0:
-                    greenpeak = 1
-                    blue += green -1.0
-                    green = 2.0 -green
-                elif green < 0.0:
-                    green = 0.0
-                else:
-                    pass
-            colors.append(pid.Color(red,green,blue))
-            i += 1
-        return colors
-
-
-
-
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10*(x-0.6)))
 
-
 def redfunc(x):
     return 1.0 / (1.0 + exp(10*(x-0.5)))
 
@@ -1098,52 +290,10 @@ def colorSpectrum(n=100):
     out2.append(out[-1])
     return out2
 
-
-def colorSpectrumSVG(n=100):
-    multiple = 10
-    if n == 1:
-        return ["rgb(255,0,0)"]
-    elif n == 2:
-        return ["rgb(255,0,0)","rgb(0,0,255)"]
-    elif n == 3:
-        return ["rgb(255,0,0)","rgb(0,255,0)","rgb(0,0,255)"]
-    N = n*multiple
-    out = [None]*N;
-    for i in range(N):
-        x = float(i)/N
-        out[i] = "rgb(%d, %d, %d)" % (redfunc(x)*255, greenfunc(x)*255, bluefunc(x)*255);
-    out2 = [out[0]]
-    step = N/float(n-1)
-    j = 0
-    for i in range(n-2):
-        j += step
-        out2.append(out[int(j)])
-    out2.append(out[-1])
-    return out2
-
-
-def BWSpectrum(n=100):
-    multiple = 10
-    if n == 1:
-        return [pid.Color(0,0,0)]
-    elif n == 2:
-        return [pid.Color(0,0,0),pid.Color(1,1,1)]
-    elif n == 3:
-        return [pid.Color(0,0,0),pid.Color(0.5,0.5,0.5),pid.Color(1,1,1)]
-
-    step = 1.0/n
-    x = 0.0
-    out = []
-    for i in range(n):
-        out.append(pid.Color(x,x,x));
-        x += step
-    return out
-
-
 def _test():
     import doctest
     doctest.testmod()
 
 
 if __name__=="__main__":
-    _test()
+    _test()
\ No newline at end of file
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index a3bb85e9..b628a0a4 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -13,10 +13,4 @@ def after_this_request(f):
     if not hasattr(g, 'after_request_callbacks'):
         g.after_request_callbacks = []
     g.after_request_callbacks.append(f)
-    return f
-
-@app.after_request
-def call_after_request_callbacks(response):
-    for callback in getattr(g, 'after_request_callbacks', ()):
-        callback(response)
-    return response
+    return f
\ No newline at end of file
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 8c97370d..8f1c916b 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -11,7 +11,7 @@ logger = getLogger(__name__ )
 class Bench(object):
     entries = collections.OrderedDict()
 
-    def __init__(self, name=None, write_output=True):
+    def __init__(self, name=None, write_output=LOG_BENCH):
         self.name = name
         self.write_output = write_output
 
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 7149e560..af306731 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -72,7 +72,7 @@ class ConvertGenoFile(object):
         yield row
 
   def process_csv(self):
-    for row_count, row in enumerate(self.process_rows()):
+    for row in self.process_rows():
       row_items = row.split("\t")
 
       this_marker = Marker()
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 128706df..510b1041 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -33,7 +33,7 @@ from pprint import pformat as pf
 from inspect import stack
 import datetime
 
-from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL, LOG_FORMAT
+from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL
 
 class GNLogger:
     """A logger class with some additional functionality, such as
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 4fc978f5..2336e722 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -90,70 +90,6 @@ PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",
 #      Accessory Functions
 #########################################
 
-def inverseCumul(p):
-    #Coefficients in rational approximations.
-    a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
-
-    b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
-
-    c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
-
-    d =  [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
-
-    #Define break-points.
-
-    p_low  = 0.02425
-    p_high = 1 - p_low
-
-    #Rational approximation for lower region.
-
-    if p > 0 and p < p_low:
-        q = sqrt(-2*log(p))
-        x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-
-    #Rational approximation for central region.
-
-    elif p>= p_low and p <= p_high:
-        q = p - 0.5
-        r = q*q
-        x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
-
-    #Rational approximation for upper region.
-
-    elif p>p_high and  p < 1:
-        q = sqrt(-2*log(1-p))
-        x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
-
-    else:
-        return None
-
-    if p>0 and p < 1:
-        e = 0.5 * erfcc(-x/sqrt(2)) - p
-        u = e * sqrt(2*pi) * exp(x*x/2)
-        x = x - u/(1 + x*u/2)
-        return x
-    else:
-        return None
-
-def erfcc(x):
-	z=abs(x)
-	t=1.0/(1.0+0.5*z)
-	ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
-	if x>=0.0:
-		return ans
-	else:
-		return 2.0-ans
-
-def U(n):
-	x=pow(0.5,1.0/n)
-	m=[1-x]
-	for i in range(2,n):
-		a=(i-0.3175)/(n+0.365)
-		m.append(a)
-	m.append(x)
-	return m
-
 def decodeEscape(str):
     a = str
     pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
@@ -952,72 +888,6 @@ def formatField(name):
     #name = name.replace("Mb Mm6", "Mb");
     return name.replace("Id", "ID")
 
-#XZ, 03/27/2009: This function is very specific.
-#It is used by AJAX_table.py, correlationPage.py and dataPage.py
-
-
-def genTableObj(tblobj=None, file="", sortby = ("", ""), tableID = "sortable", addIndex = "1", hiddenColumns=[]):
-    header = tblobj['header']
-    body = tblobj['body']
-    field, order = sortby
-
-    #ZAS 9/12/2011 - The hiddenColumns array needs to be converted into a string so they can be placed into the javascript of each up/down button
-    hiddenColumnsString = ",".join(hiddenColumns)
-
-    tbl = HT.TableLite(Class="collap b2", cellspacing=1, cellpadding=5)
-
-    hiddenColumnIdx = [] #indices of columns to hide
-    idx = -1
-    last_idx = 0 #ZS: This is the index of the last item in the regular table header (without any extra parameters). It is used to determine the index of each extra parameter.
-    for row in header:
-        hr = HT.TR()
-        for i, item in enumerate(row):
-            if (item.text == '') or (item.text not in hiddenColumns):
-                if item.sort and item.text:
-                    down = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=down&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGDESC)
-                    up = HT.Href("javascript:xmlhttpPost('%smain.py?FormID=AJAX_table', '%s', 'sort=%s&order=up&file=%s&tableID=%s&addIndex=%s&hiddenColumns=%s')" % (webqtlConfig.CGIDIR, tableID, item.text, file, tableID, addIndex, hiddenColumnsString),IMGASC)
-                    if item.text == field:
-                        idx = item.idx
-                        last_idx = idx
-                        if order == 'up':
-                            up = IMGASCON
-                        elif order == 'down':
-                            down = IMGDESCON
-                    item.html.append(HT.Div(up, down, style="float: bottom;"))
-                hr.append(item.html)
-            else:
-                hiddenColumnIdx.append(i)
-        tbl.append(hr)
-
-    for i, row in enumerate(body):
-        for j, item in enumerate(row):
-            if order == 'down':
-                if (item.val == '' or item.val == 'x' or item.val == 'None'):
-                    item.val = 0
-            if order == 'up':
-                if (item.val == '' or item.val == 'x' or item.val == 'None'):
-                    item.val = 'zzzzz'
-
-    if idx >= 0:
-        if order == 'down':
-            body.sort(lambda A, B: cmp(B[idx].val, A[idx].val), key=natsort_key)
-        elif order == 'up':
-            body.sort(lambda A, B: cmp(A[idx].val, B[idx].val), key=natsort_key)
-        else:
-            pass
-
-    for i, row in enumerate(body):
-        hr = HT.TR(Id = row[0].text)
-        for j, item in enumerate(row):
-            if (j not in hiddenColumnIdx):
-                if j == 0:
-                    if addIndex == "1":
-                        item.html.contents = [i+1] + item.html.contents
-                hr.append(item.html)
-        tbl.append(hr)
-
-    return tbl
-
 def natsort_key(string):
     r = []
     for c in string:
@@ -1027,4 +897,4 @@ def natsort_key(string):
             except: r.append(c)
         except:
             r.append(c)
-    return r
+    return r
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index c196b58b..632c2f8f 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1160,6 +1160,7 @@ class MarkerRegression(object):
         else:
             string1 = 'Mapping for Dataset: %s, mapping on Chromosome %s' % (self.dataset.group.name, self.ChrList[self.selectedChr][0])
 
+        string3 = ''
         if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
             if self.use_loco == "True":
                 string2 = 'Using GEMMA mapping method with LOCO and '
@@ -1170,7 +1171,7 @@ class MarkerRegression(object):
                 cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")])
                 string3 = cofactor_names
             else:
-                string2 += 'no cofactors.'
+                string2 += 'no cofactors'
                 string3 = ''
         elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
             string2 = 'Using R/qtl mapping method with '
@@ -1179,7 +1180,7 @@ class MarkerRegression(object):
             else:
                 string2 += 'no control for other QTLs'
         elif self.mapping_method == "plink":
-            string2 = 'Using PLINK mapping method with no control for other QTLs.'
+            string2 = 'Using PLINK mapping method with no control for other QTLs'
         else:
             string2 = 'Using Haldane mapping function with '
             if self.controlLocus and self.doControl != "false":
-- 
cgit v1.2.3


From 23ef6a91c1dce4c9258dfb2bc24ee7e0004f509d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 9 Apr 2018 23:07:33 +0000
Subject: Removed svg.py, which I know isn't used, and webqtlFormData, which
 I'm pretty sure also isn't used any more.

Also removed some other unused code from the files listed
---
 wqflask/base/webqtlFormData.py                     |  257 -----
 wqflask/utility/Plot.py                            |    1 -
 wqflask/utility/svg.py                             | 1068 --------------------
 wqflask/utility/webqtlUtil.py                      |   88 --
 wqflask/wqflask/correlation/show_corr_results.py   |   52 -
 .../marker_regression/marker_regression_gn1.py     |   16 -
 wqflask/wqflask/views.py                           |   80 +-
 7 files changed, 22 insertions(+), 1540 deletions(-)
 delete mode 100644 wqflask/base/webqtlFormData.py
 delete mode 100644 wqflask/utility/svg.py

diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
deleted file mode 100644
index 1b41b2fc..00000000
--- a/wqflask/base/webqtlFormData.py
+++ /dev/null
@@ -1,257 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-from __future__ import print_function
-from pprint import pformat as pf
-
-import string
-import os
-
-import reaper
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from utility import webqtlUtil
-
-class webqtlFormData(object):
-    'Represents data from a WebQTL form page, needed to generate the next page'
-
-    attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance'
-                'suggestive','significance','submitID','identification', 'enablevariance',
-                'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
-
-    #XZ: Attention! All attribute values must be picklable!
-
-    def __init__(self,
-                 start_vars = None,
-                 req = None):
-        # Todo: rework this whole thing
-        for item in webqtlFormData.attrs:
-            self.__dict__[item] = None
-
-        for item in start_vars:
-            self.__dict__[item] = start_vars[item]
-
-        #Todo: This can't be good below...rework
-        try:
-            self.remote_ip = req.connection.remote_ip
-        except:
-            self.remote_ip = '1.2.3.4'
-
-        self.ppolar = None
-        self.mpolar = None
-
-        if self.group:
-            _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
-
-        def set_number(stringy):
-            return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
-
-        self.nperm = set_number(self.nperm)
-        self.nboot = set_number(self.nboot)
-
-        if self.allsamplelist:
-            self.allsamplelist = self.allsamplelist.split()
-
-        if self.group == 'BXD300':
-            self.group = 'BXD'
-
-    def __getitem__(self, key):
-        return self.__dict__[key]
-
-    def get(self, key, default=None):
-        if key in self.__dict__:
-            return self.__dict__[key]
-        else:
-            return default
-
-    def __str__(self):
-        rstr = ''
-        for item in self.attrs:
-            if item != 'genotype':
-                rstr += '%s:%s\n' % (item,str(getattr(self,item)))
-        return rstr
-
-
-    def readGenotype(self):
-        '''read genotype from .geno file'''
-        if self.group == 'BXD300':
-            self.group = 'BXD'
-
-        assert self.group, "self.group needs to be set"
-
-        #genotype_1 is Dataset Object without parents and f1
-        #genotype_2 is Dataset Object with parents and f1 (not for intercross)
-
-        self.genotype_1 = reaper.Dataset()
-
-        full_filename = locate(self.group + '.geno','genotype')
-
-        # reaper barfs on unicode filenames, so here we ensure it's a string
-        full_filename = str(full_filename)
-        self.genotype_1.read(full_filename)
-
-        print("Got to after read")
-
-        try:
-            # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
-            _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group]
-        except KeyError:
-            _f1 = _f12 = _mat = _pat = None
-
-        self.genotype_2 = self.genotype_1
-        if self.genotype_1.type == "group" and _mat and _pat:
-            self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat)       #, F1=_f1)
-
-        #determine default genotype object
-        if self.incparentsf1 and self.genotype_1.type != "intercross":
-            self.genotype = self.genotype_2
-        else:
-            self.incparentsf1 = 0
-            self.genotype = self.genotype_1
-
-        self.samplelist = list(self.genotype.prgy)
-        self.f1list = []
-        self.parlist = []
-
-        if _f1 and _f12:
-            self.f1list = [_f1, _f12]
-        if _mat and _pat:
-            self.parlist = [_mat, _pat]
-
-
-    def readData(self, samplelist, incf1=None):
-        '''read user input data or from trait data and analysis form'''
-
-        if incf1 == None:
-            incf1 = []
-
-        if not self.genotype:
-            self.readGenotype()
-        if not samplelist:
-            if incf1:
-                samplelist = self.f1list + self.samplelist
-            else:
-                samplelist = self.samplelist
-
-        traitfiledata = getattr(self, "traitfile", None)
-        traitpastedata = getattr(self, "traitpaste", None)
-        variancefiledata = getattr(self, "variancefile", None)
-        variancepastedata = getattr(self, "variancepaste", None)
-        Nfiledata = getattr(self, "Nfile", None)
-
-        #### Todo: Rewrite below when we get to someone submitting their own trait #####
-
-        def to_float(item):
-            try:
-                return float(item)
-            except ValueError:
-                return None
-
-        print("bottle samplelist is:", samplelist)
-        if traitfiledata:
-            tt = traitfiledata.split()
-            values = map(webqtlUtil.StringAsFloat, tt)
-        elif traitpastedata:
-            tt = traitpastedata.split()
-            values = map(webqtlUtil.StringAsFloat, tt)
-        else:
-            print("mapping formdataasfloat")
-            #values = map(self.FormDataAsFloat, samplelist)
-            values = [to_float(getattr(self, key)) for key in samplelist]
-
-
-        if len(values) < len(samplelist):
-            values += [None] * (len(samplelist) - len(values))
-        elif len(values) > len(samplelist):
-            values = values[:len(samplelist)]
-
-        if variancefiledata:
-            tt = variancefiledata.split()
-            variances = map(webqtlUtil.StringAsFloat, tt)
-        elif variancepastedata:
-            tt = variancepastedata.split()
-            variances = map(webqtlUtil.StringAsFloat, tt)
-        else:
-            variances = map(self.FormVarianceAsFloat, samplelist)
-
-        if len(variances) < len(samplelist):
-            variances += [None]*(len(samplelist) - len(variances))
-        elif len(variances) > len(samplelist):
-            variances = variances[:len(samplelist)]
-
-        if Nfiledata:
-            tt = string.split(Nfiledata)
-            nsamples = map(webqtlUtil.IntAsFloat, tt)
-            if len(nsamples) < len(samplelist):
-                nsamples += [None]*(len(samplelist) - len(nsamples))
-        else:
-            nsamples = map(self.FormNAsFloat, samplelist)
-
-        ##values, variances, nsamples is obsolete
-        self.allTraitData = {}
-        for i, _sample in enumerate(samplelist):
-            if values[i] != None:
-                self.allTraitData[_sample] = webqtlCaseData(
-                    _sample, values[i], variances[i], nsamples[i])
-
-    def informativeStrains(self, samplelist=None, include_variances = None):
-        '''if readData was called, use this to output informative samples (sample with values)'''
-
-        if not samplelist:
-            samplelist = self.samplelist
-
-        samples = []
-        values = []
-        variances = []
-
-        for sample in samplelist:
-            if sample in self.allTraitData:
-                _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
-                if _val != None:
-                    if include_variances:
-                        if _var != None:
-                            samples.append(sample)
-                            values.append(_val)
-                            variances.append(_var)
-                    else:
-                        samples.append(sample)
-                        values.append(_val)
-                        variances.append(None)
-
-        return samples, values, variances, len(samples)
-
-    def FormVarianceAsFloat(self, key):
-        try:
-            return float(self.formdata.getfirst('V' + key))
-        except:
-            return None
-
-    def FormNAsFloat(self, key):
-        try:
-            return int(self.formdata.getfirst('N' + key))
-        except:
-            return None
\ No newline at end of file
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index dbcee331..529cd117 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -37,7 +37,6 @@ from numarray import ones, array, dot, swapaxes
 
 import reaper
 
-import svg
 import webqtlUtil
 import corestats
 from base import webqtlConfig
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
deleted file mode 100644
index 512bc9e6..00000000
--- a/wqflask/utility/svg.py
+++ /dev/null
@@ -1,1068 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#!/usr/bin/env python
-##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
-##All rights reserved.
-##
-##Redistribution and use in source and binary forms, with or without modification,
-##are permitted provided that the following conditions are met:
-##
-##Redistributions of source code must retain the above copyright notice, this
-##list of conditions and the following disclaimer.
-##
-##Redistributions in binary form must reproduce the above copyright notice,
-##this list of conditions and the following disclaimer in the documentation and/or
-##other materials provided with the distribution.
-##
-##Neither the name of the Stichting Farmaceutische Kengetallen nor the names of
-##its contributors may be used to endorse or promote products derived from this
-##software without specific prior written permission.
-##
-##THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-##AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-##IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-##DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
-##FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-##DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-##SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-##CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-##OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-##OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-##Thanks to Gerald Rosennfellner for his help and useful comments.
-
-__doc__="""Use SVGdraw to generate your SVGdrawings.
-
-SVGdraw uses an object model drawing and a method toXML to create SVG graphics
-by using easy to use classes and methods usualy you start by creating a drawing eg
-
-    d=drawing()
-    #then you create a SVG root element
-    s=svg()
-    #then you add some elements eg a circle and add it to the svg root element
-    c=circle()
-    #you can supply attributes by using named arguments.
-    c=circle(fill='red',stroke='blue')
-    #or by updating the attributes attribute:
-    c.attributes['stroke-width']=1
-    s.addElement(c)
-    #then you add the svg root element to the drawing
-    d.setSVG(s)
-    #and finaly you xmlify the drawing
-    d.toXml()
-
-
-this results in the svg source of the drawing, which consists of a circle
-on a white background. Its as easy as that;)
-This module was created using the SVG specification of www.w3c.org and the
-O'Reilly (www.oreilly.com) python books as information sources. A svg viewer
-is available from www.adobe.com"""
-
-__version__="1.0"
-
-# there are two possibilities to generate svg:
-# via a dom implementation and directly using <element>text</element> strings
-# the latter is way faster (and shorter in coding)
-# the former is only used in debugging svg programs
-# maybe it will be removed alltogether after a while
-# with the following variable you indicate whether to use the dom implementation
-# Note that PyXML is required for using the dom implementation.
-# It is also possible to use the standard minidom. But I didn't try that one.
-# Anyway the text based approach is about 60 times faster than using the full dom implementation.
-use_dom_implementation=0
-
-
-import exceptions
-if use_dom_implementation<>0:
-    try:
-        from xml.dom import implementation
-        from xml.dom.ext import PrettyPrint
-    except:
-        raise exceptions.ImportError, "PyXML is required for using the dom implementation"
-#The implementation is used for the creating the XML document.
-#The prettyprint module is used for converting the xml document object to a xml file
-
-import sys
-assert sys.version_info[0]>=2
-if sys.version_info[1]<2:
-    True=1
-    False=0
-    file=open
-
-sys.setrecursionlimit=50
-#The recursion limit is set conservative so mistakes like s=svg() s.addElement(s)
-#won't eat up too much processor time.
-
-#the following code is pasted form xml.sax.saxutils
-#it makes it possible to run the code without the xml sax package installed
-#To make it possible to have <rubbish> in your text elements, it is necessary to escape the texts
-def _escape(data, entities={}):
-    """Escape &, <, and > in a string of data.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    #data = data.replace("&", "&amp;")
-    data = data.replace("<", "&lt;")
-    data = data.replace(">", "&gt;")
-    for chars, entity in entities.items():
-        data = data.replace(chars, entity)
-    return data
-
-def _quoteattr(data, entities={}):
-    """Escape and quote an attribute value.
-
-    Escape &, <, and > in a string of data, then quote it for use as
-    an attribute value.  The \" character will be escaped as well, if
-    necessary.
-
-    You can escape other strings of data by passing a dictionary as
-    the optional entities parameter.  The keys and values must all be
-    strings; each key will be replaced with its corresponding value.
-    """
-    data = _escape(data, entities)
-    if '"' in data:
-        if "'" in data:
-            data = '"%s"' % data.replace('"', "&quot;")
-        else:
-            data = "'%s'" % data
-    else:
-        data = '"%s"' % data
-    return data
-
-
-
-def _xypointlist(a):
-    """formats a list of xy pairs"""
-    s=''
-    for e in a: #this could be done more elegant
-        s+=str(e)[1:-1] +'  '
-    return s
-
-def _viewboxlist(a):
-    """formats a tuple"""
-    s=''
-    for e in a:
-        s+=str(e)+' '
-    return s
-
-def _pointlist(a):
-    """formats a list of numbers"""
-    return str(a)[1:-1]
-
-class pathdata:
-    """class used to create a pathdata object which can be used for a path.
-    although most methods are pretty straightforward it might be useful to look at the SVG specification."""
-    #I didn't test the methods below.
-    def __init__(self,x=None,y=None):
-        self.path=[]
-        if x is not None and y is not None:
-            self.path.append('M '+str(x)+' '+str(y))
-    def closepath(self):
-        """ends the path"""
-        self.path.append('z')
-    def move(self,x,y):
-        """move to absolute"""
-        self.path.append('M '+str(x)+' '+str(y))
-    def relmove(self,x,y):
-        """move to relative"""
-        self.path.append('m '+str(x)+' '+str(y))
-    def line(self,x,y):
-        """line to absolute"""
-        self.path.append('L '+str(x)+' '+str(y))
-    def relline(self,x,y):
-        """line to relative"""
-        self.path.append('l '+str(x)+' '+str(y))
-    def hline(self,x):
-        """horizontal line to absolute"""
-        self.path.append('H'+str(x))
-    def relhline(self,x):
-        """horizontal line to relative"""
-        self.path.append('h'+str(x))
-    def vline(self,y):
-        """verical line to absolute"""
-        self.path.append('V'+str(y))
-    def relvline(self,y):
-        """vertical line to relative"""
-        self.path.append('v'+str(y))
-    def bezier(self,x1,y1,x2,y2,x,y):
-        """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relbezier(self,x1,y1,x2,y2,x,y):
-        """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def smbezier(self,x2,y2,x,y):
-        """smooth bezier with xy2 to xy absolut"""
-        self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def relsmbezier(self,x2,y2,x,y):
-        """smooth bezier with xy2 to xy relative"""
-        self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
-    def qbezier(self,x1,y1,x,y):
-        """quadratic bezier with xy1 to xy absolut"""
-        self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def relqbezier(self,x1,y1,x,y):
-        """quadratic bezier with xy1 to xy relative"""
-        self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
-    def smqbezier(self,x,y):
-        """smooth quadratic bezier to xy absolut"""
-        self.path.append('T'+str(x)+','+str(y))
-    def relsmqbezier(self,x,y):
-        """smooth quadratic bezier to xy relative"""
-        self.path.append('t'+str(x)+','+str(y))
-    def ellarc(self,rx,ry,xrot,laf,sf,x,y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
-    def relellarc(self,rx,ry,xrot,laf,sf,x,y):
-        """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot)+' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
-    def __repr__(self):
-        return ' '.join(self.path)
-
-
-
-
-class SVGelement:
-    """SVGelement(type,attributes,elements,text,namespace,**args)
-    Creates a arbitrary svg element and is intended to be subclassed not used on its own.
-    This element is the base of every svg element it defines a class which resembles
-    a xml-element. The main advantage of this kind of implementation is that you don't
-    have to create a toXML method for every different graph object. Every element
-    consists of a type, attribute, optional subelements, optional text and an optional
-    namespace. Note the elements==None, if elements = None:self.elements=[] construction.
-    This is done because if you default to elements=[] every object has a reference
-    to the same empty list."""
-    def __init__(self,type='',attributes=None,elements=None,text='',namespace='',cdata=None, **args):
-        self.type=type
-        if attributes==None:
-            self.attributes={}
-        else:
-            self.attributes=attributes
-        if elements==None:
-            self.elements=[]
-        else:
-            self.elements=elements
-        self.text=text
-        self.namespace=namespace
-        self.cdata=cdata
-        for arg in args.keys():
-            arg2 = arg.replace("__", ":")
-            arg2 = arg2.replace("_", "-")
-            self.attributes[arg2]=args[arg]
-    def addElement(self,SVGelement):
-        """adds an element to a SVGelement
-
-        SVGelement.addElement(SVGelement)
-        """
-        self.elements.append(SVGelement)
-
-    def toXml(self,level,f):
-        f.write('\t'*level)
-        f.write('<'+self.type)
-        for attkey in self.attributes.keys():
-            f.write(' '+_escape(str(attkey))+'='+_quoteattr(str(self.attributes[attkey])))
-        if self.namespace:
-            f.write(' xmlns="'+ _escape(str(self.namespace))+'" xmlns:xlink="http://www.w3.org/1999/xlink"')
-        if self.elements or self.text or self.cdata:
-            f.write('>')
-        if self.elements:
-            f.write('\n')
-        for element in self.elements:
-            element.toXml(level+1,f)
-        if self.cdata:
-            f.write('\n'+'\t'*(level+1)+'<![CDATA[')
-            for line in self.cdata.splitlines():
-                f.write('\n'+'\t'*(level+2)+line)
-            f.write('\n'+'\t'*(level+1)+']]>\n')
-        if self.text:
-            if type(self.text)==type(''): #If the text is only text
-                f.write(_escape(str(self.text)))
-            else:                         #If the text is a spannedtext class
-                f.write(str(self.text))
-        if self.elements:
-            f.write('\t'*level+'</'+self.type+'>\n')
-        elif self.text:
-            f.write('</'+self.type+'>\n')
-        elif self.cdata:
-            f.write('\t'*level+'</'+self.type+'>\n')
-        else:
-            f.write('/>\n')
-
-class tspan(SVGelement):
-    """ts=tspan(text='',**args)
-
-    a tspan element can be used for applying formatting to a textsection
-    usage:
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    st=spannedtext()
-    st.addtspan(ts)
-    t=text(3,5,st)
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'tspan',**args)
-        if self.text<>None:
-            self.text=text
-    def __repr__(self):
-        s="<tspan"
-        for key,value in self.attributes.items():
-            s+= ' %s="%s"' % (key,value)
-        s+='>'
-        s+=self.text
-        s+='</tspan>'
-        return s
-
-class tref(SVGelement):
-    """tr=tref(link='',**args)
-
-    a tref element can be used for referencing text by a link to its id.
-    usage:
-    tr=tref('#linktotext')
-    st=spannedtext()
-    st.addtref(tr)
-    t=text(3,5,st)
-    """
-    def __init__(self,link,**args):
-        SVGelement.__init__(self,'tref',{'xlink:href':link},**args)
-    def __repr__(self):
-        s="<tref"
-
-        for key,value in self.attributes.items():
-            s+= ' %s="%s"' % (key,value)
-        s+='/>'
-        return s
-
-class spannedtext:
-    """st=spannedtext(textlist=[])
-
-    a spannedtext can be used for text which consists of text, tspan's and tref's
-    You can use it to add to a text element or path element. Don't add it directly
-    to a svg or a group element.
-    usage:
-
-    ts=tspan('this text is bold')
-    ts.attributes['font-weight']='bold'
-    tr=tref('#linktotext')
-    tr.attributes['fill']='red'
-    st=spannedtext()
-    st.addtspan(ts)
-    st.addtref(tr)
-    st.addtext('This text is not bold')
-    t=text(3,5,st)
-    """
-    def __init__(self,textlist=None):
-        if textlist==None:
-            self.textlist=[]
-        else:
-            self.textlist=textlist
-    def addtext(self,text=''):
-        self.textlist.append(text)
-    def addtspan(self,tspan):
-        self.textlist.append(tspan)
-    def addtref(self,tref):
-        self.textlist.append(tref)
-    def __repr__(self):
-        s=""
-        for element in self.textlist:
-            s+=str(element)
-        return s
-
-class rect(SVGelement):
-    """r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
-
-    a rectangle is defined by a width and height and a xy pair
-    """
-    def __init__(self,x=None,y=None,width=None,height=None,fill=None,stroke=None,stroke_width=None,**args):
-        if width==None or height==None:
-            if width<>None:
-                raise ValueError, 'height is required'
-            if height<>None:
-                raise ValueError, 'width is required'
-            else:
-                raise ValueError, 'both height and width are required'
-        SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-
-class ellipse(SVGelement):
-    """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
-
-    an ellipse is defined as a center and a x and y radius.
-    """
-    def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
-        if rx==None or ry== None:
-            if rx<>None:
-                raise ValueError, 'rx is required'
-            if ry<>None:
-                raise ValueError, 'ry is required'
-            else:
-                raise ValueError, 'both rx and ry are required'
-        SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-
-
-class circle(SVGelement):
-    """c=circle(x,y,radius,fill,stroke,stroke_width,**args)
-
-    The circle creates an element using a x, y and radius values eg
-    """
-    def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
-        if r==None:
-            raise ValueError, 'r is required'
-        SVGelement.__init__(self,'circle',{'r':r},**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-
-class point(circle):
-    """p=point(x,y,color)
-
-    A point is defined as a circle with a size 1 radius. It may be more efficient to use a
-    very small rectangle if you use many points because a circle is difficult to render.
-    """
-    def __init__(self,x,y,fill='black',**args):
-        circle.__init__(self,x,y,1,fill,**args)
-
-class line(SVGelement):
-    """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
-
-    A line is defined by a begin x,y pair and an end x,y pair
-    """
-    def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'line',**args)
-        if x1<>None:
-            self.attributes['x1']=x1
-        if y1<>None:
-            self.attributes['y1']=y1
-        if x2<>None:
-            self.attributes['x2']=x2
-        if y2<>None:
-            self.attributes['y2']=y2
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-
-class polyline(SVGelement):
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
-    a polyline is defined by a list of xy pairs
-    """
-    def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-
-class polygon(SVGelement):
-    """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
-
-    a polygon is defined by a list of xy pairs
-    """
-    def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
-        SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-
-class path(SVGelement):
-    """p=path(path,fill,stroke,stroke_width,**args)
-
-    a path is defined by a path object and optional width, stroke and fillcolor
-    """
-    def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
-        SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
-        if stroke<>None:
-            self.attributes['stroke']=stroke
-        if fill<>None:
-            self.attributes['fill']=fill
-        if stroke_width<>None:
-            self.attributes['stroke-width']=stroke_width
-        if id<>None:
-            self.attributes['id']=id
-
-
-class text(SVGelement):
-    """t=text(x,y,text,font_size,font_family,**args)
-
-    a text element can bge used for displaying text on the screen
-    """
-    def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
-        SVGelement.__init__(self,'text',**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if font_size<>None:
-            self.attributes['font-size']=font_size
-        if font_family<>None:
-            self.attributes['font-family']=font_family
-        if text<>None:
-            self.text=text
-        if text_anchor<>None:
-            self.attributes['text-anchor']=text_anchor
-
-
-class textpath(SVGelement):
-    """tp=textpath(text,link,**args)
-
-    a textpath places a text on a path which is referenced by a link.
-    """
-    def __init__(self,link,text=None,**args):
-        SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
-        if text<>None:
-            self.text=text
-
-class pattern(SVGelement):
-    """p=pattern(x,y,width,height,patternUnits,**args)
-
-    A pattern is used to fill or stroke an object using a pre-defined
-    graphic object which can be replicated ("tiled") at fixed intervals
-    in x and y to cover the areas to be painted.
-    """
-    def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
-        SVGelement.__init__(self,'pattern',**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-        if patternUnits<>None:
-            self.attributes['patternUnits']=patternUnits
-
-class title(SVGelement):
-    """t=title(text,**args)
-
-    a title is a text element. The text is displayed in the title bar
-    add at least one to the root svg element
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'title',**args)
-        if text<>None:
-            self.text=text
-
-class description(SVGelement):
-    """d=description(text,**args)
-
-    a description can be added to any element and is used for a tooltip
-    Add this element before adding other elements.
-    """
-    def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'desc',**args)
-        if text<>None:
-            self.text=text
-
-class lineargradient(SVGelement):
-    """lg=lineargradient(x1,y1,x2,y2,id,**args)
-
-    defines a lineargradient using two xy pairs.
-    stop elements van be added to define the gradient colors.
-    """
-    def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
-        SVGelement.__init__(self,'linearGradient',**args)
-        if x1<>None:
-            self.attributes['x1']=x1
-        if y1<>None:
-            self.attributes['y1']=y1
-        if x2<>None:
-            self.attributes['x2']=x2
-        if y2<>None:
-            self.attributes['y2']=y2
-        if id<>None:
-            self.attributes['id']=id
-
-class radialgradient(SVGelement):
-    """rg=radialgradient(cx,cy,r,fx,fy,id,**args)
-
-    defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
-    stop elements van be added to define the gradient colors.
-    """
-    def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
-        SVGelement.__init__(self,'radialGradient',**args)
-        if cx<>None:
-            self.attributes['cx']=cx
-        if cy<>None:
-            self.attributes['cy']=cy
-        if r<>None:
-            self.attributes['r']=r
-        if fx<>None:
-            self.attributes['fx']=fx
-        if fy<>None:
-            self.attributes['fy']=fy
-        if id<>None:
-            self.attributes['id']=id
-
-class stop(SVGelement):
-    """st=stop(offset,stop_color,**args)
-
-    Puts a stop color at the specified radius
-    """
-    def __init__(self,offset,stop_color=None,**args):
-        SVGelement.__init__(self,'stop',{'offset':offset},**args)
-        if stop_color<>None:
-            self.attributes['stop-color']=stop_color
-
-class style(SVGelement):
-    """st=style(type,cdata=None,**args)
-
-    Add a CDATA element to this element for defing in line stylesheets etc..
-    """
-    def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args)
-
-
-class image(SVGelement):
-    """im=image(url,width,height,x,y,**args)
-
-    adds an image to the drawing. Supported formats are .png, .jpg and .svg.
-    """
-    def __init__(self,url,x=None,y=None,width=None,height=None,**args):
-        if width==None or height==None:
-            if width<>None:
-                raise ValueError, 'height is required'
-            if height<>None:
-                raise ValueError, 'width is required'
-            else:
-                raise ValueError, 'both height and width are required'
-        SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-
-class cursor(SVGelement):
-    """c=cursor(url,**args)
-
-    defines a custom cursor for a element or a drawing
-    """
-    def __init__(self,url,**args):
-        SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
-
-
-class marker(SVGelement):
-    """m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
-
-    defines a marker which can be used as an endpoint for a line or other pathtypes
-    add an element to it which should be used as a marker.
-    """
-    def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
-        SVGelement.__init__(self,'marker',**args)
-        if id<>None:
-            self.attributes['id']=id
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-        if refx<>None:
-            self.attributes['refX']=refx
-        if refy<>None:
-            self.attributes['refY']=refy
-        if markerWidth<>None:
-            self.attributes['markerWidth']=markerWidth
-        if markerHeight<>None:
-            self.attributes['markerHeight']=markerHeight
-
-class group(SVGelement):
-    """g=group(id,**args)
-
-    a group is defined by an id and is used to contain elements
-    g.addElement(SVGelement)
-    """
-    def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'g',**args)
-        if id<>None:
-            self.attributes['id']=id
-
-class symbol(SVGelement):
-    """sy=symbol(id,viewbox,**args)
-
-    defines a symbol which can be used on different places in your graph using
-    the use element. A symbol is not rendered but you can use 'use' elements to
-    display it by referencing its id.
-    sy.addElement(SVGelement)
-    """
-
-    def __init__(self,id=None,viewBox=None,**args):
-        SVGelement.__init__(self,'symbol',**args)
-        if id<>None:
-            self.attributes['id']=id
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-
-class defs(SVGelement):
-    """d=defs(**args)
-
-    container for defining elements
-    """
-    def __init__(self,**args):
-        SVGelement.__init__(self,'defs',**args)
-
-class switch(SVGelement):
-    """sw=switch(**args)
-
-    Elements added to a switch element which are "switched" by the attributes
-    requiredFeatures, requiredExtensions and systemLanguage.
-    Refer to the SVG specification for details.
-    """
-    def __init__(self,**args):
-        SVGelement.__init__(self,'switch',**args)
-
-
-class use(SVGelement):
-    """u=use(link,x,y,width,height,**args)
-
-    references a symbol by linking to its id and its position, height and width
-    """
-    def __init__(self,link,x=None,y=None,width=None,height=None,**args):
-        SVGelement.__init__(self,'use',{'xlink:href':link},**args)
-        if x<>None:
-            self.attributes['x']=x
-        if y<>None:
-            self.attributes['y']=y
-
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-
-
-class link(SVGelement):
-    """a=link(url,**args)
-
-    a link  is defined by a hyperlink. add elements which have to be linked
-    a.addElement(SVGelement)
-    """
-    def __init__(self,link='',**args):
-        SVGelement.__init__(self,'a',{'xlink:href':link},**args)
-
-class view(SVGelement):
-    """v=view(id,**args)
-
-    a view can be used to create a view with different attributes"""
-    def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'view',**args)
-        if id<>None:
-            self.attributes['id']=id
-
-class script(SVGelement):
-    """sc=script(type,type,cdata,**args)
-
-    adds a script element which contains CDATA to the SVG drawing
-
-    """
-    def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
-
-class animate(SVGelement):
-    """an=animate(attribute,from,to,during,**args)
-
-    animates an attribute.
-    """
-    def __init__(self,attribute,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-
-class animateMotion(SVGelement):
-    """an=animateMotion(pathdata,dur,**args)
-
-    animates a SVGelement over the given path in dur seconds
-    """
-    def __init__(self,pathdata,dur,**args):
-        SVGelement.__init__(self,'animateMotion',**args)
-        if pathdata<>None:
-            self.attributes['path']=str(pathdata)
-        if dur<>None:
-            self.attributes['dur']=dur
-
-class animateTransform(SVGelement):
-    """antr=animateTransform(type,from,to,dur,**args)
-
-    transform an element from and to a value.
-    """
-    def __init__(self,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
-        #As far as I know the attributeName is always transform
-        if type<>None:
-            self.attributes['type']=type
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-class animateColor(SVGelement):
-    """ac=animateColor(attribute,type,from,to,dur,**args)
-
-    Animates the color of a element
-    """
-    def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
-        if type<>None:
-            self.attributes['type']=type
-        if fr<>None:
-            self.attributes['from']=fr
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-class set(SVGelement):
-    """st=set(attribute,to,during,**args)
-
-    sets an attribute to a value for a
-    """
-    def __init__(self,attribute,to=None,dur=None,**args):
-        SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
-        if to<>None:
-            self.attributes['to']=to
-        if dur<>None:
-            self.attributes['dur']=dur
-
-
-
-class svg(SVGelement):
-    """s=svg(viewbox,width,height,**args)
-
-    a svg or element is the root of a drawing add all elements to a svg element.
-    You can have different svg elements in one svg file
-    s.addElement(SVGelement)
-
-    eg
-    d=drawing()
-    s=svg((0,0,100,100),'100%','100%')
-    c=circle(50,50,20)
-    s.addElement(c)
-    d.setSVG(s)
-    d.toXml()
-    """
-    def __init__(self,viewBox=None, width=None, height=None,**args):
-        SVGelement.__init__(self,'svg',**args)
-        if viewBox<>None:
-            self.attributes['viewBox']=_viewboxlist(viewBox)
-        if width<>None:
-            self.attributes['width']=width
-        if height<>None:
-            self.attributes['height']=height
-        self.namespace="http://www.w3.org/2000/svg"
-
-class drawing:
-    """d=drawing()
-
-    this is the actual SVG document. It needs a svg element as a root.
-    Use the addSVG method to set the svg to the root. Use the toXml method to write the SVG
-    source to the screen or to a file
-    d=drawing()
-    d.addSVG(svg)
-    d.toXml(optionalfilename)
-    """
-
-    def __init__(self, entity={}):
-        self.svg=None
-        self.entity = entity
-    def setSVG(self,svg):
-        self.svg=svg
-        #Voeg een element toe aan de grafiek toe.
-    if use_dom_implementation==0:
-        def toXml(self, filename='',compress=False):
-            import cStringIO
-            xml=cStringIO.StringIO()
-            xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
-            xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
-            if self.entity:
-                xml.write(" [\n")
-                for item in self.entity.keys():
-                    xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
-                xml.write("]")
-            xml.write(">\n")
-            self.svg.toXml(0,xml)
-            if not filename:
-                if compress:
-                    import gzip
-                    f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                if filename[-4:]=='svgz':
-                    import gzip
-                    f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
-                    f.write(xml.getvalue())
-                    f.close()
-                else:
-                    f=file(filename,'w')
-                    f.write(xml.getvalue())
-                    f.close()
-
-    else:
-        def toXml(self,filename='',compress=False):
-            """drawing.toXml()        ---->to the screen
-            drawing.toXml(filename)---->to the file
-            writes a svg drawing to the screen or to a file
-            compresses if filename ends with svgz or if compress is true
-            """
-            doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
-
-            global root
-            #root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
-            #that is a bit messy.
-            root=implementation.createDocument(None,None,doctype)
-            #Create the xml document.
-            global appender
-            def appender(element,elementroot):
-                """This recursive function appends elements to an element and sets the attributes
-                and type. It stops when alle elements have been appended"""
-                if element.namespace:
-                    e=root.createElementNS(element.namespace,element.type)
-                else:
-                    e=root.createElement(element.type)
-                if element.text:
-                    textnode=root.createTextNode(element.text)
-                    e.appendChild(textnode)
-                for attribute in element.attributes.keys():   #in element.attributes is supported from python 2.2
-                    e.setAttribute(attribute,str(element.attributes[attribute]))
-                if element.elements:
-                    for el in element.elements:
-                        e=appender(el,e)
-                elementroot.appendChild(e)
-                return elementroot
-            root=appender(self.svg,root)
-            if not filename:
-                import cStringIO
-                xml=cStringIO.StringIO()
-                PrettyPrint(root,xml)
-                if compress:
-                    import gzip
-                    f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
-                    zf.write(xml.getvalue())
-                    zf.close()
-                    f.seek(0)
-                    return f.read()
-                else:
-                    return xml.getvalue()
-            else:
-                try:
-                    if filename[-4:]=='svgz':
-                        import gzip
-                        import cStringIO
-                        xml=cStringIO.StringIO()
-                        PrettyPrint(root,xml)
-                        f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
-                        f.write(xml.getvalue())
-                        f.close()
-                    else:
-                        f=open(filename,'w')
-                        PrettyPrint(root,f)
-                        f.close()
-                except:
-                    print "Cannot write SVG file: " + filename
-    def validate(self):
-        try:
-            import xml.parsers.xmlproc.xmlval
-        except:
-            raise exceptions.ImportError,'PyXml is required for validating SVG'
-        svg=self.toXml()
-        xv=xml.parsers.xmlproc.xmlval.XMLValidator()
-        try:
-            xv.feed(svg)
-        except:
-            raise "SVG is not well formed, see messages above"
-        else:
-            print "SVG well formed"
-if __name__=='__main__':
-
-
-    d=drawing()
-    s=svg((0,0,100,100))
-    r=rect(-100,-100,300,300,'cyan')
-    s.addElement(r)
-
-    t=title('SVGdraw Demo')
-    s.addElement(t)
-    g=group('animations')
-    e=ellipse(0,0,5,2)
-    g.addElement(e)
-    c=circle(0,0,1,'red')
-    g.addElement(c)
-    pd=pathdata(0,-10)
-    for i in range(6):
-        pd.relsmbezier(10,5,0,10)
-        pd.relsmbezier(-10,5,0,10)
-    an=animateMotion(pd,10)
-    an.attributes['rotate']='auto-reverse'
-    an.attributes['repeatCount']="indefinite"
-    g.addElement(an)
-    s.addElement(g)
-    for i in range(20,120,20):
-        u=use('#animations',i,0)
-        s.addElement(u)
-    for i in range(0,120,20):
-        for j in range(5,105,10):
-            c=circle(i,j,1,'red','black',.5)
-            s.addElement(c)
-    d.setSVG(s)
-
-    print d.toXml()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 2336e722..94dd7cbf 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -34,9 +34,6 @@ from htmlgen import HTMLgen2 as HT
 
 from base import webqtlConfig
 
-
-
-
 # NL, 07/27/2010. moved from webqtlForm.py
 #Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
 ParInfo ={
@@ -64,43 +61,10 @@ ParInfo ={
 'SXM':['SMF1', 'MSF1', 'Steptoe','Morex']
 }
 
-
-# NL, 07/27/2010. moved from template.py
-IMGSTEP1 = HT.Image('/images/step1.gif', alt='STEP 1',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP2 = HT.Image('/images/step2.gif', alt='STEP 2',border=0) #XZ, Only be used in inputPage.py
-IMGSTEP3 = HT.Image('/images/step3.gif', alt='STEP 3',border=0) #XZ, Only be used in inputPage.py
-IMGNEXT = HT.Image('/images/arrowdown.gif', alt='NEXT',border=0) #XZ, Only be used in inputPage.py
-
-IMGASC = HT.Image("/images/sortup.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-
-"""
-IMGASC = HT.Image("/images/sortup_icon.gif", border=0)
-IMGASCON = HT.Image("/images/sortupon.gif", border=0)
-IMGDESC = HT.Image("/images/sortdown_icon.gif", border=0)
-IMGDESCON = HT.Image("/images/sortdownon.gif", border=0)
-IMG_UNSORTED = HT.Image("/images/unsorted_icon.gif", border=0)
-"""
-
-PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",border=0)
-
 #########################################
 #      Accessory Functions
 #########################################
 
-def decodeEscape(str):
-    a = str
-    pattern = re.compile('(%[0-9A-Fa-f][0-9A-Fa-f])')
-    match = pattern.findall(a)
-    matched = []
-    for item in match:
-        if item not in matched:
-            a = a.replace(item, '%c' % eval("0x"+item[-2:]))
-        matched.append(item)
-    return a
-
 def exportData(hddn, tdata, NP = None):
     for key in tdata.keys():
         _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
@@ -136,37 +100,6 @@ def genShortStrainName(RISet='', input_strainName=''):
             pass
     return strainName
 
-def toInt(in_str):
-    "Converts an arbitrary string to an unsigned integer"
-    start = -1
-    end = -1
-    for i, char in enumerate(in_str):
-        if char >= '0' and char <= '9':
-            if start < 0:
-                start = i
-            end = i+1
-        else:
-            if start >= 0:
-                break
-    if start < end:
-        return int(in_str[start:end])
-    else:
-        return  -1
-
-def transpose(m):
-    'transpose a matrix'
-    n = len(m)
-    return [[m[j][i] for i in range(len(m[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m[0]))]
-
-def asymTranspose(m):
-    'transpose a matrix'
-    t = max(map(len, m))
-    n = len(m)
-    m2 = [["-"]]*n
-    for i in range(n):
-        m2[i] = m[i] + [""]*(t- len(m[i]))
-    return [[m2[j][i] for i in range(len(m2[0])) for j in range(n)][k*n:k*n+n] for k in range(len(m2[0]))]
-
 def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
     from random import choice
     _str = prefix[:]
@@ -174,27 +107,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
         _str += choice(chars)
     return _str
 
-def generate_session():
-    import sha
-    return sha.new(str(time.time())).hexdigest()
-
-def cvt2Dict(x):
-    tmp = {}
-    for key in x.keys():
-        tmp[key] = x[key]
-    return tmp
-
-def dump_session(session_obj, filename):
-    "It seems mod python can only cPickle most basic data type"
-    import cPickle
-    session_file = open(filename, 'wb')
-    #try:
-    #       pass
-    #except:
-    #       pass
-    cPickle.dump(session_obj, session_file)
-    session_file.close()
-
 def StringAsFloat(str):
     'Converts string to float but catches any exception and returns None'
     try:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 73072423..abf9fc89 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -296,60 +296,8 @@ class CorrelationResults(object):
             if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
                 self.do_tissue_correlation_for_trait_list()
 
-            #print("self.correlation_results: ", pf(self.correlation_results))
-
         self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
 
-        #XZ, 09/18/2008: get all information about the user selected database.
-        #target_db_name = fd.corr_dataset
-        #self.target_db_name = start_vars['corr_dataset']
-
-        # Zach said this is ok
-        # Auth if needed
-        #try:
-        #    auth_user_for_db(self.db, self.cursor, self.target_db_name, self.privilege, self.userName)
-        #except AuthException as e:
-        #    detail = [e.message]
-        #    return self.error(detail)
-
-        #XZ, 09/18/2008: filter out the strains that have no value.
-        #self.sample_names, vals, vars, N = fd.informativeStrains(sample_list)
-
-        #print("samplenames is:", pf(self.sample_names))
-        #CF - If less than a minimum number of strains/cases in common, don't calculate anything
-        #if len(self.sample_names) < self.corr_min_informative:
-        #    detail = ['Fewer than %d strain data were entered for %s data set. No calculation of correlation has been attempted.' % (self.corr_min_informative, fd.RISet)]
-        #    self.error(heading=None, detail=detail)
-
-        #correlation_method = self.CORRELATION_METHODS[self.method]
-        #rankOrder = self.RANK_ORDERS[self.method]
-
-        # CF - Number of results returned
-        # Todo: Get rid of self.returnNumber
-
-        #self.record_count = 0
-
-        #myTrait = get_custom_trait(fd, self.cursor)
-
-
-        # We will not get Literature Correlations if there is no GeneId because there is nothing
-        # to look against
-        #self.geneid = self.this_trait.geneid
-
-        # We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
-        #self.trait_symbol = myTrait.symbol
-
-
-        #XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
-        #self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.dataset.group.species, self.geneid)
-
-        #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)'
-        #self.tissue_probeset_freeze_id = 1
-
-        #traitList = self.correlate()
-
-        #print("Done doing correlation calculation")
-
 ############################################################################################################################################
 
     def get_formatted_corr_type(self):
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 632c2f8f..81da8976 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -190,21 +190,6 @@ class MarkerRegression(object):
             self.js_data = start_vars['js_data']
         self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
 
-        #ZS: Think I can just get all this from dataset object now
-        #RISet and Species
-        #if not fd.genotype:
-        #    fd.readGenotype()
-        #
-        #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
-        #
-        #if ((fd.parentsf14regression == 'on') and fd.genotype_2):
-        #    fd.genotype = fd.genotype_2
-        #else:
-        #    fd.genotype = fd.genotype_1
-        #fd.strainlist = list(fd.genotype.prgy)
-        #
-        #self.species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=fd.RISet)
-
         if self.dataset.group.species == "rat":
             self._ucscDb = "rn3"
         elif self.dataset.group.species == "mouse":
@@ -212,7 +197,6 @@ class MarkerRegression(object):
         else:
             self._ucscDb = ""
 
-
         #####################################
         # Options
         #####################################
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3c2cca94..8ff359a7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -57,7 +57,6 @@ from utility import temp_data
 from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
 from utility.helper_functions import get_species_groups
 
-from base import webqtlFormData
 from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.benchmark import Bench
 
@@ -163,62 +162,37 @@ def css(filename):
 def twitter(filename):
     return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename)
 
-#@app.route("/data_sharing")
-#def data_sharing_page():
-#    logger.info("In data_sharing")
-#    fd = webqtlFormData.webqtlFormData(request.args)
-#    logger.info("1Have fd")
-#    sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-#    info, htmlfilelist = sharingInfoObject.getBody(infoupdate="")
-#    logger.info("type(htmlfilelist):", type(htmlfilelist))
-#    htmlfilelist = htmlfilelist.encode("utf-8")
-#    #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None)
-#    logger.info("1 Made it to rendering")
-#    return render_template("data_sharing.html",
-#                            info=info,
-#                            htmlfilelist=htmlfilelist)
-
-
 @app.route("/search", methods=('GET',))
 def search_page():
     logger.info("in search_page")
     logger.info(request.url)
-    if 'info_database' in request.args:
-        logger.info("Going to sharing_info_page")
-        template_vars = sharing_info_page()
-        if template_vars.redirect_url:
-            logger.info("Going to redirect")
-            return flask.redirect(template_vars.redirect_url)
-        else:
-            return render_template("data_sharing.html", **template_vars.__dict__)
+    result = None
+    if USE_REDIS:
+        with Bench("Trying Redis cache"):
+            key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
+            logger.debug("key is:", pf(key))
+            result = Redis.get(key)
+            if result:
+                logger.info("Redis cache hit on search results!")
+                result = pickle.loads(result)
     else:
-        result = None
-        if USE_REDIS:
-            with Bench("Trying Redis cache"):
-                key = "search_results:v1:" + json.dumps(request.args, sort_keys=True)
-                logger.debug("key is:", pf(key))
-                result = Redis.get(key)
-                if result:
-                    logger.info("Redis cache hit on search results!")
-                    result = pickle.loads(result)
-        else:
-            logger.info("Skipping Redis cache (USE_REDIS=False)")
+        logger.info("Skipping Redis cache (USE_REDIS=False)")
 
-        logger.info("request.args is", request.args)
-        the_search = search_results.SearchResultPage(request.args)
-        result = the_search.__dict__
-        valid_search = result['search_term_exists']
+    logger.info("request.args is", request.args)
+    the_search = search_results.SearchResultPage(request.args)
+    result = the_search.__dict__
+    valid_search = result['search_term_exists']
 
-        logger.debugf("result", result)
+    logger.debugf("result", result)
 
-        if USE_REDIS and valid_search:
-            Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
-            Redis.expire(key, 60*60)
+    if USE_REDIS and valid_search:
+        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+        Redis.expire(key, 60*60)
 
-        if valid_search:
-            return render_template("search_result_page.html", **result)
-        else:
-            return render_template("search_error.html")
+    if valid_search:
+        return render_template("search_result_page.html", **result)
+    else:
+        return render_template("search_error.html")
 
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
@@ -741,7 +715,6 @@ def network_graph_page():
 def corr_compute_page():
     logger.info("In corr_compute, request.form is:", pf(request.form))
     logger.info(request.url)
-    #fd = webqtlFormData.webqtlFormData(request.form)
     template_vars = show_corr_results.CorrelationResults(request.form)
     return render_template("correlation_page.html", **template_vars.__dict__)
 
@@ -777,15 +750,6 @@ def submit_bnw():
     template_vars = get_bnw_input(request.form)
     return render_template("empty_collection.html", **{'tool':'Correlation Matrix'})
 
-# Todo: Can we simplify this? -Sam
-def sharing_info_page():
-    """Info page displayed when the user clicks the "Info" button next to the dataset selection"""
-    logger.info("In sharing_info_page")
-    logger.info(request.url)
-    fd = webqtlFormData.webqtlFormData(request.args)
-    template_vars = SharingInfoPage.SharingInfoPage(fd)
-    return template_vars
-
 # Take this out or secure it before putting into production
 @app.route("/get_temp_data")
 def get_temp_data():
-- 
cgit v1.2.3


From d8cec0ef94b7683f42946ce182a937484ad1034a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 10 Apr 2018 21:30:33 +0000
Subject: Most code in webqtlUtil.py has been removed. There is so little left
 that the remaining could should be migrated to the files that use them at
 some point.

Some of this code was in the correlation code but not being used, so it wss removed from there as well.
---
 wqflask/utility/webqtlUtil.py                      | 700 +--------------------
 .../wqflask/correlation/correlation_functions.py   |  56 --
 wqflask/wqflask/correlation/show_corr_results.py   |  30 -
 3 files changed, 1 insertion(+), 785 deletions(-)

diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 94dd7cbf..83fa90b7 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -65,41 +65,6 @@ ParInfo ={
 #      Accessory Functions
 #########################################
 
-def exportData(hddn, tdata, NP = None):
-    for key in tdata.keys():
-        _val, _var, _N = tdata[key].val, tdata[key].var, tdata[key].N
-        if _val != None:
-            hddn[key] = _val
-            if _var != None:
-                hddn['V'+key] = _var
-            if NP and _N != None:
-                hddn['N'+key] = _N
-
-def genShortStrainName(RISet='', input_strainName=''):
-    #aliasStrainDict = {'C57BL/6J':'B6','DBA/2J':'D2'}
-    strainName = input_strainName
-    if RISet != 'AXBXA':
-        if RISet == 'BXD300':
-            this_RISet = 'BXD'
-        elif RISet == 'BDF2-2005':
-            this_RISet = 'CASE05_'
-        else:
-            this_RISet = RISet
-        strainName = string.replace(strainName,this_RISet,'')
-        strainName = string.replace(strainName,'CASE','')
-        try:
-            strainName = "%02d" % int(strainName)
-        except:
-            pass
-    else:
-        strainName = string.replace(strainName,'AXB','A')
-        strainName = string.replace(strainName,'BXA','B')
-        try:
-            strainName = strainName[0] + "%02d" % int(strainName[1:])
-        except:
-            pass
-    return strainName
-
 def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
     from random import choice
     _str = prefix[:]
@@ -107,63 +72,6 @@ def genRandStr(prefix = "", length=8, chars=string.letters+string.digits):
         _str += choice(chars)
     return _str
 
-def StringAsFloat(str):
-    'Converts string to float but catches any exception and returns None'
-    try:
-        return float(str)
-    except:
-        return None
-
-def IntAsFloat(str):
-    'Converts string to Int but catches any exception and returns None'
-    try:
-        return int(str)
-    except:
-        return None
-
-def FloatAsFloat(flt):
-    'Converts float to string but catches any exception and returns None'
-    try:
-        return float("%2.3f" % flt)
-    except:
-        return None
-
-def RemoveZero(flt):
-    'Converts string to float but catches any exception and returns None'
-    try:
-        if abs(flt) < 1e-6:
-            return None
-        else:
-            return flt
-    except:
-        return None
-
-
-def SciFloat(d):
-    'Converts string to float but catches any exception and returns None'
-
-    try:
-        if abs(d) <= 1.0e-4:
-            return "%1.2e" % d
-        else:
-            return "%1.5f" % d
-    except:
-        return None
-
-###To be removed
-def FloatList2String(lst):
-    'Converts float list to string but catches any exception and returns None'
-    tt=''
-    try:
-        for item in lst:
-            if item == None:
-                tt += 'X '
-            else:
-                tt += '%f ' % item
-        return tt
-    except:
-        return ""
-
 def ListNotNull(lst):
     '''Obsolete - Use built in function any (or all or whatever)
 
@@ -176,427 +84,6 @@ def ListNotNull(lst):
             return 1
     return None
 
-###To be removed
-def FileDataProcess(str):
-    'Remove the description text from the input file if theres any'
-    i=0
-    while i<len(str):
-        if str[i]<'\x7f' and str[i]>'\x20':
-            break
-        else:
-            i+=1
-    str=str[i:]
-    str=string.join(string.split(str,'\000'),'')
-    i=string.find(str,"*****")
-    if i>-1:
-        return str[i+5:]
-    else:
-        return str
-
-def rank(a,lst,offset=0):
-    """Calculate the integer rank of a number in an array, can be used to calculate p-value"""
-    n = len(lst)
-    if n == 2:
-        if a <lst[0]:
-            return offset
-        elif a > lst[1]:
-            return offset + 2
-        else:
-            return offset +1
-    elif n == 1:
-        if a <lst[0]:
-            return offset
-        else:
-            return offset +1
-    elif n== 0:
-        return offset
-    else:
-        mid = n/2
-        if a < lst[mid]:
-            return rank(a,lst[:mid-1],offset)
-        else:
-            return rank(a,lst[mid:],offset+mid)
-
-def cmpScanResult(A,B):
-    try:
-        if A.LRS > B.LRS:
-            return 1
-        elif A.LRS == B.LRS:
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-
-def cmpScanResult2(A,B):
-    try:
-        if A.LRS < B.LRS:
-            return 1
-        elif A.LRS == B.LRS:
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpOrder(A,B):
-    try:
-        if A[1] < B[1]:
-            return -1
-        elif A[1] == B[1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-def cmpOrder2(A,B):
-    try:
-        if A[-1] < B[-1]:
-            return -1
-        elif A[-1] == B[-1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-
-
-
-def calRank(xVals, yVals, N): ###  Zach Sloan, February 4 2010
-    """
-    Returns a ranked set of X and Y values. These are used when generating
-    a Spearman scatterplot. Bear in mind that this sets values equal to each
-    other as the same rank.
-    """
-    XX = []
-    YY = []
-    X = [0]*len(xVals)
-    Y = [0]*len(yVals)
-    j = 0
-
-    for i in range(len(xVals)):
-
-        if xVals[i] != None and yVals[i] != None:
-            XX.append((j, xVals[i]))
-            YY.append((j, yVals[i]))
-            j = j + 1
-
-    NN = len(XX)
-
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-
-    j = 1
-    rank = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    return (X,Y)
-
-def calCorrelationRank(xVals,yVals,N):
-    """
-    Calculated Spearman Ranked Correlation. The algorithm works
-    by setting all tied ranks to the average of those ranks (for
-    example, if ranks 5-10 all have the same value, each will be set
-    to rank 7.5).
-    """
-
-    XX = []
-    YY = []
-    j = 0
-
-    for i in range(len(xVals)):
-        if (xVals[i]!= None and yVals[i]!= None) and (xVals[i] != "None" and yVals[i] != "None"):
-            XX.append((j,xVals[i]))
-            YY.append((j,yVals[i]))
-            j = j+1
-
-    NN = len(XX)
-    if NN <6:
-        return (0.0,NN)
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-    X = [0]*NN
-    Y = [0]*NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sx = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            t = jt-j
-            sx = sx + (t*t*t-t)
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sy = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            t = jt - j
-            sy = sy + (t*t*t-t)
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    D = 0.0
-
-    for i in range(NN):
-        D += (X[i]-Y[i])*(X[i]-Y[i])
-
-    fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
-    return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
-def calCorrelationRankText(dbdata,userdata,N): ### dcrowell = David Crowell, July 2008
-    """Calculates correlation ranks with data formatted from the text file.
-    dbdata, userdata are lists of strings.  N is an int.  Returns a float.
-    Used by correlationPage"""
-    XX = []
-    YY = []
-    j = 0
-    for i in range(N):
-        if (dbdata[i]!= None and userdata[i]!=None) and (dbdata[i]!= 'None' and userdata[i]!='None'):
-            XX.append((j,float(dbdata[i])))
-            YY.append((j,float(userdata[i])))
-            j += 1
-    NN = len(XX)
-    if NN <6:
-        return (0.0,NN)
-    XX.sort(cmpOrder2)
-    YY.sort(cmpOrder2)
-    X = [0]*NN
-    Y = [0]*NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sx = 0.0
-
-    while j < NN:
-
-        if XX[j][1] != XX[j-1][1]:
-            X[XX[j-1][0]] = j
-            j = j+1
-
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (XX[jt][1] != XX[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                X[XX[ji][0]] = rank
-            t = jt-j
-            sx = sx + (t*t*t-t)
-            if (jt == NN-1):
-                if (XX[jt][1] == XX[j-1][1]):
-                    X[XX[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if X[XX[NN-1][0]] == 0:
-            X[XX[NN-1][0]] = NN
-
-    j = 1
-    rank = 0.0
-    t = 0.0
-    sy = 0.0
-
-    while j < NN:
-
-        if YY[j][1] != YY[j-1][1]:
-            Y[YY[j-1][0]] = j
-            j = j+1
-        else:
-            jt = j+1
-            ji = j
-            for jt in range(j+1, NN):
-                if (YY[jt][1] != YY[j-1][1]):
-                    break
-            rank = 0.5*(j+jt)
-            for ji in range(j-1, jt):
-                Y[YY[ji][0]] = rank
-            t = jt - j
-            sy = sy + (t*t*t-t)
-            if (jt == NN-1):
-                if (YY[jt][1] == YY[j-1][1]):
-                    Y[YY[NN-1][0]] = rank
-            j = jt+1
-
-    if j == NN:
-        if Y[YY[NN-1][0]] == 0:
-            Y[YY[NN-1][0]] = NN
-
-    D = 0.0
-
-    for i in range(NN):
-        D += (X[i]-Y[i])*(X[i]-Y[i])
-
-    fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
-    return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-
-
-def calCorrelation(dbdata,userdata,N):
-    X = []
-    Y = []
-    for i in range(N):
-        if dbdata[i]!= None and userdata[i]!= None:
-            X.append(dbdata[i])
-            Y.append(userdata[i])
-    NN = len(X)
-    if NN <6:
-        return (0.0,NN)
-    sx = reduce(lambda x,y:x+y,X,0.0)
-    sy = reduce(lambda x,y:x+y,Y,0.0)
-    meanx = sx/NN
-    meany = sy/NN
-    xyd = 0.0
-    sxd = 0.0
-    syd = 0.0
-    for i in range(NN):
-        xyd += (X[i] - meanx)*(Y[i]-meany)
-        sxd += (X[i] - meanx)*(X[i] - meanx)
-        syd += (Y[i] - meany)*(Y[i] - meany)
-    try:
-        corr = xyd/(sqrt(sxd)*sqrt(syd))
-    except:
-        corr = 0
-    return (corr,NN)
-
-def calCorrelationText(dbdata,userdata,N): ### dcrowell July 2008
-    """Calculates correlation coefficients with values formatted from text files. dbdata, userdata are lists of strings.  N is an int.  Returns a float
-    Used by correlationPage"""
-    X = []
-    Y = []
-    for i in range(N):
-        #if (dbdata[i]!= None and userdata[i]!= None) and (dbdata[i]!= 'None' and userdata[i]!= 'None'):
-        #               X.append(float(dbdata[i]))
-        #               Y.append(float(userdata[i]))
-        if dbdata[i] == None or dbdata[i] == 'None' or userdata[i] == None or userdata[i] == 'None':
-            continue
-        else:
-            X.append(float(dbdata[i]))
-            Y.append(float(userdata[i]))
-    NN = len(X)
-    if NN <6:
-        return (0.0,NN)
-    sx = sum(X)
-    sy = sum(Y)
-    meanx = sx/float(NN)
-    meany = sy/float(NN)
-    xyd = 0.0
-    sxd = 0.0
-    syd = 0.0
-    for i in range(NN):
-        x1 = X[i]-meanx
-        y1 = Y[i]-meany
-        xyd += x1*y1
-        sxd += x1**2
-        syd += y1**2
-    try:
-        corr = xyd/(sqrt(sxd)*sqrt(syd))
-    except:
-        corr = 0
-    return (corr,NN)
-
-
 def readLineCSV(line): ### dcrowell July 2008
     """Parses a CSV string of text and returns a list containing each element as a string.
     Used by correlationPage"""
@@ -605,45 +92,6 @@ def readLineCSV(line): ### dcrowell July 2008
     returnList[0]=returnList[0][1:]
     return returnList
 
-
-def cmpCorr(A,B):
-    try:
-        if abs(A[1]) < abs(B[1]):
-            return 1
-        elif abs(A[1]) == abs(B[1]):
-            return 0
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpLitCorr(A,B):
-    try:
-        if abs(A[3]) < abs(B[3]): return 1
-        elif abs(A[3]) == abs(B[3]):
-            if abs(A[1]) < abs(B[1]): return 1
-            elif abs(A[1]) == abs(B[1]): return 0
-            else: return -1
-        else: return -1
-    except:
-        return 0
-
-def cmpPValue(A,B):
-    try:
-        if A.corrPValue < B.corrPValue:
-            return -1
-        elif A.corrPValue == B.corrPValue:
-            if abs(A.corr) > abs(B.corr):
-                return -1
-            elif abs(A.corr) < abs(B.corr):
-                return 1
-            else:
-                return 0
-        else:
-            return 1
-    except:
-        return 0
-
 def cmpEigenValue(A,B):
     try:
         if A[0] > B[0]:
@@ -655,80 +103,6 @@ def cmpEigenValue(A,B):
     except:
         return 0
 
-
-def cmpLRSFull(A,B):
-    try:
-        if A[0] < B[0]:
-            return -1
-        elif A[0] == B[0]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-def cmpLRSInteract(A,B):
-    try:
-        if A[1] < B[1]:
-            return -1
-        elif A[1] == B[1]:
-            return 0
-        else:
-            return 1
-    except:
-        return 0
-
-
-def cmpPos(A,B):
-    try:
-        try:
-            AChr = int(A.chr)
-        except:
-            AChr = 20
-        try:
-            BChr = int(B.chr)
-        except:
-            BChr = 20
-        if AChr > BChr:
-            return 1
-        elif AChr == BChr:
-            if A.mb > B.mb:
-                return 1
-            if A.mb == B.mb:
-                return 0
-            else:
-                return -1
-        else:
-            return -1
-    except:
-        return 0
-
-def cmpGenoPos(A,B):
-    try:
-        A1 = A.chr
-        B1 = B.chr
-        try:
-            A1 = int(A1)
-        except:
-            A1 = 25
-        try:
-            B1 = int(B1)
-        except:
-            B1 = 25
-        if A1 > B1:
-            return 1
-        elif A1 == B1:
-            if A.mb > B.mb:
-                return 1
-            if A.mb == B.mb:
-                return 0
-            else:
-                return -1
-        else:
-            return -1
-    except:
-        return 0
-
 def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
     access_to_confidential_phenotype_trait = 0
     if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
@@ -737,76 +111,4 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users)
         AuthorizedUsersList=map(string.strip, string.split(authorized_users, ','))
         if AuthorizedUsersList.__contains__(userName):
             access_to_confidential_phenotype_trait = 1
-    return access_to_confidential_phenotype_trait
-
-
-class VisualizeException(Exception):
-    def __init__(self, message):
-        self.message = message
-    def __str__(self):
-        return self.message
-
-# safeConvert : (string -> A) -> A -> A
-# to convert a string to type A, using the supplied default value
-# if the given conversion function doesn't work
-def safeConvert(f, value, default):
-    try:
-        return f(value)
-    except:
-        return default
-
-# safeFloat : string -> float -> float
-# to convert a string to a float safely
-def safeFloat(value, default):
-    return safeConvert(float, value, default)
-
-# safeInt: string -> int -> int
-# to convert a string to an int safely
-def safeInt(value, default):
-    return safeConvert(int, value, default)
-
-# safeString : string -> (arrayof string) -> string -> string
-# if a string is not in a list of strings to pick a default value
-# for that string
-def safeString(value, validChoices, default):
-    if value in validChoices:
-        return value
-    else:
-        return default
-
-# yesNoToInt: string -> int
-# map "yes" -> 1 and "no" -> 0
-def yesNoToInt(value):
-    if value == "yes":
-        return 1
-    elif value == "no":
-        return 0
-    else:
-        return None
-
-# IntToYesNo: int -> string
-# map 1 -> "yes" and 0 -> "no"
-def intToYesNo(value):
-    if value == 1:
-        return "yes"
-    elif value == 0:
-        return "no"
-    else:
-        return None
-
-def formatField(name):
-    name = name.replace("_", " ")
-    name = name.title()
-    #name = name.replace("Mb Mm6", "Mb");
-    return name.replace("Id", "ID")
-
-def natsort_key(string):
-    r = []
-    for c in string:
-        try:
-            c = int(c)
-            try: r[-1] = r[-1] * 10 + c
-            except: r.append(c)
-        except:
-            r.append(c)
-    return r
\ No newline at end of file
+    return access_to_confidential_phenotype_trait
\ No newline at end of file
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index 80a0818c..1ee9b558 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -491,62 +491,6 @@ pcor.rec <- function(x,y,z,method="p",na.rm=T){
     return allcorrelations
 
 
-
-#XZ, April 30, 2010: The input primaryTrait and targetTrait are instance of webqtlTrait
-#XZ: The primaryTrait and targetTrait should have executed retrieveData function
-def calZeroOrderCorr(primaryTrait, targetTrait, method='pearson'):
-
-    #primaryTrait.retrieveData()
-
-    #there is no None value in primary_val
-    primary_strain, primary_val, primary_var = primaryTrait.exportInformative()
-
-    #targetTrait.retrieveData()
-
-    #there might be None value in target_val
-    target_val = targetTrait.exportData(primary_strain, type="val")
-
-    R_primary = rpy2.robjects.FloatVector(range(len(primary_val)))
-    for i in range(len(primary_val)):
-        R_primary[i] = primary_val[i]
-
-    N = len(target_val)
-
-    if None in target_val:
-        goodIndex = []
-        for i in range(len(target_val)):
-            if target_val[i] != None:
-                goodIndex.append(i)
-
-        N = len(goodIndex)
-
-        R_primary = rpy2.robjects.FloatVector(range(len(goodIndex)))
-        for i in range(len(goodIndex)):
-            R_primary[i] = primary_val[goodIndex[i]]
-
-        R_target = rpy2.robjects.FloatVector(range(len(goodIndex)))
-        for i in range(len(goodIndex)):
-            R_target[i] = target_val[goodIndex[i]]
-
-    else:
-        R_target = rpy2.robjects.FloatVector(range(len(target_val)))
-        for i in range(len(target_val)):
-            R_target[i] = target_val[i]
-
-    R_corr_test = rpy2.robjects.r['cor.test']
-
-    if method == 'spearman':
-        R_result = R_corr_test(R_primary, R_target, method='spearman')
-    else:
-        R_result = R_corr_test(R_primary, R_target)
-
-    corr_result = []
-    corr_result.append( R_result[3][0] )
-    corr_result.append( N )
-    corr_result.append( R_result[2][0] )
-
-    return corr_result
-
 #####################################################################################
 #Input: primaryValue(list): one list of expression values of one probeSet,
 #       targetValue(list): one list of expression values of one probeSet,
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index abf9fc89..85a8c0ef 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -555,21 +555,6 @@ class CorrelationResults(object):
 
         self.record_count = len(traits) #ZS: This isn't a good way to get this value, so I need to change it later
 
-        #XZ, 3/31/2010: Theoretically, we should create one function 'comTissueCorr'
-        #to compare each trait by their tissue corr p values.
-        #But because the tissue corr p values are generated by permutation test,
-        #the top ones always have p value 0. So comparing p values actually does nothing.
-        #In addition, for the tissue data in our database, the N is always the same.
-        #So it's safe to compare with tissue corr statistic value.
-        #That's the same as literature corr.
-        #if self.method in [METHOD_LIT, METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] and self.gene_id:
-        #    traits.sort(webqtlUtil.cmpLitCorr)
-        #else:
-        #if self.method in TISSUE_METHODS:
-        #    sort(traits, key=lambda A: math.fabs(A.tissue_corr))
-        #elif self.method == METHOD_LIT:
-        #    traits.sort(traits, key=lambda A: math.fabs(A.lit_corr))
-        #else:
         traits = sortTraitCorrelations(traits, self.method)
 
         # Strip to the top N correlations
@@ -1069,21 +1054,6 @@ class CorrelationResults(object):
 
         return (symbolCorrDict, symbolPvalueDict)
 
-
-    def correlate(self):
-        self.correlation_data = collections.defaultdict(list)
-        for trait, values in self.target_dataset.trait_data.iteritems():
-            values_1 = []
-            values_2 = []
-            for index,sample in enumerate(self.target_dataset.samplelist):
-                target_value = values[index]
-                if sample in self.sample_data.keys():
-                    this_value = self.sample_data[sample]
-                    values_1.append(this_value)
-                    values_2.append(target_value)
-            correlation = calCorrelation(values_1, values_2)
-            self.correlation_data[trait] = correlation
-
     def getFileName(self, target_db_name):  ### dcrowell  August 2008
         """Returns the name of the reference database file with which correlations are calculated.
         Takes argument cursor which is a cursor object of any instance of a subclass of templatePage
-- 
cgit v1.2.3


From 9750e63d64849d7fa9e1e681f56b73cae96905df Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 11 Apr 2018 20:39:24 +0000
Subject: Added tissue correlation p value to correlation page results, since
 it was missing before

Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
---
 wqflask/base/mrna_assay_tissue_data.py             |  65 +-
 wqflask/wqflask/collect.py                         |   8 -
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  16 +-
 .../wqflask/correlation/correlation_functions.py   | 786 +------------------
 wqflask/wqflask/correlation/show_corr_results.py   | 844 ---------------------
 .../wqflask/correlation_matrix/show_corr_matrix.py |   1 -
 wqflask/wqflask/ctl/ctl_analysis.py                |  63 +-
 wqflask/wqflask/templates/correlation_page.html    |   9 +-
 8 files changed, 33 insertions(+), 1759 deletions(-)

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 53f7c16a..6fec5dcd 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -21,17 +21,8 @@ class MrnaAssayTissueData(object):
         if self.gene_symbols == None:
             self.gene_symbols = []
 
-        #print("self.gene_symbols:", self.gene_symbols)
-
         self.data = collections.defaultdict(Bunch)
 
-        #self.gene_id_dict ={}
-        #self.data_id_dict = {}
-        #self.chr_dict = {}
-        #self.mb_dict = {}
-        #self.desc_dict = {}
-        #self.probe_target_desc_dict = {}
-
         query =  '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
                         from (
                         select Symbol, max(Mean) as maxmean
@@ -51,7 +42,6 @@ class MrnaAssayTissueData(object):
             in_clause = db_tools.create_in_clause(gene_symbols)
 
             #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
-
             query += ''' Symbol in {} group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
                 and t.Mean = x.maxmean;
@@ -66,9 +56,7 @@ class MrnaAssayTissueData(object):
 
         for result in results:
             symbol = result[0]
-            #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]:
             if symbol.lower() in lower_symbols:
-                #gene_symbols.append(symbol)
                 symbol = symbol.lower()
 
                 self.data[symbol].gene_id = result.GeneId
@@ -78,8 +66,6 @@ class MrnaAssayTissueData(object):
                 self.data[symbol].description = result.description
                 self.data[symbol].probe_target_description = result.Probe_Target_Description
 
-        print("self.data: ", pf(self.data))
-
     ###########################################################################
     #Input: cursor, symbolList (list), dataIdDict(Dict)
     #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
@@ -106,53 +92,4 @@ class MrnaAssayTissueData(object):
                 else:
                     symbol_values_dict[result.Symbol.lower()].append(result.value)
 
-        #for symbol in self.data:
-        #    data_id = self.data[symbol].data_id
-        #    symbol_values_dict[symbol] = self.get_tissue_values(data_id)
-
-
-        return symbol_values_dict
-
-
-    #def get_tissue_values(self, data_id):
-    #    """Gets the tissue values for a particular gene"""
-    #
-    #    tissue_values=[]
-    #
-    #    query = """SELECT value, id
-    #               FROM TissueProbeSetData
-    #               WHERE Id IN {}""".format(db_tools.create_in_clause(data_id))
-    #
-    #    #try :
-    #    results = g.db.execute(query).fetchall()
-    #    for result in results:
-    #        tissue_values.append(result.value)
-    #    #symbol_values_dict[symbol] = value_list
-    #    #except:
-    #    #    symbol_values_pairs[symbol] = None
-    #
-    #    return tissue_values
-
-########################################################################################################
-#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
-#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
-#        key is symbol, value is one list of expression values of one probeSet.
-#function: wrapper function for getSymbolValuePairDict function
-#          build gene symbol list if necessary, cut it into small lists if necessary,
-#          then call getSymbolValuePairDict function and merge the results.
-########################################################################################################
-
-#def get_trait_symbol_and_tissue_values(symbol_list=None):
-#    tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
-#
-#    #symbolList,
-#    #geneIdDict,
-#    #dataIdDict,
-#    #ChrDict,
-#    #MbDict,
-#    #descDict,
-#    #pTargetDescDict = getTissueProbeSetXRefInfo(
-#    #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-#
-#    if len(tissue_data.gene_symbols):
-#        return get_symbol_values_pairs(tissue_data)
+        return symbol_values_dict
\ No newline at end of file
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index ffc698de..04035e96 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -40,13 +40,6 @@ import logging
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
-def get_collection():
-    if g.user_session.logged_in:
-        return UserCollection()
-    else:
-        return AnonCollection()
-    #else:
-    #    CauseError
 
 class AnonCollection(object):
     """User is not logged in"""
@@ -282,7 +275,6 @@ def create_new(collection_name):
         db_session.commit()
         return redirect(url_for('view_collection', uc_id=uc.id))
     else:
-        current_collections = user_manager.AnonUser().get_collections()
         ac = AnonCollection(collection_name)
         ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
         ac.add_traits(params)
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index a08cd759..94711c67 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -19,37 +19,31 @@ class CorrScatterPlot(object):
             width = int(params['width'])
         except:
             width = 800
-        self.width = width
 
         try:
             height = int(params['height'])
         except:
             height = 600
-        self.height = height
 
         try:
             circle_color = params['circle_color']
         except:
             circle_color = '#3D85C6'
-        self.circle_color = circle_color
 
         try:
             circle_radius = int(params['circle_radius'])
         except:
             circle_radius = 5
-        self.circle_radius = circle_radius
 
         try:
             line_color = params['line_color']
         except:
             line_color = '#FF0000'
-        self.line_color = line_color
 
         try:
             line_width = int(params['line_width'])
         except:
             line_width = 1
-        self.line_width = line_width
 
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
@@ -66,14 +60,14 @@ class CorrScatterPlot(object):
 
         x = np.array(vals_1)
         y = np.array(vals_2)
-        slope, intercept, r_value, p_value, std_err = stats.linregress(x, y)
+        slope, intercept, r_value, p_value, _std_err = stats.linregress(x, y)
         
         rx = stats.rankdata(x)
         ry = stats.rankdata(y)        
         self.rdata = []
         self.rdata.append(rx.tolist())
         self.rdata.append(ry.tolist())        
-        srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry)
+        srslope, srintercept, srr_value, srp_value, _srstd_err = stats.linregress(rx, ry)
 
         self.js_data = dict(
             data = self.data,
@@ -86,17 +80,17 @@ class CorrScatterPlot(object):
             num_overlap = num_overlap,
             vals_1 = vals_1,
             vals_2 = vals_2,
-            
+
             slope = slope,
             intercept = intercept,
             r_value = r_value,
             p_value = p_value,
-            
+
             srslope = srslope,
             srintercept = srintercept,
             srr_value = srr_value,
             srp_value = srp_value,
-            
+
             width = width,
             height = height,
             circle_color = circle_color,
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index 1ee9b558..06dec795 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -28,468 +28,12 @@ from __future__ import absolute_import, print_function, division
 
 import math
 import rpy2.robjects
-import pp
 import string
 
-from utility import webqtlUtil
 from base.mrna_assay_tissue_data import MrnaAssayTissueData
-from base.trait import GeneralTrait
-from db import webqtlDatabaseFunction
 
 from flask import Flask, g
 
-#XZ: The input 'controls' is String. It contains the full name of control traits.
-#XZ: The input variable 'strainlst' is List. It contains the strain names of primary trait.
-#XZ: The returned tcstrains is the list of list [[],[]...]. So are tcvals and tcvars. The last returned parameter is list of numbers.
-#XZ, 03/29/2010: For each returned control trait, there is no None value in it.
-def controlStrains(controls, strainlst):
-
-    controls = controls.split(',')
-
-    cvals = {}
-    for oneTraitName in controls:
-        oneTrait = webqtlTrait(fullname=oneTraitName, cursor=webqtlDatabaseFunction.getCursor() )
-        oneTrait.retrieveData()
-        cvals[oneTraitName] = oneTrait.data
-
-    tcstrains = []
-    tcvals = []
-    tcvars = []
-
-    for oneTraitName in controls:
-        strains = []
-        vals = []
-        vars = []
-
-        for _strain in strainlst:
-            if cvals[oneTraitName].has_key(_strain):
-                _val = cvals[oneTraitName][_strain].val
-                if _val != None:
-                    strains.append(_strain)
-                    vals.append(_val)
-                    vars.append(None)
-
-        tcstrains.append(strains)
-        tcvals.append(vals)
-        tcvars.append(vars)
-
-    return tcstrains, tcvals, tcvars, [len(x) for x in tcstrains]
-
-
-
-#XZ, 03/29/2010: After execution of functon "controlStrains" and "fixStrains", primary trait and control traits have the same strains and in the same order. There is no 'None' value in them.
-def fixStrains(_strains,_controlstrains,_vals,_controlvals,_vars,_controlvars):
-    """Corrects strains, vals, and vars so that all contrain only those strains common
-    to the reference trait and all control traits."""
-
-    def dictify(strains,vals,vars):
-        subdict = {}
-        for i in xrange(len(strains)):
-            subdict[strains[i]] = (vals[i],vars[i])
-        return subdict
-
-    #XZ: The 'dicts' is a list of dictionary. The first element is the dictionary of reference trait. The rest elements are for control traits.
-    dicts = []
-    dicts.append(dictify(_strains,_vals,_vars))
-
-    nCstrains = len(_controlstrains)
-    for i in xrange(nCstrains):
-        dicts.append(dictify(_controlstrains[i],_controlvals[i],_controlvars[i]))
-
-    _newstrains = []
-    _vals = []
-    _vars = []
-    _controlvals = [[] for x in xrange(nCstrains)]
-    _controlvars = [[] for x in xrange(nCstrains)]
-
-    for strain in _strains:
-        inall = True
-        for d in dicts:
-            if strain not in d:
-                inall = False
-                break
-        if inall:
-            _newstrains.append(strain)
-            _vals.append(dicts[0][strain][0])
-            _vars.append(dicts[0][strain][1])
-            for i in xrange(nCstrains):
-                _controlvals[i].append(dicts[i+1][strain][0])
-                _controlvars[i].append(dicts[i+1][strain][1])
-
-    return _newstrains,  _vals, _controlvals, _vars, _controlvars
-
-
-#XZ, 6/15/2010: If there is no identical control traits, the returned list is empty.
-#else, the returned list has two elements of control trait name.
-def findIdenticalControlTraits ( controlVals, controlNames ):
-    nameOfIdenticalTraits = []
-
-    controlTraitNumber = len(controlVals)
-
-    if controlTraitNumber > 1:
-
-        #XZ: reset the precision of values and convert to string type
-        for oneTraitVal in controlVals:
-            for oneStrainVal in oneTraitVal:
-                oneStrainVal = '%.3f' % oneStrainVal
-
-        for i, oneTraitVal in enumerate( controlVals ):
-            for j in range(i+1, controlTraitNumber):
-                if oneTraitVal == controlVals[j]:
-                    nameOfIdenticalTraits.append(controlNames[i])
-                    nameOfIdenticalTraits.append(controlNames[j])
-
-    return nameOfIdenticalTraits
-
-#XZ, 6/15/2010: If there is no identical control traits, the returned list is empty.
-#else, the returned list has two elements of control trait name.
-#primaryVal is of list type. It contains value of primary trait.
-#primaryName is of string type.
-#controlVals is of list type. Each element is list too. Each element contain value of one control trait.
-#controlNames is of list type.
-def findIdenticalTraits (primaryVal, primaryName, controlVals, controlNames ):
-    nameOfIdenticalTraits = []
-
-    #XZ: reset the precision of values and convert to string type
-    for oneStrainVal in primaryVal:
-        oneStrainVal = '%.3f' % oneStrainVal
-
-    for oneTraitVal in controlVals:
-        for oneStrainVal in oneTraitVal:
-            oneStrainVal = '%.3f' % oneStrainVal
-
-    controlTraitNumber = len(controlVals)
-
-    if controlTraitNumber > 1:
-        for i, oneTraitVal in enumerate( controlVals ):
-            for j in range(i+1, controlTraitNumber):
-                if oneTraitVal == controlVals[j]:
-                    nameOfIdenticalTraits.append(controlNames[i])
-                    nameOfIdenticalTraits.append(controlNames[j])
-                    break
-
-    if len(nameOfIdenticalTraits) == 0:
-        for i, oneTraitVal in enumerate( controlVals ):
-            if primaryVal == oneTraitVal:
-                nameOfIdenticalTraits.append(primaryName)
-                nameOfIdenticalTraits.append(controlNames[i])
-                break
-
-    return nameOfIdenticalTraits
-
-
-
-#XZ, 03/29/2010: The strains in primaryVal, controlVals, targetVals must be of the same number and in same order.
-#XZ: No value in primaryVal and controlVals could be None.
-
-def determinePartialsByR (primaryVal, controlVals, targetVals, targetNames, method='p'):
-
-    def compute_partial ( primaryVal, controlVals, targetVals, targetNames, method ):
-
-        rpy2.robjects.r("""
-pcor.test <- function(x,y,z,use="mat",method="p",na.rm=T){
-        # The partial correlation coefficient between x and y given z
-        #
-        # pcor.test is free and comes with ABSOLUTELY NO WARRANTY.
-        #
-        # x and y should be vectors
-        #
-        # z can be either a vector or a matrix
-        #
-        # use: There are two methods to calculate the partial correlation coefficient.
-        #        One is by using variance-covariance matrix ("mat") and the other is by using recursive formula ("rec").
-        #        Default is "mat".
-        #
-        # method: There are three ways to calculate the correlation coefficient,
-        #           which are Pearson's ("p"), Spearman's ("s"), and Kendall's ("k") methods.
-        #           The last two methods which are Spearman's and Kendall's coefficient are based on the non-parametric analysis.
-        #           Default is "p".
-        #
-        # na.rm: If na.rm is T, then all the missing samples are deleted from the whole dataset, which is (x,y,z).
-        #        If not, the missing samples will be removed just when the correlation coefficient is calculated.
-        #          However, the number of samples for the p-value is the number of samples after removing
-        #          all the missing samples from the whole dataset.
-        #          Default is "T".
-
-        x <- c(x)
-        y <- c(y)
-        z <- as.data.frame(z)
-
-        if(use == "mat"){
-                p.use <- "Var-Cov matrix"
-                pcor = pcor.mat(x,y,z,method=method,na.rm=na.rm)
-        }else if(use == "rec"){
-                p.use <- "Recursive formula"
-                pcor = pcor.rec(x,y,z,method=method,na.rm=na.rm)
-        }else{
-                stop("use should be either rec or mat!\n")
-        }
-
-        # print the method
-        if(gregexpr("p",method)[[1]][1] == 1){
-                p.method <- "Pearson"
-        }else if(gregexpr("s",method)[[1]][1] == 1){
-                p.method <- "Spearman"
-        }else if(gregexpr("k",method)[[1]][1] == 1){
-                p.method <- "Kendall"
-        }else{
-                stop("method should be pearson or spearman or kendall!\n")
-        }
-
-        # sample number
-        n <- dim(na.omit(data.frame(x,y,z)))[1]
-
-        # given variables' number
-        gn <- dim(z)[2]
-
-        # p-value
-        if(p.method == "Kendall"){
-                statistic <- pcor/sqrt(2*(2*(n-gn)+5)/(9*(n-gn)*(n-1-gn)))
-                p.value <- 2*pnorm(-abs(statistic))
-
-        }else{
-                statistic <- pcor*sqrt((n-2-gn)/(1-pcor^2))
-                p.value <- 2*pnorm(-abs(statistic))
-        }
-
-        data.frame(estimate=pcor,p.value=p.value,statistic=statistic,n=n,gn=gn,Method=p.method,Use=p.use)
-}
-
-# By using var-cov matrix
-pcor.mat <- function(x,y,z,method="p",na.rm=T){
-
-        x <- c(x)
-        y <- c(y)
-        z <- as.data.frame(z)
-
-        if(dim(z)[2] == 0){
-                stop("There should be given data\n")
-        }
-
-        data <- data.frame(x,y,z)
-
-        if(na.rm == T){
-                data = na.omit(data)
-        }
-
-        xdata <- na.omit(data.frame(data[,c(1,2)]))
-        Sxx <- cov(xdata,xdata,m=method)
-
-        xzdata <- na.omit(data)
-        xdata <- data.frame(xzdata[,c(1,2)])
-        zdata <- data.frame(xzdata[,-c(1,2)])
-        Sxz <- cov(xdata,zdata,m=method)
-
-        zdata <- na.omit(data.frame(data[,-c(1,2)]))
-        Szz <- cov(zdata,zdata,m=method)
-
-        # is Szz positive definite?
-        zz.ev <- eigen(Szz)$values
-        if(min(zz.ev)[1]<0){
-                stop("\'Szz\' is not positive definite!\n")
-        }
-
-        # partial correlation
-        Sxx.z <- Sxx - Sxz %*% solve(Szz) %*% t(Sxz)
-
-        rxx.z <- cov2cor(Sxx.z)[1,2]
-
-        rxx.z
-}
-
-# By using recursive formula
-pcor.rec <- function(x,y,z,method="p",na.rm=T){
-        #
-
-        x <- c(x)
-        y <- c(y)
-        z <- as.data.frame(z)
-
-        if(dim(z)[2] == 0){
-                stop("There should be given data\n")
-        }
-
-        data <- data.frame(x,y,z)
-
-        if(na.rm == T){
-                data = na.omit(data)
-        }
-
-        # recursive formula
-        if(dim(z)[2] == 1){
-                tdata <- na.omit(data.frame(data[,1],data[,2]))
-                rxy <- cor(tdata[,1],tdata[,2],m=method)
-
-                tdata <- na.omit(data.frame(data[,1],data[,-c(1,2)]))
-                rxz <- cor(tdata[,1],tdata[,2],m=method)
-
-                tdata <- na.omit(data.frame(data[,2],data[,-c(1,2)]))
-                ryz <- cor(tdata[,1],tdata[,2],m=method)
-
-                rxy.z <- (rxy - rxz*ryz)/( sqrt(1-rxz^2)*sqrt(1-ryz^2) )
-
-                return(rxy.z)
-        }else{
-                x <- c(data[,1])
-                y <- c(data[,2])
-                z0 <- c(data[,3])
-                zc <- as.data.frame(data[,-c(1,2,3)])
-
-                rxy.zc <- pcor.rec(x,y,zc,method=method,na.rm=na.rm)
-                rxz0.zc <- pcor.rec(x,z0,zc,method=method,na.rm=na.rm)
-                ryz0.zc <- pcor.rec(y,z0,zc,method=method,na.rm=na.rm)
-
-                rxy.z <- (rxy.zc - rxz0.zc*ryz0.zc)/( sqrt(1-rxz0.zc^2)*sqrt(1-ryz0.zc^2) )
-                return(rxy.z)
-        }
-}
-""")
-
-        R_pcorr_function = rpy2.robjects.r['pcor.test']
-        R_corr_test = rpy2.robjects.r['cor.test']
-
-        primary = rpy2.robjects.FloatVector(range(len(primaryVal)))
-        for i in range(len(primaryVal)):
-            primary[i] = primaryVal[i]
-
-        control = rpy2.robjects.r.matrix(rpy2.robjects.FloatVector( range(len(controlVals)*len(controlVals[0])) ), ncol=len(controlVals))
-        for i in range(len(controlVals)):
-            for j in range(len(controlVals[0])):
-                control[i*len(controlVals[0]) + j] = controlVals[i][j]
-
-        allcorrelations = []
-
-        for targetIndex, oneTargetVals in enumerate(targetVals):
-
-            this_primary = None
-            this_control = None
-            this_target = None
-
-            if None in oneTargetVals:
-
-                goodIndex = []
-                for i in range(len(oneTargetVals)):
-                    if oneTargetVals[i] != None:
-                        goodIndex.append(i)
-
-                this_primary = rpy2.robjects.FloatVector(range(len(goodIndex)))
-                for i in range(len(goodIndex)):
-                    this_primary[i] = primaryVal[goodIndex[i]]
-
-                this_control = rpy2.robjects.r.matrix(rpy2.robjects.FloatVector( range(len(controlVals)*len(goodIndex)) ), ncol=len(controlVals))
-                for i in range(len(controlVals)):
-                    for j in range(len(goodIndex)):
-                        this_control[i*len(goodIndex) + j] = controlVals[i][goodIndex[j]]
-
-                this_target = rpy2.robjects.FloatVector(range(len(goodIndex)))
-                for i in range(len(goodIndex)):
-                    this_target[i] = oneTargetVals[goodIndex[i]]
-
-            else:
-                this_primary = primary
-                this_control = control
-                this_target = rpy2.robjects.FloatVector(range(len(oneTargetVals)))
-                for i in range(len(oneTargetVals)):
-                    this_target[i] = oneTargetVals[i]
-
-            one_name = targetNames[targetIndex]
-            one_N = len(this_primary)
-
-            #calculate partial correlation
-            one_pc_coefficient = 'NA'
-            one_pc_p = 1
-
-            try:
-                if method == 's':
-                    result = R_pcorr_function(this_primary, this_target, this_control, method='s')
-                else:
-                    result = R_pcorr_function(this_primary, this_target, this_control)
-
-                #XZ: In very few cases, the returned coefficient is nan.
-                #XZ: One way to detect nan is to compare the number to itself. NaN is always != NaN
-                if result[0][0] == result[0][0]:
-                    one_pc_coefficient = result[0][0]
-                    #XZ: when the coefficient value is 1 (primary trait and target trait are the same),
-                    #XZ: occationally, the returned p value is nan instead of 0.
-                    if result[1][0] == result[1][0]:
-                        one_pc_p = result[1][0]
-                    elif abs(one_pc_coefficient - 1) < 0.0000001:
-                        one_pc_p = 0
-            except:
-                pass
-
-            #calculate zero order correlation
-            one_corr_coefficient = 0
-            one_corr_p = 1
-
-            try:
-                if method == 's':
-                    R_result = R_corr_test(this_primary, this_target, method='spearman')
-                else:
-                    R_result = R_corr_test(this_primary, this_target)
-
-                one_corr_coefficient = R_result[3][0]
-                one_corr_p = R_result[2][0]
-            except:
-                pass
-
-            traitinfo = [ one_name, one_N, one_pc_coefficient, one_pc_p, one_corr_coefficient, one_corr_p ]
-
-            allcorrelations.append(traitinfo)
-
-        return allcorrelations
-    #End of function compute_partial
-
-
-    allcorrelations = []
-
-    target_trait_number = len(targetVals)
-
-    if target_trait_number < 1000:
-        allcorrelations = compute_partial ( primaryVal, controlVals, targetVals, targetNames, method )
-    else:
-        step = 1000
-        job_number = math.ceil( float(target_trait_number)/step )
-
-        job_targetVals_lists = []
-        job_targetNames_lists = []
-
-        for job_index in range( int(job_number) ):
-            starti = job_index*step
-            endi = min((job_index+1)*step, target_trait_number)
-
-            one_job_targetVals_list = []
-            one_job_targetNames_list = []
-
-            for i in range( starti, endi ):
-                one_job_targetVals_list.append( targetVals[i] )
-                one_job_targetNames_list.append( targetNames[i] )
-
-            job_targetVals_lists.append( one_job_targetVals_list )
-            job_targetNames_lists.append( one_job_targetNames_list )
-
-        ppservers = ()
-        # Creates jobserver with automatically detected number of workers
-        job_server = pp.Server(ppservers=ppservers)
-
-        jobs = []
-        results = []
-
-        for i, one_job_targetVals_list in enumerate( job_targetVals_lists ):
-            one_job_targetNames_list = job_targetNames_lists[i]
-            #pay attention to modules from outside
-            jobs.append( job_server.submit(func=compute_partial, args=( primaryVal, controlVals, one_job_targetVals_list, one_job_targetNames_list, method), depfuncs=(), modules=("rpy2.robjects",)) )
-
-        for one_job in jobs:
-            one_result = one_job()
-            results.append( one_result )
-
-        for one_result in results:
-            for one_traitinfo in one_result:
-                allcorrelations.append( one_traitinfo )
-
-    return allcorrelations
-
 
 #####################################################################################
 #Input: primaryValue(list): one list of expression values of one probeSet,
@@ -529,170 +73,6 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
     return corr_result
 
 
-
-
-def batchCalTissueCorr(primaryTraitValue=[], SymbolValueDict={}, method='pearson'):
-
-    def cal_tissue_corr(primaryTraitValue, oneSymbolValueDict, method ):
-
-        oneSymbolCorrDict = {}
-        oneSymbolPvalueDict = {}
-
-        R_corr_test = rpy2.robjects.r['cor.test']
-
-        R_primary = rpy2.robjects.FloatVector(range(len(primaryTraitValue)))
-
-        for i in range(len(primaryTraitValue)):
-            R_primary[i] = primaryTraitValue[i]
-
-        for (oneTraitSymbol, oneTraitValue) in oneSymbolValueDict.iteritems():
-            R_target = rpy2.robjects.FloatVector(range(len(oneTraitValue)))
-            for i in range(len(oneTraitValue)):
-                R_target[i] = oneTraitValue[i]
-
-            if method =='spearman':
-                R_result = R_corr_test(R_primary, R_target, method='spearman')
-            else:
-                R_result = R_corr_test(R_primary, R_target)
-
-            oneSymbolCorrDict[oneTraitSymbol] = R_result[3][0]
-            oneSymbolPvalueDict[oneTraitSymbol] = R_result[2][0]
-
-        return(oneSymbolCorrDict, oneSymbolPvalueDict)
-
-
-
-    symbolCorrDict = {}
-    symbolPvalueDict = {}
-
-    items_number = len(SymbolValueDict)
-
-    if items_number <= 1000:
-        symbolCorrDict, symbolPvalueDict = cal_tissue_corr(primaryTraitValue, SymbolValueDict, method)
-    else:
-        items_list = SymbolValueDict.items()
-
-        step = 1000
-        job_number = math.ceil( float(items_number)/step )
-
-        job_oneSymbolValueDict_list = []
-
-        for job_index in range( int(job_number) ):
-            starti = job_index*step
-            endi = min((job_index+1)*step, items_number)
-
-            oneSymbolValueDict = {}
-
-            for i in range( starti, endi ):
-                one_item = items_list[i]
-                one_symbol = one_item[0]
-                one_value = one_item[1]
-                oneSymbolValueDict[one_symbol] = one_value
-
-            job_oneSymbolValueDict_list.append( oneSymbolValueDict )
-
-
-        ppservers = ()
-        # Creates jobserver with automatically detected number of workers
-        job_server = pp.Server(ppservers=ppservers)
-
-        jobs = []
-        results = []
-
-        for i, oneSymbolValueDict in enumerate( job_oneSymbolValueDict_list ):
-
-            #pay attention to modules from outside
-            jobs.append( job_server.submit(func=cal_tissue_corr, args=(primaryTraitValue, oneSymbolValueDict, method), depfuncs=(), modules=("rpy2.robjects",)) )
-
-        for one_job in jobs:
-            one_result = one_job()
-            results.append( one_result )
-
-        for one_result in results:
-            oneSymbolCorrDict, oneSymbolPvalueDict = one_result
-            symbolCorrDict.update( oneSymbolCorrDict )
-            symbolPvalueDict.update( oneSymbolPvalueDict )
-
-    return (symbolCorrDict, symbolPvalueDict)
-
-###########################################################################
-#Input: cursor, GeneNameLst (list), TissueProbeSetFreezeId
-#output: geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict (Dict)
-#function: get multi dicts for short and long label functions, and for getSymbolValuePairDict and
-# getGeneSymbolTissueValueDict to build dict to get CorrPvArray
-#Note: If there are multiple probesets for one gene, select the one with highest mean.
-###########################################################################
-def getTissueProbeSetXRefInfo(GeneNameLst=[],TissueProbeSetFreezeId=0):
-    Symbols =""
-    symbolList =[]
-    geneIdDict ={}
-    dataIdDict = {}
-    ChrDict = {}
-    MbDict = {}
-    descDict = {}
-    pTargetDescDict = {}
-
-    count = len(GeneNameLst)
-
-    # Added by NL 01/06/2011
-    # Note that:inner join is necessary in this query to get distinct record in one symbol group with highest mean value
-    # Duo to the limit size of TissueProbeSetFreezeId table in DB, performance of inner join is acceptable.
-    if count==0:
-        query='''
-                        select t.Symbol,t.GeneId, t.DataId,t.Chr, t.Mb,t.description,t.Probe_Target_Description
-                        from (
-                                select Symbol, max(Mean) as maxmean
-                                from TissueProbeSetXRef
-                                where TissueProbeSetFreezeId=%s and Symbol!='' and Symbol Is Not Null group by Symbol)
-                        as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean;
-                '''%TissueProbeSetFreezeId
-
-    else:
-        for i, item in enumerate(GeneNameLst):
-
-            if i == count-1:
-                Symbols += "'%s'" %item
-            else:
-                Symbols += "'%s'," %item
-
-        Symbols = "("+ Symbols+")"
-        query='''
-                        select t.Symbol,t.GeneId, t.DataId,t.Chr, t.Mb,t.description,t.Probe_Target_Description
-                        from (
-                                select Symbol, max(Mean) as maxmean
-                                from TissueProbeSetXRef
-                                where TissueProbeSetFreezeId=%s and Symbol in %s group by Symbol)
-                        as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean;
-                '''% (TissueProbeSetFreezeId,Symbols)
-
-    try:
-        cursor.execute(query)
-        results =cursor.fetchall()
-        resultCount = len(results)
-        # Key in all dicts is the lower-cased symbol
-        for i, item in enumerate(results):
-            symbol = item[0]
-            symbolList.append(symbol)
-
-            key =symbol.lower()
-            geneIdDict[key]=item[1]
-            dataIdDict[key]=item[2]
-            ChrDict[key]=item[3]
-            MbDict[key]=item[4]
-            descDict[key]=item[5]
-            pTargetDescDict[key]=item[6]
-
-    except:
-        symbolList = None
-        geneIdDict=None
-        dataIdDict=None
-        ChrDict=None
-        MbDict=None
-        descDict=None
-        pTargetDescDict=None
-
-    return symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict
-
 ###########################################################################
 #Input: cursor, symbolList (list), dataIdDict(Dict)
 #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
@@ -701,7 +81,6 @@ def getTissueProbeSetXRefInfo(GeneNameLst=[],TissueProbeSetFreezeId=0):
 #Attention! All keys are lower case!
 ###########################################################################
 def get_symbol_value_pairs(tissue_data):
-
     id_list = [tissue_data[symbol.lower()].data_id for item in tissue_data]
 
     symbol_value_pairs = {}
@@ -719,23 +98,6 @@ def get_symbol_value_pairs(tissue_data):
     except:
         symbol_value_pairs[symbol] = None
 
-    #for symbol in symbol_list:
-    #    if tissue_data.has_key(symbol):
-    #        data_id = tissue_data[symbol].data_id
-    #
-    #        query = """select value, id
-    #                   from TissueProbeSetData
-    #                   where Id={}""".format(escape(data_id))
-    #        try :
-    #            results = g.db.execute(query).fetchall()
-    #            for item in results:
-    #                item = item[0]
-    #                value_list.append(item)
-    #            symbol_value_pairs[symbol] = value_list
-    #            value_list=[]
-    #        except:
-    #            symbol_value_pairs[symbol] = None
-
     return symbol_value_pairs
 
 
@@ -752,150 +114,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
     tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
 
     if len(tissue_data.gene_symbols):
-        return tissue_data.get_symbol_values_pairs()
-
-    #symbolList,
-    #geneIdDict,
-    #dataIdDict,
-    #ChrDict,
-    #MbDict,
-    #descDict,
-    #pTargetDescDict = getTissueProbeSetXRefInfo(
-    #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-
-    #limit_num=1000
-    #count = len(symbol_list)
-    #
-    #symbol_value_pairs = {}
-    #
-    #if count !=0 and count <= limit_num:
-    #    symbol_value_pairs = getSymbolValuePairDict(cursor=cursor,symbolList=symbol_list,dataIdDict=dataIdDict)
-    #
-    #elif count > limit_num:
-    #    n = count/limit_num
-    #    start = 0
-    #    stop = 0
-    #
-    #    for i in range(n):
-    #        stop =limit_num*(i+1)
-    #        gList1 = symbolList[start:stop]
-    #        PairDict1 = getSymbolValuePairDict(cursor=cursor,symbolList=gList1,dataIdDict=dataIdDict)
-    #        start =limit_num*(i+1)
-    #
-    #        SymbolValuePairDict.update(PairDict1)
-    #
-    #    if stop < count:
-    #        stop = count
-    #        gList2 = symbolList[start:stop]
-    #        PairDict2 = getSymbolValuePairDict(cursor=cursor,symbolList=gList2,dataIdDict=dataIdDict)
-    #        SymbolValuePairDict.update(PairDict2)
-    #
-    #return SymbolValuePairDict
-
-########################################################################################################
-#input: cursor, GeneNameLst (list), TissueProbeSetFreezeId(int)
-#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
-#        key is symbol, value is one list of expression values of one probeSet.
-#function: wrapper function of getGeneSymbolTissueValueDict function
-#          for CorrelationPage.py
-########################################################################################################
-
-#def get_trait_symbol_and_tissue_values(cursor=None,GeneNameLst=[],TissueProbeSetFreezeId=0):
-#    SymbolValuePairDict={}
-#
-#    symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict = getTissueProbeSetXRefInfo(
-#        cursor=cursor,GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-#
-#    if symbolList:
-#        SymbolValuePairDict = get_gene_symbol_and_tissue_values(symbolList=symbolList,
-#                                                                dataIdDict=dataIdDict)
-#
-#    return SymbolValuePairDict
-
-########################################################################################################
-#Input: cursor(cursor): MySQL connnection cursor;
-#       priGeneSymbolList(list): one list of gene symbol;
-#       symbolValuepairDict(dictionary): one dictionary of Symbol and Value Pair,
-#               key is symbol, value is one list of expression values of one probeSet;
-#Output: corrArray(array): array of Correlation Value,
-#        pvArray(array): array of PValue;
-#Function: build corrArray, pvArray for display by calling  calculation function:calZeroOrderCorrForTiss
-########################################################################################################
-
-def getCorrPvArray(cursor=None,priGeneSymbolList=[],symbolValuepairDict={}):
-    # setting initial value for corrArray, pvArray equal to 0
-    Num = len(priGeneSymbolList)
-
-    corrArray = [([0] * (Num))[:] for i in range(Num)]
-    pvArray = [([0] * (Num))[:] for i in range(Num)]
-    i = 0
-    for pkey in priGeneSymbolList:
-        j = 0
-        pkey = pkey.strip().lower()# key in symbolValuepairDict is low case
-        if symbolValuepairDict.has_key(pkey):
-            priValue = symbolValuepairDict[pkey]
-            for tkey in priGeneSymbolList:
-                tkey = tkey.strip().lower()# key in symbolValuepairDict is low case
-                if priValue and symbolValuepairDict.has_key(tkey):
-                    tarValue = symbolValuepairDict[tkey]
-
-                    if tarValue:
-                        if i>j:
-                            # corrArray stores Pearson Correlation values
-                            # pvArray stores Pearson P-Values
-                            pcorr_result =calZeroOrderCorrForTiss(primaryValue=priValue,targetValue=tarValue)
-                            corrArray[i][j] =pcorr_result[0]
-                            pvArray[i][j] =pcorr_result[2]
-                        elif i<j:
-                            # corrArray stores Spearman Correlation values
-                            # pvArray stores Spearman P-Values
-                            scorr_result =calZeroOrderCorrForTiss(primaryValue=priValue,targetValue=tarValue,method='spearman')
-                            corrArray[i][j] =scorr_result[0]
-                            pvArray[i][j] =scorr_result[2]
-                        else:
-                            # on the diagonal line, correlation value is 1, P-Values is 0
-                            corrArray[i][j] =1
-                            pvArray[i][j] =0
-                        j+=1
-                    else:
-                        corrArray[i][j] = None
-                        pvArray[i][j] = None
-                        j+=1
-                else:
-                    corrArray[i][j] = None
-                    pvArray[i][j] = None
-                    j+=1
-        else:
-            corrArray[i][j] = None
-            pvArray[i][j] = None
-
-        i+=1
-
-    return corrArray, pvArray
-
-########################################################################################################
-#Input: cursor(cursor): MySQL connnection cursor;
-#       primaryTraitSymbol(string): one gene symbol;
-#               TissueProbeSetFreezeId (int): Id of related TissueProbeSetFreeze
-#       method: '0' default value, Pearson Correlation; '1', Spearman Correlation
-#Output: symbolCorrDict(Dict): Dict of Correlation Value, key is symbol
-#        symbolPvalueDict(Dict): Dict of PValue,key is symbol ;
-#Function: build symbolCorrDict, symbolPvalueDict for display by calling  calculation function:calZeroOrderCorrForTiss
-########################################################################################################
-def calculateCorrOfAllTissueTrait(cursor=None, primaryTraitSymbol=None, TissueProbeSetFreezeId=None,method='0'):
-
-    symbolCorrDict = {}
-    symbolPvalueDict = {}
-
-    primaryTraitSymbolValueDict = getGeneSymbolTissueValueDictForTrait(cursor=cursor, GeneNameLst=[primaryTraitSymbol], TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-    primaryTraitValue = primaryTraitSymbolValueDict.values()[0]
-
-    SymbolValueDict = getGeneSymbolTissueValueDictForTrait(cursor=cursor, GeneNameLst=[], TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-
-    if method =='1':
-        symbolCorrDict, symbolPvalueDict = batchCalTissueCorr(primaryTraitValue,SymbolValueDict,method='spearman')
-    else:
-        symbolCorrDict, symbolPvalueDict = batchCalTissueCorr(primaryTraitValue,SymbolValueDict)
-
-
-    return (symbolCorrDict, symbolPvalueDict)
+        return tissue_data.get_symbol_values_pairs()
\ No newline at end of file
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 85a8c0ef..9f3f7982 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -21,9 +21,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-# sys.path.append(".") Never in a running webserver
 
-import gc
 import string
 import cPickle
 import os
@@ -64,8 +62,6 @@ from flask import Flask, g
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-METHOD_SAMPLE_PEARSON = "1"
-METHOD_SAMPLE_RANK = "2"
 METHOD_LIT = "3"
 METHOD_TISSUE_PEARSON = "4"
 METHOD_TISSUE_RANK = "5"
@@ -74,26 +70,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
 
 TISSUE_MOUSE_DB = 1
 
-def print_mem(stage=""):
-    mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
-    #print("{}: {}".format(stage, mem/1024))
-
-class AuthException(Exception):
-    pass
-
 class CorrelationResults(object):
-
-    corr_min_informative = 4
-
-    #PAGE_HEADING = "Correlation Table"
-    #CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
-    #                       "2" : "Genetic Correlation (Spearman's rho)",
-    #                       "3" : "SGO Literature Correlation",
-    #                       "4" : "Tissue Correlation (Pearson's r)",
-    #                       "5" : "Tissue Correlation (Spearman's rho)"}
-    #
-    #RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
-
     def __init__(self, start_vars):
         # get trait list from db (database name)
         # calculate correlation with Base vector and targets
@@ -167,16 +144,12 @@ class CorrelationResults(object):
                 self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
 
             self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
-            # print("self.sample_data.keys: %s" % self.sample_data.keys)
             self.target_dataset.get_trait_data(self.sample_data.keys())
 
             self.correlation_results = []
 
             self.correlation_data = {}
 
-            db_filename = self.getFileName(target_db_name = self.target_dataset.name)
-            cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR)
-
             if self.corr_type == "tissue":
                 self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol")
 
@@ -196,24 +169,6 @@ class CorrelationResults(object):
                     self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
 
             elif self.corr_type == "sample":
-              #ZS: Commented out since parallel correlation has issues with gunicorn
-                # if self.dataset.type == "ProbeSet" and cache_available:
-                    # dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
-
-                    ##XZ, 01/08/2009: read the first line
-                    # line = dataset_file.readline()
-                    # dataset_strains = webqtlUtil.readLineCSV(line)[1:]
-
-                    # self.this_trait_vals = []
-                    # for item in dataset_strains:
-                        # if item in self.sample_data:
-                            # self.this_trait_vals.append(self.sample_data[item])
-                        # else:
-                            # self.this_trait_vals.append("None")
-                    # num_overlap = len(self.this_trait_vals)
-                    # logger.debug("DOING PARALLEL")
-                    # self.do_parallel_correlation(db_filename, num_overlap)
-                # else:
                 for trait, values in self.target_dataset.trait_data.iteritems():
                     self.get_sample_r_and_p_values(trait, values)
 
@@ -256,9 +211,6 @@ class CorrelationResults(object):
                         trait_object.sample_p,
                         trait_object.num_overlap) = self.correlation_data[trait]
 
-                        #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
-                        #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
-
                         # Set some sane defaults
                         trait_object.tissue_corr = 0
                         trait_object.tissue_pvalue = 0
@@ -274,9 +226,6 @@ class CorrelationResults(object):
                         trait_object.sample_p,
                         trait_object.num_overlap) = self.correlation_data[trait]
 
-                        #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
-                        #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
-
                         # Set some sane defaults
                         trait_object.tissue_corr = 0
                         trait_object.tissue_pvalue = 0
@@ -323,13 +272,6 @@ class CorrelationResults(object):
 
         if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
             primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
-
-            #gene_symbol_list = []
-            #
-            #for trait in self.correlation_results:
-            #    if hasattr(trait, 'symbol'):
-            #        gene_symbol_list.append(trait.symbol)
-
             gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol]
 
             corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
@@ -346,17 +288,6 @@ class CorrelationResults(object):
                     trait.tissue_corr = result[0]
                     trait.tissue_pvalue = result[2]
 
-        #        else:
-        #            trait.tissue_corr = None
-        #            trait.tissue_pvalue = None
-        #else:
-        #    for trait in self.correlation_results:
-        #        trait.tissue_corr = None
-        #        trait.tissue_pvalue = None
-
-        #return self.correlation_results
-
-
     def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
         #Gets tissue expression values for the primary trait
         primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
@@ -377,7 +308,6 @@ class CorrelationResults(object):
             for trait, symbol in self.trait_symbol_dict.iteritems():
                 if symbol and symbol.lower() in corr_result_tissue_vals_dict:
                     this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
-                    #print("this_trait_tissue_values: ", pf(this_trait_tissue_values))
 
                     result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
                                                                           this_trait_tissue_values,
@@ -390,7 +320,6 @@ class CorrelationResults(object):
 
             return tissue_corr_data
 
-
     def do_lit_correlation_for_trait_list(self):
 
         input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
@@ -529,219 +458,6 @@ class CorrelationResults(object):
         if num_overlap > 5:
             self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
 
-
-        """
-        correlations = []
-
-        #XZ: Use the fast method only for probeset dataset, and this dataset must have been created.
-        #XZ: Otherwise, use original method
-        #print("Entering correlation")
-
-        #db_filename = self.getFileName(target_db_name=self.target_db_name)
-        #
-        #cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR)
-
-         # If the cache file exists, do a cached correlation for probeset data
-        if self.dataset.type == "ProbeSet":
-#           if self.method in [METHOD_SAMPLE_PEARSON, METHOD_SAMPLE_RANK] and cache_available:
-#               traits = do_parallel_correlation()
-#
-#           else:
-
-            traits = self.get_traits(self.vals)
-
-            for trait in traits:
-                trait.calculate_correlation(vals, self.method)
-
-        self.record_count = len(traits) #ZS: This isn't a good way to get this value, so I need to change it later
-
-        traits = sortTraitCorrelations(traits, self.method)
-
-        # Strip to the top N correlations
-        traits = traits[:min(self.returnNumber, len(traits))]
-
-        addLiteratureCorr = False
-        addTissueCorr = False
-
-        trait_list = []
-        for trait in traits:
-            db_trait = webqtlTrait(db=self.db, name=trait.name, cursor=self.cursor)
-            db_trait.retrieveInfo( QTL='Yes' )
-
-            db_trait.Name = trait.name
-            db_trait.corr = trait.correlation
-            db_trait.nOverlap = trait.overlap
-            db_trait.corrPValue = trait.p_value
-
-            # NL, 07/19/2010
-            # js function changed, add a new parameter rankOrder for js function 'showTissueCorrPlot'
-            db_trait.RANK_ORDER = self.RANK_ORDERS[self.method]
-
-            #XZ, 26/09/2008: Method is 4 or 5. Have fetched tissue corr, but no literature correlation yet.
-            if self.method in TISSUE_METHODS:
-                db_trait.tissueCorr = trait.tissue_corr
-                db_trait.tissuePValue = trait.p_tissue
-                addTissueCorr = True
-
-
-            #XZ, 26/09/2008: Method is 3,  Have fetched literature corr, but no tissue corr yet.
-            elif self.method == METHOD_LIT:
-                db_trait.LCorr = trait.lit_corr
-                db_trait.mouse_geneid = self.translateToMouseGeneID(self.species, db_trait.geneid)
-                addLiteratureCorr = True
-
-            #XZ, 26/09/2008: Method is 1 or 2. Have NOT fetched literature corr and tissue corr yet.
-            # Phenotype data will not have geneid, and neither will some probes
-            # we need to handle this because we will get an attribute error
-            else:
-                if self.input_trait_mouse_gene_id and self.db.type=="ProbeSet":
-                    addLiteratureCorr = True
-                if self.trait_symbol and self.db.type=="ProbeSet":
-                    addTissueCorr = True
-
-            trait_list.append(db_trait)
-
-        if addLiteratureCorr:
-            trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id,
-                                                    self.species, trait_list)
-        if addTissueCorr:
-            trait_list = self.getTissueCorrelationByList(
-                        primaryTraitSymbol = self.trait_symbol,
-                        traitList = trait_list,
-                        TissueProbeSetFreezeId = TISSUE_MOUSE_DB,
-                        method=self.method)
-
-        return trait_list
-        """
-
-
-    def do_tissue_corr_for_all_traits_2(self):
-        """Comments Possibly Out of Date!!!!!
-
-        Uses get_temp_tissue_corr_table to generate table of tissue correlations
-
-        This function then gathers that data and pairs it with the TraitID string.
-        Takes as its arguments a formdata instance, and a dataset instance.
-        Returns a dictionary of 'TraitID':(tissueCorr, tissuePValue)
-        for the requested correlation
-
-        Used when the user selects the tissue correlation method; i.e. not for the
-        column that is appended to all probeset trait correlation tables
-
-        """
-
-        # table name string
-        temp_table = self.get_temp_tissue_corr_table(tissue_probesetfreeze_id=TISSUE_MOUSE_DB,
-                                                    method=method)
-
-        query = """SELECT ProbeSet.Name, {}.Correlation, {}.PValue
-                FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
-                LEFT JOIN {} ON {}.Symbol=ProbeSet.Symbol
-                WHERE ProbeSetFreeze.Name = '{}'
-                and ProbeSetFreeze.Id=ProbeSetXRef.ProbeSetFreezeId
-                and ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                and ProbeSet.Symbol IS NOT NULL
-                and {}.Correlation IS NOT NULL""".format(dataset.mescape(
-                    temp_table, temp_table, temp_table, temp_table,
-                    self.dataset.name, temp_table))
-
-        results = g.db.execute(query).fetchall()
-
-        tissue_corr_dict = {}
-
-        for entry in results:
-            trait_name, tissue_corr, tissue_pvalue = entry
-            tissue_corr_dict[trait_name] = (tissue_corr, tissue_pvalue)
-    #symbolList,
-    #geneIdDict,
-    #dataIdDict,
-    #ChrDict,
-    #MbDict,
-    #descDict,
-    #pTargetDescDict = getTissueProbeSetXRefInfo(
-    #                    GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-
-        g.db.execute('DROP TEMPORARY TABLE {}'.format(escape(temp_table)))
-
-        return tissue_corr_dict
-
-
-    #XZ, 09/23/2008: In tissue correlation tables, there is no record of GeneId1 == GeneId2
-    #XZ, 09/24/2008: Note that the correlation value can be negative.
-    def get_temp_tissue_corr_table(self,
-                                   tissue_probesetfreeze_id=0,
-                                   method="",
-                                   return_number=0):
-
-
-        def cmp_tisscorr_absolute_value(A, B):
-            try:
-                if abs(A[1]) < abs(B[1]): return 1
-                elif abs(A[1]) == abs(B[1]):
-                    return 0
-                else: return -1
-            except:
-                return 0
-
-        symbol_corr_dict, symbol_pvalue_dict = self.calculate_corr_for_all_tissues(
-                                                                tissue_dataset_id=TISSUE_MOUSE_DB)
-
-        symbol_corr_list = symbol_corr_dict.items()
-
-        symbol_corr_list.sort(cmp_tisscorr_absolute_value)
-        symbol_corr_list = symbol_corr_list[0 : 2*return_number]
-
-        tmp_table_name = webqtlUtil.genRandStr(prefix="TOPTISSUE")
-
-        q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmp_table_name
-        self.cursor.execute(q1)
-
-        for one_pair in symbol_corr_list:
-            one_symbol = one_pair[0]
-            one_corr = one_pair[1]
-            one_p_value = symbol_pvalue_dict[one_symbol]
-
-            self.cursor.execute( "INSERT INTO %s (Symbol, Correlation, PValue) VALUES ('%s',%f,%f)" % (tmpTableName, one_symbol, float(one_corr), float(one_p_value)) )
-
-        return tmp_table_name
-
-
-    def calculate_corr_for_all_tissues(self, tissue_dataset_id=None):
-
-        symbol_corr_dict = {}
-        symbol_pvalue_dict = {}
-
-        primary_trait_symbol_value_dict = correlation_functions.make_gene_tissue_value_dict(
-                                                    GeneNameLst=[self.this_trait.symbol],
-                                                    TissueProbeSetFreezeId=tissue_dataset_id)
-        primary_trait_value = primary_trait_symbol_value_dict.values()[0]
-
-        symbol_value_dict = correlation_functions.make_gene_tissue_value_dict(
-                                        gene_name_list=[],
-                                        tissue_dataset_id=tissue_dataset_id)
-
-        symbol_corr_dict, symbol_pvalue_dict = correlation_functions.batch_cal_tissue_corr(
-                primaryTraitValue,
-                SymbolValueDict,
-                method=self.corr_method)
-        #else:
-        #    symbol_corr_dict, symbol_pvalue_dict = correlation_functions.batch_cal_tissue_corr(
-        #        primaryTraitValue,
-        #        SymbolValueDict)
-
-        return (symbolCorrDict, symbolPvalueDict)
-
-    ##XZ, 12/16/2008: the input geneid is of mouse type
-    #def checkSymbolForTissueCorr(self, tissueProbeSetFreezeId=0, symbol=""):
-    #    q = "SELECT 1 FROM  TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol)
-    #    self.cursor.execute(q)
-    #    try:
-    #        x = self.cursor.fetchone()
-    #        if x: return True
-    #        else: raise
-    #    except: return False
-
-
     def process_samples(self, start_vars, sample_names, excluded_samples=None):
         if not excluded_samples:
             excluded_samples = ()
@@ -754,566 +470,6 @@ class CorrelationResults(object):
                     if not value.strip().lower() == 'x':
                         self.sample_data[str(sample)] = float(value)
 
-    ##XZ, 12/16/2008: the input geneid is of mouse type
-    #def checkForLitInfo(self,geneId):
-    #    q = 'SELECT 1 FROM LCorrRamin3 WHERE GeneId1=%s LIMIT 1' % geneId
-    #    self.cursor.execute(q)
-    #    try:
-    #        x = self.cursor.fetchone()
-    #        if x: return True
-    #        else: raise
-    #    except: return False
-
-
-
-    def fetchAllDatabaseData(self, species, GeneId, GeneSymbol, strains, db, method, returnNumber, tissueProbeSetFreezeId):
-
-        StrainIds = []
-        for item in strains:
-            self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE Strain.Name="%s" and Strain.SpeciesId=Species.Id and Species.name = "%s" ''' % (item, species))
-            Id = self.cursor.fetchone()[0]
-            StrainIds.append('%d' % Id)
-
-        # break it into smaller chunks so we don't overload the MySql server
-        nnn = len(StrainIds) / 25
-        if len(StrainIds) % 25:
-            nnn += 1
-        oridata = []
-
-        #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
-        tempTable = None
-        if GeneId and db.type == "ProbeSet":
-            if method == "3":
-                tempTable = self.getTempLiteratureTable(species=species, input_species_geneid=GeneId, returnNumber=returnNumber)
-
-            if method == "4" or method == "5":
-                tempTable = self.getTempTissueCorrTable(primaryTraitSymbol=GeneSymbol, TissueProbeSetFreezeId=TISSUE_MOUSE_DB, method=method, returnNumber=returnNumber)
-
-        for step in range(nnn):
-            temp = []
-            StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
-            for item in StrainIdstep: temp.append('T%s.value' % item)
-
-            if db.type == "Publish":
-                query = "SELECT PublishXRef.Id, "
-                dataStartPos = 1
-                query += string.join(temp,', ')
-                query += ' FROM (PublishXRef, PublishFreeze)'
-                #XZ, 03/04/2009: Xiaodong changed Data to PublishData
-                for item in StrainIdstep:
-                    query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item)
-                query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Name = '%s'" % (db.name, )
-            #XZ, 09/20/2008: extract literature correlation value together with gene expression values.
-            #XZ, 09/20/2008: notice the difference between the code in next block.
-            #elif tempTable:
-            #    # we can get a little performance out of selecting our LitCorr here
-            #    # but also we need to do this because we are unconcerned with probes that have no geneId associated with them
-            #    # as we would not have litCorr data.
-            #
-            #    if method == "3":
-            #        query = "SELECT %s.Name, %s.value," %  (db.type,tempTable)
-            #        dataStartPos = 2
-            #    if method == "4" or method == "5":
-            #        query = "SELECT %s.Name, %s.Correlation, %s.PValue," %  (db.type,tempTable, tempTable)
-            #        dataStartPos = 3
-            #
-            #    query += string.join(temp,', ')
-            #    query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type)
-            #    if method == "3":
-            #        query += ' LEFT JOIN %s ON %s.GeneId2=ProbeSet.GeneId ' % (tempTable,tempTable)
-            #    if method == "4" or method == "5":
-            #        query += ' LEFT JOIN %s ON %s.Symbol=ProbeSet.Symbol ' % (tempTable,tempTable)
-            #    #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
-            #    for item in StrainIdstep:
-            #        query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
-            #
-            #    if method == "3":
-            #        query += "WHERE ProbeSet.GeneId IS NOT NULL AND %s.value IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s'  and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-            #    if method == "4" or method == "5":
-            #        query += "WHERE ProbeSet.Symbol IS NOT NULL AND %s.Correlation IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s'  and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-            else:
-                query = "SELECT %s.Name," %  db.type
-                dataStartPos = 1
-                query += string.join(temp,', ')
-                query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type)
-                #XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
-                for item in StrainIdstep:
-                    query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
-                query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s'  and %s.Id = %sXRef.%sId order by %s.Id" % (db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-
-            self.cursor.execute(query)
-            results = self.cursor.fetchall()
-            oridata.append(results)
-
-        datasize = len(oridata[0])
-        traits = []
-        # put all of the separate data together into a huge list of lists
-        for j in range(datasize):
-            traitdata = list(oridata[0][j])
-            for i in range(1,nnn):
-                traitdata += list(oridata[i][j][dataStartPos:])
-
-            trait = Trait(traitdata[0], traitdata[dataStartPos:])
-
-            if method == METHOD_LIT:
-                trait.lit_corr = traitdata[1]
-
-            if method in TISSUE_METHODS:
-                trait.tissue_corr = traitdata[1]
-                trait.p_tissue = traitdata[2]
-
-            traits.append(trait)
-
-        if tempTable:
-            self.cursor.execute( 'DROP TEMPORARY TABLE %s' % tempTable )
-
-        return traits
-
-
-
-
-    # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name.
-    # XZ, 09/20/2008: It stores top literature correlation values associated with the input geneId.
-    # XZ, 09/20/2008: Attention: In each row, the input geneId is always in column GeneId1.
-    #XZ, 12/16/2008: the input geneid can be of mouse, rat or human type
-    def getTempLiteratureTable(self, species, input_species_geneid, returnNumber):
-        # according to mysql the TEMPORARY TABLE name should not have to be unique because
-        # it is only available to the current connection. This program will be invoked via command line, but if it
-        # were to be invoked over mod_python this could cuase problems.  mod_python will keep the connection alive
-        # in its executing threads ( i think) so there is a potential for the table not being dropped between users.
-        #XZ, 01/29/2009: To prevent the potential risk, I generate random table names and drop the tables after use them.
-
-
-        # the 'input_species_geneid' could be rat or human geneid, need to translate it to mouse geneid
-        translated_mouse_geneid = self.translateToMouseGeneID (species, input_species_geneid)
-
-        tmpTableName_1 = webqtlUtil.genRandStr(prefix="LITERATURE")
-
-        q1 = 'CREATE TEMPORARY TABLE %s (GeneId1 int(12) unsigned, GeneId2 int(12) unsigned PRIMARY KEY, value double)' % tmpTableName_1
-        q2 = 'INSERT INTO %s (GeneId1, GeneId2, value) SELECT GeneId1,GeneId2,value FROM LCorrRamin3 WHERE GeneId1=%s' % (tmpTableName_1, translated_mouse_geneid)
-        q3 = 'INSERT INTO %s (GeneId1, GeneId2, value) SELECT GeneId2,GeneId1,value FROM LCorrRamin3 WHERE GeneId2=%s AND GeneId1!=%s' % (tmpTableName_1, translated_mouse_geneid,translated_mouse_geneid)
-        for x in [q1,q2,q3]: self.cursor.execute(x)
-
-        #XZ, 09/23/2008: Just use the top records insteard of using all records
-        tmpTableName_2 = webqtlUtil.genRandStr(prefix="TOPLITERATURE")
-
-        q1 = 'CREATE TEMPORARY TABLE %s (GeneId1 int(12) unsigned, GeneId2 int(12) unsigned PRIMARY KEY, value double)' % tmpTableName_2
-        self.cursor.execute(q1)
-        q2 = 'SELECT GeneId1, GeneId2, value FROM %s ORDER BY value DESC' % tmpTableName_1
-        self.cursor.execute(q2)
-        result = self.cursor.fetchall()
-
-        counter = 0 #this is to count how many records being inserted into table
-        for one_row in result:
-            mouse_geneid1, mouse_geneid2, lit_corr_alue = one_row
-
-            #mouse_geneid1 has been tested before, now should test if mouse_geneid2 has corresponding geneid in other species
-            translated_species_geneid = 0
-            if species == 'mouse':
-                translated_species_geneid = mouse_geneid2
-            elif species == 'rat':
-                self.cursor.execute( "SELECT rat FROM GeneIDXRef WHERE mouse=%d" % int(mouse_geneid2) )
-                record = self.cursor.fetchone()
-                if record:
-                    translated_species_geneid = record[0]
-            elif species == 'human':
-                self.cursor.execute( "SELECT human FROM GeneIDXRef WHERE mouse=%d" % int(mouse_geneid2) )
-                record = self.cursor.fetchone()
-                if record:
-                    translated_species_geneid = record[0]
-
-            if translated_species_geneid:
-                self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) )
-                counter = counter + 1
-
-            #pay attention to the number
-            if (counter > 2*returnNumber):
-                break
-
-        self.cursor.execute('DROP TEMPORARY TABLE %s' % tmpTableName_1)
-
-        return tmpTableName_2
-
-
-
-    #XZ, 01/09/2009: This function was created by David Crowell. Xiaodong cleaned up and modified it.
-    def fetchLitCorrelations(self, species, GeneId, db, returnNumber): ### Used to generate Lit Correlations when calculations are done from text file.  dcrowell August 2008
-        """Uses getTempLiteratureTable to generate table of literatire correlations.  This function then gathers that data and
-        pairs it with the TraitID string.  Takes as its arguments a formdata instance, and a database instance.
-        Returns a dictionary of 'TraitID':'LitCorr' for the requested correlation"""
-
-        tempTable = self.getTempLiteratureTable(species=species, input_species_geneid=GeneId, returnNumber=returnNumber)
-
-        query = "SELECT %s.Name, %s.value" %  (db.type,tempTable)
-        query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type)
-        query += ' LEFT JOIN %s ON %s.GeneId2=ProbeSet.GeneId ' % (tempTable,tempTable)
-        query += "WHERE ProbeSet.GeneId IS NOT NULL AND %s.value IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s'  and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable, db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-
-        self.cursor.execute(query)
-        results = self.cursor.fetchall()
-
-        litCorrDict = {}
-
-        for entry in results:
-            traitName,litcorr = entry
-            litCorrDict[traitName] = litcorr
-
-        self.cursor.execute('DROP TEMPORARY TABLE %s' % tempTable)
-
-        return litCorrDict
-
-
-    def get_traits(self, vals):
-
-        #Todo: Redo cached stuff using memcached
-        if False:
-            lit_corrs = {}
-            tissue_corrs = {}
-            use_lit = False
-            if self.method == METHOD_LIT:
-                lit_corrs = self.fetchLitCorrelations(species=self.species, GeneId=self.gene_id, db=self.db, returnNumber=self.returnNumber)
-                use_lit = True
-
-            use_tissue_corr = False
-            if self.method in TISSUE_METHODS:
-                tissue_corrs = self.fetch_tissue_correlations(method=self.method, return_number = self.return_number)
-                use_tissue_corr = True
-
-            DatabaseFileName = self.getFileName( target_db_name=self.target_db_name )
-            datasetFile = open(webqtlConfig.CACHEDIR+DatabaseFileName,'r')
-
-            #XZ, 01/08/2009: read the first line
-            line = datasetFile.readline()
-            cached_sample_names = webqtlUtil.readLineCSV(line)[1:]
-
-            #XZ, 01/08/2009: This step is critical. It is necessary for this new method.
-            #XZ: The original function fetchAllDatabaseData uses all strains stored in variable _strains to
-            #XZ: retrieve the values of each strain from database in real time.
-            #XZ: The new method uses all strains stored in variable dataset_strains to create a new variable
-            #XZ: _newvals. _newvals has the same length as dataset_strains. The items in _newvals is in
-            #XZ: the same order of items in dataset_strains. The value of each item in _newvals is either
-            #XZ: the value of correspinding strain in _vals or 'None'.
-            new_vals = []
-            for name in cached_sample_names:
-                if name in self.sample_names:
-                    new_vals.append(float(vals[self.sample_names.index(name)]))
-                else:
-                    new_vals.append('None')
-
-            nnCorr = len(new_vals)
-
-            #XZ, 01/14/2009: If literature corr or tissue corr is selected,
-            #XZ: there is no need to use parallel computing.
-
-            traits = []
-            data_start = 1
-            for line in datasetFile:
-                raw_trait = webqtlUtil.readLineCSV(line)
-                trait = Trait.from_csv(raw_trait, data_start)
-                trait.lit_corr = lit_corrs.get(trait.name)
-                trait.tissue_corr, trait.p_tissue = tissue_corrs.get(trait.name, (None, None))
-                traits.append(trait)
-
-            return traits, new_vals
-
-        else:
-            traits = self.fetchAllDatabaseData(species=self.dataset.species,
-                                               GeneId=self.gene_id,
-                                               GeneSymbol=self.trait.symbol,
-                                               strains=self.sample_names,
-                                               db=self.db,
-                                               method=self.method,
-                                               returnNumber=self.returnNumber,
-                                               tissueProbeSetFreezeId= self.tissue_probeset_freeze_id)
-            totalTraits = len(traits) #XZ, 09/18/2008: total trait number
-
-        return traits
-
-    def calculate_corr_for_all_tissues(self, tissue_dataset_id=None):
-
-        symbol_corr_dict = {}
-        symbol_pvalue_dict = {}
-
-        primary_trait_symbol_value_dict = correlation_functions.make_gene_tissue_value_dict(
-                                                    GeneNameLst=[self.this_trait.symbol],
-                                                    TissueProbeSetFreezeId=tissue_dataset_id)
-        primary_trait_value = primary_trait_symbol_value_dict.values()[0]
-
-        symbol_value_dict = correlation_functions.make_gene_tissue_value_dict(
-                                        gene_name_list=[],
-                                        tissue_dataset_id=tissue_dataset_id)
-
-        symbol_corr_dict, symbol_pvalue_dict = correlation_functions.batch_cal_tissue_corr(
-                primaryTraitValue,
-                SymbolValueDict,
-                method=self.corr_method)
-        #else:
-        #    symbol_corr_dict, symbol_pvalue_dict = correlation_functions.batch_cal_tissue_corr(
-        #        primaryTraitValue,
-        #        SymbolValueDict)
-
-        return (symbolCorrDict, symbolPvalueDict)
-
-    def getFileName(self, target_db_name):  ### dcrowell  August 2008
-        """Returns the name of the reference database file with which correlations are calculated.
-        Takes argument cursor which is a cursor object of any instance of a subclass of templatePage
-        Used by correlationPage"""
-
-        dataset_id = str(self.target_dataset.id)
-        dataset_fullname = self.target_dataset.fullname.replace(' ','_')
-        dataset_fullname = dataset_fullname.replace('/','_')
-
-        FileName = 'ProbeSetFreezeId_' + dataset_id + '_FullName_' + dataset_fullname + '.txt'
-
-        return FileName
-
-    def do_parallel_correlation(self, db_filename, num_overlap):
-
-        #XZ, 01/14/2009: This method is for parallel computing only.
-        #XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
-        #XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected
-        def compute_corr(input_nnCorr, input_trait, input_list, corr_method):
-
-            import math
-            import reaper
-
-            def cmpOrder2(A,B):
-                try:
-                    if A[-1] < B[-1]:
-                        return -1
-                    elif A[-1] == B[-1]:
-                        return 0
-                    else:
-                        return 1
-                except:
-                    return 0
-
-            def calCorrelation(dbdata,userdata,N):
-                X = []
-                Y = []
-                for i in range(N):
-                    if (dbdata[i] != None and userdata[i] != None) and (dbdata[i] != "None" and userdata[i] != "None"):
-                        X.append(float(dbdata[i]))
-                        Y.append(float(userdata[i]))
-                NN = len(X)
-                if NN <6:
-                    return (0.0,NN)
-                sx = reduce(lambda x,y:x+y,X,0.0)
-                sy = reduce(lambda x,y:x+y,Y,0.0)
-                meanx = sx/NN
-                meany = sy/NN
-                xyd = 0.0
-                sxd = 0.0
-                syd = 0.0
-                for i in range(NN):
-                    xyd += (X[i] - meanx)*(Y[i]-meany)
-                    sxd += (X[i] - meanx)*(X[i] - meanx)
-                    syd += (Y[i] - meany)*(Y[i] - meany)
-                try:
-                    corr = xyd/(math.sqrt(sxd)*math.sqrt(syd))
-                except:
-                    corr = 0
-                return (corr,NN)
-
-            def calCorrelationRank(xVals,yVals,N):
-                """
-                Calculated Spearman Ranked Correlation. The algorithm works
-                by setting all tied ranks to the average of those ranks (for
-                example, if ranks 5-10 all have the same value, each will be set
-                to rank 7.5).
-                """
-
-                XX = []
-                YY = []
-                j = 0
-
-                for i in range(len(xVals)):
-                    if (xVals[i]!= None and yVals[i]!= None) and (xVals[i] != "None" and yVals[i] != "None"):
-                        XX.append((j,float(xVals[i])))
-                        YY.append((j,float(yVals[i])))
-                        j = j+1
-
-                NN = len(XX)
-                if NN <6:
-                    return (0.0,NN)
-                XX.sort(cmpOrder2)
-                YY.sort(cmpOrder2)
-                X = [0]*NN
-                Y = [0]*NN
-
-                j = 1
-                rank = 0.0
-                t = 0.0
-                sx = 0.0
-
-                while j < NN:
-
-                    if XX[j][1] != XX[j-1][1]:
-                        X[XX[j-1][0]] = j
-                        j = j+1
-
-                    else:
-                        jt = j+1
-                        ji = j
-                        for jt in range(j+1, NN):
-                            if (XX[jt][1] != XX[j-1][1]):
-                                break
-                        rank = 0.5*(j+jt)
-                        for ji in range(j-1, jt):
-                            X[XX[ji][0]] = rank
-                        t = jt-j
-                        sx = sx + (t*t*t-t)
-                        if (jt == NN-1):
-                            if (XX[jt][1] == XX[j-1][1]):
-                                X[XX[NN-1][0]] = rank
-                        j = jt+1
-
-                if j == NN:
-                    if X[XX[NN-1][0]] == 0:
-                        X[XX[NN-1][0]] = NN
-
-                j = 1
-                rank = 0.0
-                t = 0.0
-                sy = 0.0
-
-                while j < NN:
-
-                    if YY[j][1] != YY[j-1][1]:
-                        Y[YY[j-1][0]] = j
-                        j = j+1
-                    else:
-                        jt = j+1
-                        ji = j
-                        for jt in range(j+1, NN):
-                            if (YY[jt][1] != YY[j-1][1]):
-                                break
-                        rank = 0.5*(j+jt)
-                        for ji in range(j-1, jt):
-                            Y[YY[ji][0]] = rank
-                        t = jt - j
-                        sy = sy + (t*t*t-t)
-                        if (jt == NN-1):
-                            if (YY[jt][1] == YY[j-1][1]):
-                                Y[YY[NN-1][0]] = rank
-                        j = jt+1
-
-                if j == NN:
-                    if Y[YY[NN-1][0]] == 0:
-                        Y[YY[NN-1][0]] = NN
-
-                D = 0.0
-
-                for i in range(NN):
-                    D += (X[i]-Y[i])*(X[i]-Y[i])
-
-                fac = (1.0 -sx/(NN*NN*NN-NN))*(1.0-sy/(NN*NN*NN-NN))
-
-                return ((1-(6.0/(NN*NN*NN-NN))*(D+(sx+sy)/12.0))/math.sqrt(fac),NN)
-
-            # allcorrelations = []
-
-            correlation_data = {}
-            for i, line in enumerate(input_list):
-                if i == 0:
-                    continue
-                tokens = line.split('","')
-                tokens[-1] = tokens[-1][:-2] #remove the last "
-                tokens[0] = tokens[0][1:] #remove the first "
-
-                traitdataName = tokens[0]
-                database_trait = tokens[1:]
-
-                #print("database_trait:", database_trait)
-
-                #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
-                # if corr_method == 'pearson':
-                    # sample_r, sample_p = scipy.stats.pearsonr(input_trait, database_trait)
-                # else:
-                    # sample_r, sample_p = scipy.stats.spearmanr(input_trait, database_trait)
-
-                if corr_method == "pearson": #XZ: Pearson's r
-                    sample_r, nOverlap = calCorrelation(input_trait, database_trait, input_nnCorr)
-                else: #XZ: Spearman's rho
-                    sample_r, nOverlap = calCorrelationRank(input_trait, database_trait, input_nnCorr)
-
-                #XZ: calculate corrPValue
-                if nOverlap < 3:
-                    sample_p = 1.0
-                else:
-                    if abs(sample_r) >= 1.0:
-                        sample_p = 0.0
-                    else:
-                        z_value = 0.5*math.log((1.0+sample_r)/(1.0-sample_r))
-                        z_value = z_value*math.sqrt(nOverlap-3)
-                        sample_p = 2.0*(1.0 - reaper.normp(abs(z_value)))
-
-                correlation_data[traitdataName] = [sample_r, sample_p, nOverlap]
-
-                # traitinfo = [traitdataName, sample_r, nOverlap]
-                # allcorrelations.append(traitinfo)
-
-            return correlation_data
-            # return allcorrelations
-
-
-        datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r')
-
-        print("Invoking parallel computing")
-        input_line_list = datasetFile.readlines()
-        print("Read lines from the file")
-        all_line_number = len(input_line_list)
-
-        step = 1000
-        job_number = math.ceil( float(all_line_number)/step )
-
-        print("JOB NUMBER", job_number)
-
-        job_input_lists = []
-
-        print("Configuring jobs")
-
-        for job_index in range( int(job_number) ):
-            starti = job_index*step
-            endi = min((job_index+1)*step, all_line_number)
-
-            one_job_input_list = []
-
-            for i in range( starti, endi ):
-                one_job_input_list.append( input_line_list[i] )
-
-            job_input_lists.append( one_job_input_list )
-
-        print("Creating pp servers")
-
-        ppservers = ()
-        # Creates jobserver with automatically detected number of workers
-        job_server = pp.Server(ppservers=ppservers)
-
-        print("Done creating servers")
-
-        jobs = []
-        results = []
-
-        print("Starting parallel computation, submitting jobs")
-        for one_job_input_list in job_input_lists: #pay attention to modules from outside
-            jobs.append( job_server.submit(func=compute_corr, args=(num_overlap, self.this_trait_vals, one_job_input_list, self.corr_method), depfuncs=(), modules=("webqtlUtil",)) )
-        print("Done submitting jobs")
-
-        for one_job in jobs:
-            one_result = one_job()
-            self.correlation_data.update(one_result)
-            # one_result = one_job()
-            # results.append( one_result )
-
-        #print("CORRELATION DATA:", self.correlation_data)
-
-        # print("Acquiring results")
-
-        # for one_result in results:
-            # for one_traitinfo in one_result:
-                # allcorrelations.append( one_traitinfo )
-
 def generate_corr_json(corr_results, this_trait, dataset, target_dataset):
     results_list = []
     for i, trait in enumerate(corr_results):
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 077386a3..4bb4d65d 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -23,7 +23,6 @@ from __future__ import absolute_import, print_function, division
 import sys
 # sys.path.append(".")   Never do this in a webserver!
 
-import gc
 import string
 import cPickle
 import os
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 9515d23a..6fda02fd 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -2,7 +2,6 @@
 # Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
 import sys
 from numpy import *
-import scipy as sp                            # SciPy
 import rpy2.robjects as ro                    # R Objects
 import rpy2.rinterface as ri
 
@@ -24,60 +23,38 @@ from utility import helper_functions
 from utility.tools import locate
 
 from rpy2.robjects.packages import importr
-utils = importr("utils")
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
 
 ## Get pointers to some common R functions
 r_library       = ro.r["library"]             # Map the library function
 r_options       = ro.r["options"]             # Map the options function
-r_read_csv      = ro.r["read.csv"]            # Map the read.csv function
-r_dim           = ro.r["dim"]                 # Map the dim function
-r_c             = ro.r["c"]                   # Map the c function
 r_t             = ro.r["t"]                   # Map the t function
-r_cat           = ro.r["cat"]                 # Map the cat function
-r_paste         = ro.r["paste"]               # Map the paste function
-r_unlist        = ro.r["unlist"]              # Map the unlist function
-r_head          = ro.r["head"]                # Map the unlist function
-r_unique        = ro.r["unique"]              # Map the unique function
-r_length        = ro.r["length"]              # Map the length function
 r_unlist        = ro.r["unlist"]              # Map the unlist function
 r_list          = ro.r.list                   # Map the list function
-r_matrix        = ro.r.matrix                 # Map the matrix function
-r_seq           = ro.r["seq"]                 # Map the seq function
-r_table         = ro.r["table"]               # Map the table function
-r_names         = ro.r["names"]               # Map the names function
-r_sink          = ro.r["sink"]                # Map the sink function
-r_is_NA         = ro.r["is.na"]               # Map the is.na function
-r_file          = ro.r["file"]                # Map the file function
 r_png           = ro.r["png"]                 # Map the png function for plotting
 r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
-r_save_image    = ro.r["save.image"]          # Map the save.image function
-r_class         = ro.r["class"]               # Map the class function
-r_save          = ro.r["save"]                # Map the save function
 r_write_table   = ro.r["write.table"]         # Map the write.table function
-r_read_table   = ro.r["read.table"]         # Map the read.table function
-r_as_data_frame = ro.r["as.data.frame"]         # Map the write.table function
 r_data_frame    = ro.r["data.frame"]         # Map the write.table function
 r_as_numeric    = ro.r["as.numeric"]         # Map the write.table function
 
 class CTL(object):
     def __init__(self):
-        print("Initialization of CTL")
+        logger.info("Initialization of CTL")
         #log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
-        #r_sink(log)                                  # Uncomment the r_sink() commands to log output from stdout/stderr to a file
+        #r_sink(log)                                                       # Uncomment the r_sink() commands to log output from stdout/stderr to a file
         #r_sink(log, type = "message")
-        r_library("ctl")                                                  # Load CTL - Should only be done once, since it is quite expensive
+        r_library("ctl")                                                   # Load CTL - Should only be done once, since it is quite expensive
         r_options(stringsAsFactors = False)
-        print("Initialization of CTL done, package loaded in R session")
+        logger.info("Initialization of CTL done, package loaded in R session")
         self.r_CTLscan            = ro.r["CTLscan"]                        # Map the CTLscan function
         self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
         self.r_lineplot           = ro.r["ctl.lineplot"]                   # Map the ctl.lineplot function
-        self.r_CTLsignificant     = ro.r["CTLsignificant"]                 # Map the CTLsignificant function
-        self.r_CTLnetwork         = ro.r["CTLnetwork"]                     # Map the CTLnetwork function
-        self.r_CTLprofiles        = ro.r["CTLprofiles"]                    # Map the CTLprofiles function
         self.r_plotCTLobject      = ro.r["plot.CTLobject"]                 # Map the CTLsignificant function
         self.nodes_list = []
         self.edges_list = []
-        print("Obtained pointers to CTL functions")
+        logger.info("Obtained pointers to CTL functions")
 
     def addNode(self, gt):
         node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name),
@@ -100,20 +77,20 @@ class CTL(object):
         self.edges_list.append(edge_dict)
 
     def run_analysis(self, requestform):
-        print("Starting CTL analysis on dataset")
+        logger.info("Starting CTL analysis on dataset")
         self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
         self.trait_db_list = [x for x in self.trait_db_list if x]
 
-        print("strategy:", requestform.get("strategy"))
+        logger.debug("strategy:", requestform.get("strategy"))
         strategy = requestform.get("strategy")
 
-        print("nperm:", requestform.get("nperm"))
+        logger.debug("nperm:", requestform.get("nperm"))
         nperm = int(requestform.get("nperm"))
 
-        print("parametric:", requestform.get("parametric"))
+        logger.debug("parametric:", requestform.get("parametric"))
         parametric = bool(requestform.get("parametric"))
 
-        print("significance:", requestform.get("significance"))
+        logger.debug("significance:", requestform.get("significance"))
         significance = float(requestform.get("significance"))
 
         # Get the name of the .geno file belonging to the first phenotype
@@ -123,7 +100,7 @@ class CTL(object):
         genofilelocation = locate(dataset.group.name + ".geno", "genotype")
         parser = genofile_parser.ConvertGenoFile(genofilelocation)
         parser.process_csv()
-        print(dataset.group)
+        logger.debug("dataset group: ", dataset.group)
         # Create a genotype matrix
         individuals = parser.individuals
         markers = []
@@ -133,14 +110,14 @@ class CTL(object):
           markers.append(marker["genotypes"])
 
         genotypes = list(itertools.chain(*markers))
-        print(len(genotypes) / len(individuals), "==", len(parser.markers))
+        logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers))
 
         rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames = r_list(markernames, individuals), byrow=True))
 
         # Create a phenotype matrix
         traits = []
         for trait in self.trait_db_list:
-          print("retrieving data for", trait)
+          logger.debug("retrieving data for", trait)
           if trait != "":
             ts = trait.split(':')
             gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1])
@@ -153,7 +130,7 @@ class CTL(object):
 
         rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True))
 
-        print(rPheno)
+        logger.debug(rPheno)
 
         # Use a data frame to store the objects
         rPheno = r_data_frame(rPheno, check_names = False)
@@ -196,10 +173,9 @@ class CTL(object):
         sys.stdout.flush()
 
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
-        print(type(significant))
         if not type(significant) == ri.RNULLType:
           for x in range(len(significant[0])):
-            print(significant[0][x], significant[1][x], significant[2][x])            # Debug to console
+            logger.debug(significant[0][x], significant[1][x], significant[2][x])     # Debug to console
             tsS = significant[0][x].split(':')                                        # Source
             tsT = significant[2][x].split(':')                                        # Target
             gtS = TRAIT.GeneralTrait(name = tsS[0], dataset_name = tsS[1])            # Retrieve Source info from the DB
@@ -214,7 +190,6 @@ class CTL(object):
         self.elements = json.dumps(self.nodes_list + self.edges_list)
 
     def loadImage(self, path, name):
-        print("pre-loading imgage results:", self.results[path])
         imgfile = open(self.results[path], 'rb')
         imgdata = imgfile.read()
         imgB64 = imgdata.encode("base64")
@@ -229,7 +204,7 @@ class CTL(object):
           n = n + 1
 
     def process_results(self, results):
-        print("Processing CTL output")
+        logger.info("Processing CTL output")
         template_vars = {}
         template_vars["results"] = self.results
         template_vars["elements"] = self.elements
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index fb4e19a1..05136ad8 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -94,12 +94,14 @@
                         <th>Sample p(r)</th>
                         <th>Lit r</th>
                         <th>Tissue r</th>
+                        <th>Tissue p(r)</th>
                         {% else %}
                         <th>Sample rho</th>
                         <th>N</th>
                         <th>Sample p(rho)</th>
                         <th>Lit r</th>
                         <th>Tissue rho</th>
+                        <th>Tissue p(rho)</th>
                         {% endif %}
                     {% elif target_dataset.type == "Publish" %}
                         {% if corr_method == 'pearson' %}
@@ -156,8 +158,10 @@
                         {% endif %}
                         {% if trait.tissue_corr == "" or trait.tissue_corr == 0.000 %}
                         <td align="right">--</td>
+                        <td align="right">--</td>
                         {% else %}
                         <td align="right">{{'%0.3f'|format(trait.tissue_corr)}}</td>
+                        <td align="right">{{'%0.3e'|format(trait.tissue_pvalue)}}</td>
                         {% endif %}
                       {% elif target_dataset.type == "Publish" %}
                         <td>{{ trait.description_display }}</td>
@@ -319,7 +323,7 @@
                        title: 'correlation_results',
                        fieldBoundary: '"',
                        exportOptions: {
-                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14]
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]
                        }
                     }
                 ],
@@ -342,7 +346,8 @@
                     { "type": "natural" },
                     { "type": "scientific" },
                     { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural" },
+                    { "type": "scientific" }
                 ],
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
-- 
cgit v1.2.3


From 55cc4c63478de9587e282522540334e5375aebf1 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 13 Apr 2018 15:33:39 +0300
Subject: Use single entry-point for tests

* Remove the run-integration-tests.py, and use the test-website.py as
  the entry point for all tests. This simplifies running the tests for
  the site.
---
 test/requests/run-integration-tests.py | 34 -----------------------------
 test/requests/test-website.py          | 40 ++++++++++++++++++++++++++++++++++
 2 files changed, 40 insertions(+), 34 deletions(-)
 delete mode 100644 test/requests/run-integration-tests.py

diff --git a/test/requests/run-integration-tests.py b/test/requests/run-integration-tests.py
deleted file mode 100644
index 5e816549..00000000
--- a/test/requests/run-integration-tests.py
+++ /dev/null
@@ -1,34 +0,0 @@
-import sys
-from test_login_local import TestLoginLocal
-from test_login_orcid import TestLoginOrcid
-from test_login_github import TestLoginGithub
-from test_registration import TestRegistration
-from unittest import TestSuite, TextTestRunner, TestLoader
-
-test_cases = [
-    TestRegistration
-    , TestLoginLocal
-    , TestLoginGithub
-    , TestLoginOrcid
-]
-
-def suite(gn2_url, es_url):
-    the_suite = TestSuite()
-    for case in test_cases:
-        the_suite.addTests(initTest(case, gn2_url, es_url))
-    return the_suite
-
-def initTest(klass, gn2_url, es_url):
-    loader = TestLoader()
-    methodNames = loader.getTestCaseNames(klass)
-    return [klass(mname, gn2_url, es_url) for mname in methodNames]
-
-def main(gn2_url, es_url):
-    runner = TextTestRunner()
-    runner.run(suite(gn2_url, es_url))
-
-if __name__ == "__main__":
-    if len(sys.argv) < 3:
-        raise Exception("Required arguments missing:\n\tTry running `run-integration-test.py <gn2-url> <es-url>`")
-    else:
-        main(sys.argv[1], sys.argv[2])
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index a33fe708..b2e09bc4 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -12,6 +12,15 @@ from main_web_functionality import check_main_web_functionality
 import link_checker
 import sys
 
+# Imports for integration tests
+from wqflask import app
+from test_login_local import TestLoginLocal
+from test_login_orcid import TestLoginOrcid
+from test_login_github import TestLoginGithub
+from test_registration import TestRegistration
+from test_forgot_password import TestForgotPassword
+from unittest import TestSuite, TextTestRunner, TestLoader
+
 print("Mechanical Rob firing up...")
 
 def run_all(args_obj, parser):
@@ -30,6 +39,33 @@ def print_help(args_obj, parser):
 def dummy(args_obj, parser):
     print("Not implemented yet.")
 
+def integration_tests(args_obj, parser):
+    gn2_url = args_obj.host
+    es_url = app.config.get("ELASTICSEARCH_HOST")+":"+str(app.config.get("ELASTICSEARCH_PORT"))
+    run_integration_tests(gn2_url, es_url)
+
+def initTest(klass, gn2_url, es_url):
+    loader = TestLoader()
+    methodNames = loader.getTestCaseNames(klass)
+    return [klass(mname, gn2_url, es_url) for mname in methodNames]
+
+def integration_suite(gn2_url, es_url):
+    test_cases = [
+        TestRegistration
+        , TestLoginLocal
+        , TestLoginGithub
+        , TestLoginOrcid
+        , TestForgotPassword
+    ]
+    the_suite = TestSuite()
+    for case in test_cases:
+        the_suite.addTests(initTest(case, gn2_url, es_url))
+    return the_suite
+
+def run_integration_tests(gn2_url, es_url):
+    runner = TextTestRunner()
+    runner.run(integration_suite(gn2_url, es_url))
+
 
 desc = """
 This is Mechanical-Rob - an automated web server tester for
@@ -64,6 +100,10 @@ parser.add_argument("-m", "--mapping", dest="accumulate"
                     , action="store_const", const=check_mapping, default=print_help
                     , help="Checks for mapping.")
 
+parser.add_argument("-i", "--integration-tests", dest="accumulate"
+                    , action="store_const", const=integration_tests, default=print_help
+                    , help="Runs integration tests.")
+
 # Navigation tests deactivated since system relies on Javascript
 # parser.add_argument("-n", "--navigation", dest="accumulate"
 #                     , action="store_const", const=check_navigation, default=print_help
-- 
cgit v1.2.3


From 90da7aa5028d64437f3fcaf903075cbda293b575 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 13 Apr 2018 15:39:47 +0300
Subject: Fix logging in tests

* Use the LOG_LEVEL provided by the application settings to enable easy
  control of logging when running tests. It helps avoid a lot of
  verbosity when running tests.
---
 test/requests/parametrized_test.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/requests/parametrized_test.py b/test/requests/parametrized_test.py
index abf98fce..c585e910 100644
--- a/test/requests/parametrized_test.py
+++ b/test/requests/parametrized_test.py
@@ -1,5 +1,6 @@
 import logging
 import unittest
+from wqflask import app
 from elasticsearch import Elasticsearch, TransportError
 
 class ParametrizedTest(unittest.TestCase):
@@ -14,6 +15,7 @@ class ParametrizedTest(unittest.TestCase):
         self.es_cleanup = []
 
         es_logger = logging.getLogger("elasticsearch")
+        es_logger.setLevel(app.config.get("LOG_LEVEL"))
         es_logger.addHandler(
             logging.FileHandler("/tmp/es_TestRegistrationInfo.log"))
         es_trace_logger = logging.getLogger("elasticsearch.trace")
-- 
cgit v1.2.3


From 9396ba78aa204a7f9474c314ca5a519c48ba042c Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Fri, 13 Apr 2018 15:41:31 +0300
Subject: Check email provided on forgot password

* Ensure that the user actually provides an email address when they try
  to use the forgot password feature.
---
 wqflask/wqflask/user_manager.py | 32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5f6c818e..9d09dbf6 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -727,31 +727,33 @@ def logout():
     return response
 
 
-@app.route("/n/forgot_password")
+@app.route("/n/forgot_password", methods=['GET'])
 def forgot_password():
     """Entry point for forgotten password"""
-    return render_template("new_security/forgot_password.html")
+    print("ARGS: ", request.args)
+    errors = {"no-email": request.args.get("no-email")}
+    print("ERRORS: ", errors)
+    return render_template("new_security/forgot_password.html", errors=errors)
 
 @app.route("/n/forgot_password_submit", methods=('POST',))
 def forgot_password_submit():
     """When a forgotten password form is submitted we get here"""
     params = request.form
     email_address = params['email_address']
-    logger.debug("Wants to send password E-mail to ",email_address)
-    es = get_elasticsearch_connection()
-    user_details = get_user_by_unique_column(es, "email_address", email_address)
-    if user_details:
-        ForgotPasswordEmail(user_details["email_address"])
-    # try:
-    #     user = model.User.query.filter_by(email_address=email_address).one()
-    # except orm.exc.NoResultFound:
-    #     flash("Couldn't find a user associated with the email address {}. Sorry.".format(
-    #         email_address))
-    #     return redirect(url_for("login"))
-    # ForgotPasswordEmail(user)
-    return render_template("new_security/forgot_password_step2.html",
+    next_page = None
+    if email_address != "":
+        logger.debug("Wants to send password E-mail to ",email_address)
+        es = get_elasticsearch_connection()
+        user_details = get_user_by_unique_column(es, "email_address", email_address)
+        if user_details:
+            ForgotPasswordEmail(user_details["email_address"])
+            return render_template("new_security/forgot_password_step2.html",
                             subject=ForgotPasswordEmail.subject)
 
+    else:
+        flash("You MUST provide an email", "alert-danger")
+        return redirect(url_for("forgot_password"))
+
 @app.errorhandler(401)
 def unauthorized(error):
     return redirect(url_for('login'))
-- 
cgit v1.2.3


From ea099c2820fbca3f935fb8dc657b88e71224cded Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Sun, 15 Apr 2018 09:53:21 +0300
Subject: Fix issue with indentation

* Ensure the return is at the correct indentation level so that it is
  executed correctly.
---
 wqflask/wqflask/user_manager.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 9d09dbf6..d652f2e9 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -747,8 +747,9 @@ def forgot_password_submit():
         user_details = get_user_by_unique_column(es, "email_address", email_address)
         if user_details:
             ForgotPasswordEmail(user_details["email_address"])
-            return render_template("new_security/forgot_password_step2.html",
-                            subject=ForgotPasswordEmail.subject)
+
+        return render_template("new_security/forgot_password_step2.html",
+                               subject=ForgotPasswordEmail.subject)
 
     else:
         flash("You MUST provide an email", "alert-danger")
-- 
cgit v1.2.3


From e3e98b0533460837c4ea2eac67c4281eb0ba0012 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Sun, 15 Apr 2018 11:48:06 +0300
Subject: Use existing code. Delay after delete.

* Use existing code to get the elasticsearch connection. This should
  prevent tests from failing in case the way connections to
  elasticsearch are made change.
* Delay a while after deleting to allow elasticsearch to re-index the
  data, thus preventing subtle bugs in the test.
---
 test/requests/parametrized_test.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/requests/parametrized_test.py b/test/requests/parametrized_test.py
index c585e910..50003850 100644
--- a/test/requests/parametrized_test.py
+++ b/test/requests/parametrized_test.py
@@ -1,6 +1,7 @@
 import logging
 import unittest
 from wqflask import app
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column
 from elasticsearch import Elasticsearch, TransportError
 
 class ParametrizedTest(unittest.TestCase):
@@ -11,7 +12,7 @@ class ParametrizedTest(unittest.TestCase):
         self.es_url = es_url
 
     def setUp(self):
-        self.es = Elasticsearch([self.es_url])
+        self.es = get_elasticsearch_connection()
         self.es_cleanup = []
 
         es_logger = logging.getLogger("elasticsearch")
@@ -23,7 +24,9 @@ class ParametrizedTest(unittest.TestCase):
             logging.FileHandler("/tmp/es_TestRegistrationTrace.log"))
 
     def tearDown(self):
+        from time import sleep
         self.es.delete_by_query(
             index="users"
             , doc_type="local"
             , body={"query":{"match":{"email_address":"test@user.com"}}})
+        sleep(1)
-- 
cgit v1.2.3


From 9ac9f94f3b1409ae3a47c8a9e890f578a69b020f Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Sun, 15 Apr 2018 11:56:00 +0300
Subject: Add tests for Forgot Password feature

* Add tests to ensure the "Forgot Password" feature works appropriately.
---
 test/requests/test_forgot_password.py | 52 +++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)
 create mode 100644 test/requests/test_forgot_password.py

diff --git a/test/requests/test_forgot_password.py b/test/requests/test_forgot_password.py
new file mode 100644
index 00000000..2bf34c5c
--- /dev/null
+++ b/test/requests/test_forgot_password.py
@@ -0,0 +1,52 @@
+import requests
+from wqflask import user_manager
+from utility.elasticsearch_tools import get_user_by_unique_column
+from parameterized import parameterized
+from parametrized_test import ParametrizedTest
+
+passwork_reset_link = ''
+forgot_password_page = None
+
+class TestForgotPassword(ParametrizedTest):
+
+    def setUp(self):
+        super(TestForgotPassword, self).setUp()
+        self.forgot_password_url = self.gn2_url+"/n/forgot_password_submit"
+        def send_email(to_addr, msg, fromaddr="no-reply@genenetwork.org"):
+            print("CALLING: send_email_mock()")
+            email_data = {
+                "to_addr": to_addr
+                , "msg": msg
+                , "fromaddr": from_addr}
+
+        data = {
+            "es_connection": self.es,
+            "email_address": "test@user.com",
+            "full_name": "Test User",
+            "organization": "Test Organisation",
+            "password": "test_password",
+            "password_confirm": "test_password"
+        }
+        user_manager.basic_info = lambda : { "basic_info": "basic" }
+        user_manager.RegisterUser(data)
+
+    def testWithoutEmail(self):
+        data = {"email_address": ""}
+        error_notification = '<div class="alert alert-danger">You MUST provide an email</div>'
+        result = requests.post(self.forgot_password_url, data=data)
+        self.assertEqual(result.url, self.gn2_url+"/n/forgot_password")
+        self.assertTrue(
+            result.content.find(error_notification) >= 0
+            , "Error message should be displayed but was not")
+
+    def testWithNonExistingEmail(self):
+        # Monkey patching doesn't work, so simply test that getting by email
+        # returns the correct data
+        user = get_user_by_unique_column(self.es, "email_address", "non-existent@domain.com")
+        self.assertTrue(user is None, "Should not find non-existent user")
+
+    def testWithExistingEmail(self):
+        # Monkey patching doesn't work, so simply test that getting by email
+        # returns the correct data
+        user = get_user_by_unique_column(self.es, "email_address", "test@user.com")
+        self.assertTrue(user is not None, "Should find user")
-- 
cgit v1.2.3


From fdd28defcaf3326f3c6b6507124708d83a1da119 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Sun, 15 Apr 2018 11:57:09 +0300
Subject: Deactivate analysis of email_address field

* Prevent elasticsearch from analysing and tokenising the email_address
  field so as to avoid issue with getting back all email addresses with
  the same domain as the one being searched for.
---
 wqflask/utility/elasticsearch_tools.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index d35cb5ee..7d2ee8c9 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -24,6 +24,8 @@ def get_elasticsearch_connection():
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
         }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
+        setup_users_index(es)
+
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)
         es_logger.addHandler(logging.NullHandler())
@@ -33,6 +35,17 @@ def get_elasticsearch_connection():
 
     return es
 
+def setup_users_index(es_connection):
+    if es_connection:
+        index_settings = {
+            "properties": {
+                "email_address": {
+                    "type": "string"
+                    , "index": "not_analyzed"}}}
+
+        es_connection.indices.create(index='users', ignore=400)
+        es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+
 def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
     return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
 
-- 
cgit v1.2.3


From dda4697505aea2cd950533dfb3a0dfb0e66ec018 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 16 Apr 2018 09:00:52 +0000
Subject: Docs on elasticsearch use

---
 README.md                              | 24 ++++++++++++++------
 bin/test-website                       |  2 +-
 wqflask/utility/elasticsearch_tools.py | 41 ++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index 3e7e64d0..59645994 100644
--- a/README.md
+++ b/README.md
@@ -17,25 +17,35 @@ deploy GN2 and dependencies as a self contained unit on any machine.
 The database can be run separately as well as the source tree (for
 developers).  See the [installation docs](doc/README.org).
 
-## Test
+## Run
 
 Once installed GN2 can be run online through a browser interface
 
 ```sh
-./bin/genenetwork2
+genenetwork2
 ```
 
-(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL
-see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
+(default is http://localhost:5003/). For full examples (you'll need to
+set a number of environment variables), including running scripts and
+a Python REPL, see the startup script
+[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
 
+## Testing
 
-We are building up automated
-testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with
+We are building 'Mechanical Rob' automated testing using Python
+[requests](https://github.com/genenetwork/genenetwork2/tree/master/test/lib)
+which can be run with something like
 
 ```sh
-./bin/test-website
+env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
 ```
 
+The GN2_PROFILE is the Guix profile that contains all
+dependencies. The ./bin/genenetwork2 script sets up the environment
+and executes test-website.py in a Python interpreter. The -a switch
+says to run all tests and the URL points to the running GN2 http
+server.
+
 ## Documentation
 
 User documentation can be found
diff --git a/bin/test-website b/bin/test-website
index 5935f016..7fbcfd2f 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -2,6 +2,6 @@
 
 if [ -z $GN2_PROFILE ]; then
   echo "Run request tests with something like"
-  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
   exit 1
 fi
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 7d2ee8c9..4d4a9844 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -1,3 +1,44 @@
+# Elasticsearch support
+#
+# Some helpful commands to view the database:
+#
+# You can test the server being up with
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200
+#
+# List all indices
+#
+#   curl -H 'Content-Type: application/json' 'localhost:9200/_cat/indices?v'
+#
+# To see the users index 'table'
+#
+#   curl http://localhost:9200/users
+#
+# To list all user ids
+#
+# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+# {
+#     "query" : {
+#         "match_all" : {}
+#     },
+#     "stored_fields": []
+# }'
+#
+# To view a record
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+#   {
+#     "query" : {
+#       "match" : { "email_address": "pjotr2017@thebird.nl"}
+#     }
+#   }'
+#
+#
+# To delete the users index and data (dangerous!)
+#
+#   curl -XDELETE -H 'Content-Type: application/json' 'localhost:9200/users'
+
+
 from elasticsearch import Elasticsearch, TransportError
 import logging
 
-- 
cgit v1.2.3


From bc1672f8617c56684ae3aeda7018362e818c46d6 Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 16 Apr 2018 17:25:14 +0300
Subject: Update mappings for Elasticsearch 6.2. Update logger

* Update the indexes mappings to be compatible with the newer
  Elasticsearch 6.2.* series.
  Close the index before updating it, and reopen it after to help with
  the re-indexing of the data.

* Update the error logger to include the exception that was thrown.
---
 wqflask/utility/elasticsearch_tools.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 7d2ee8c9..0dc59d43 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -29,8 +29,8 @@ def get_elasticsearch_connection():
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)
         es_logger.addHandler(logging.NullHandler())
-    except:
-        logger.error("Failed to get elasticsearch connection")
+    except Exception as e:
+        logger.error("Failed to get elasticsearch connection", e)
         es = None
 
     return es
@@ -40,11 +40,12 @@ def setup_users_index(es_connection):
         index_settings = {
             "properties": {
                 "email_address": {
-                    "type": "string"
-                    , "index": "not_analyzed"}}}
+                    "type": "keyword"}}}
 
         es_connection.indices.create(index='users', ignore=400)
+        es_connection.indices.close(index="users")
         es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+        es_connection.indices.open(index="users")
 
 def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
     return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
-- 
cgit v1.2.3


From ebbc8c67c13b44df98ea3c2b355e86f77572543b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 16 Apr 2018 15:02:16 +0000
Subject: login messages improved

---
 wqflask/wqflask/templates/new_security/login_user.html | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 4a857c60..27b20ebf 100644
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -31,16 +31,19 @@
 	    <div>
 	      {% if external_login["github"]: %}
 	      <a href="{{external_login['github']}}" title="Login with GitHub" class="btn btn-info btn-group">Login with Github</a>
+              {% else %}
+              <p>Github login is not available right now</p>
 	      {% endif %}
 
 	      {% if external_login["orcid"]: %}
 	      <a href="{{external_login['orcid']}}" title="Login with ORCID" class="btn btn-info btn-group">Login with ORCID</a>
+              {% else %}
+              <p>ORCID login is not available right now</p>
 	      {% endif %}
 	    </div>
 	    {% else: %}
 	    <div class="alert alert-warning">
-	      <p>You cannot login with external services at this time.<br />
-		Please try again later.</p>
+	      <p>Sorry, you cannot login with Github or ORCID at this time.</p>
 	    </div>
 	    {% endif %}
 	    <hr />
-- 
cgit v1.2.3


From fcc43dd4008692b27935d90fcfd134d6c5d9495e Mon Sep 17 00:00:00 2001
From: Muriithi Frederick Muriuki
Date: Mon, 16 Apr 2018 18:46:29 +0300
Subject: Remove statements that might be causing issues

* I can't swear on this, but it seems the presence of these statements
  was causing elasticsearch to act weird.
---
 wqflask/utility/elasticsearch_tools.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 76dcaebf..cce210c3 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -84,9 +84,7 @@ def setup_users_index(es_connection):
                     "type": "keyword"}}}
 
         es_connection.indices.create(index='users', ignore=400)
-        es_connection.indices.close(index="users")
         es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
-        es_connection.indices.open(index="users")
 
 def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
     return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
-- 
cgit v1.2.3


From 2e2698641d0dc8d8315f48b45c170290641d7b0f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Apr 2018 21:21:25 +0000
Subject: Removed a bunch of unused code from the following files:

marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
---
 wqflask/wqflask/do_search.py                       |  88 --
 wqflask/wqflask/export_traits.py                   |   1 -
 wqflask/wqflask/heatmap/heatmap.py                 | 173 +---
 wqflask/wqflask/interval_analyst/GeneUtil.py       |   2 +-
 .../wqflask/marker_regression/marker_regression.py |  59 +-
 .../marker_regression/marker_regression_gn1.py     | 886 +--------------------
 .../new/javascript/dataset_menu_structure.json     |  67 +-
 wqflask/wqflask/templates/heatmap.html             |   1 -
 8 files changed, 81 insertions(+), 1196 deletions(-)

diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 07c67384..e2a0a479 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -79,38 +79,6 @@ class DoSearch(object):
         else:
             return None
 
-class QuickMrnaAssaySearch(DoSearch):
-    """A general search for mRNA assays"""
-
-    DoSearch.search_types['quick_mrna_assay'] = "QuickMrnaAssaySearch"
-
-    base_query = """SELECT ProbeSet.Name as ProbeSet_Name,
-                ProbeSet.Symbol as ProbeSet_Symbol,
-                ProbeSet.description as ProbeSet_Description,
-                ProbeSet.Chr_num as ProbeSet_Chr_Num,
-                ProbeSet.Mb as ProbeSet_Mb,
-                ProbeSet.name_num as ProbeSet_name_num
-                FROM ProbeSet """
-
-    header_fields = ['Index',
-                     'Record',
-                     'Symbol',
-                     'Location']
-
-    def run(self):
-        """Generates and runs a search for assays across all mRNA expression datasets"""
-
-        logger.debug("Running ProbeSetSearch")
-        query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
-                    ProbeSet.description,
-                    ProbeSet.symbol,
-                    ProbeSet.alias)
-                    AGAINST ('%s' IN BOOLEAN MODE))
-                            """ % (escape(self.search_term[0]))
-
-        return self.execute(query)
-
-
 class MrnaAssaySearch(DoSearch):
     """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
 
@@ -311,54 +279,6 @@ class PhenotypeSearch(DoSearch):
 
         return self.execute(query)
 
-class QuickPhenotypeSearch(PhenotypeSearch):
-    """A search across all phenotype datasets"""
-
-    DoSearch.search_types['quick_phenotype'] = "QuickPhenotypeSearch"
-
-    base_query = """SELECT Species.Name as Species_Name,
-                PublishFreeze.FullName as Dataset_Name,
-                PublishFreeze.Name,
-                PublishXRef.Id,
-                PublishFreeze.createtime as thistable,
-                Publication.PubMed_ID as Publication_PubMed_ID,
-                Phenotype.Post_publication_description as Phenotype_Name
-                FROM Phenotype,
-                    PublishFreeze,
-                    Publication,
-                    PublishXRef,
-                    InbredSet,
-                    Species """
-
-    search_fields = ('Phenotype.Post_publication_description',
-                    'Phenotype.Pre_publication_description',
-                    'Phenotype.Pre_publication_abbreviation',
-                    'Phenotype.Post_publication_abbreviation',
-                    'Phenotype.Lab_code',
-                    'Publication.PubMed_ID',
-                    'Publication.Abstract',
-                    'Publication.Title',
-                    'Publication.Authors')
-
-    def compile_final_query(self, where_clause = ''):
-        """Generates the final query string"""
-
-        query = (self.base_query +
-                 """WHERE %s
-                    PublishXRef.PhenotypeId = Phenotype.Id and
-                    PublishXRef.PublicationId = Publication.Id and
-                    PublishXRef.InbredSetId = InbredSet.Id and
-                    InbredSet.SpeciesId = Species.Id""" % where_clause)
-
-        return query
-
-    def run(self):
-        """Generates and runs a search across all phenotype datasets"""
-
-        query = self.compile_final_query(where_clause = self.get_where_clause())
-
-        return self.execute(query)
-
 class GenotypeSearch(DoSearch):
     """A search within a genotype dataset"""
 
@@ -767,14 +687,6 @@ class MeanSearch(MrnaAssaySearch):
 
         return where_clause
 
-    def get_final_query(self):
-        self.where_clause = self.get_where_clause()
-        logger.debug("where_clause is:", pf(self.where_clause))
-
-        self.query = self.compile_final_query(where_clause = self.where_clause)
-
-        return self.query
-
     def run(self):
         self.where_clause = self.get_where_clause()
         logger.debug("where_clause is:", pf(self.where_clause))
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index f8fce929..ab4c0d7c 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,6 +1,5 @@
 from __future__ import print_function, division
 
-import operator
 import csv
 import xlsxwriter
 import StringIO 
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 56ff11cd..af75d441 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -3,7 +3,6 @@ from __future__ import absolute_import, print_function, division
 import sys
 # sys.path.append(".") Never in a running webserver
 
-import gc
 import string
 import cPickle
 import os
@@ -16,7 +15,6 @@ import resource
 
 import scipy
 import numpy as np
-from scipy import linalg
 
 from pprint import pformat as pf
 
@@ -82,21 +80,16 @@ class Heatmap(object):
             this_trait = trait_db[0]
             this_sample_data = this_trait.data
 
-            #self.sample_data[this_trait.name] = []
             this_trait_vals = []
             for sample in self.all_sample_list:
                 if sample in this_sample_data:
                     this_trait_vals.append(this_sample_data[sample].value)
-                    #self.sample_data[this_trait.name].append(this_sample_data[sample].value)
                 else:
                     this_trait_vals.append('')
-                    #self.sample_data[this_trait.name].append('')
             self.sample_data.append(this_trait_vals)
 
         self.gen_reaper_results()
-        #self.gen_pylmm_results()
 
-        #chrnames = []
         lodnames = []
         chr_pos = []
         pos = []
@@ -106,9 +99,6 @@ class Heatmap(object):
             lodnames.append(trait)
 
         for marker in self.dataset.group.markers.markers:
-            #if marker['chr'] not in chrnames:
-            #    chr_ob = [marker['chr'], "filler"]
-            #    chrnames.append(chr_ob)
             chr_pos.append(marker['chr'])
             pos.append(marker['Mb'])
             markernames.append(marker['name'])
@@ -126,9 +116,6 @@ class Heatmap(object):
             json_data = self.json_data
         )
 
-        print("self.js_data:", self.js_data)
-
-
     def gen_reaper_results(self):
         self.trait_results = {}
         for trait_db in self.trait_list:
@@ -145,172 +132,14 @@ class Heatmap(object):
                     trimmed_samples.append(samples[i])
                     trimmed_values.append(values[i])
 
-            self.lrs_array = genotype.permutation(strains = trimmed_samples,
-                                                       trait = trimmed_values,
-                                                       nperm= self.num_permutations)
-
-            #self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)]
-            #self.significant = self.lrs_array[int(self.num_permutations*0.95-1)]
-
             reaper_results = genotype.regression(strains = trimmed_samples,
                                                  trait = trimmed_values)
 
-
             lrs_values = [float(qtl.lrs) for qtl in reaper_results]
-            print("lrs_values:", lrs_values)
-            #self.dataset.group.markers.add_pvalues(p_values)
 
             self.trait_results[this_trait.name] = []
             for qtl in reaper_results:
                 if qtl.additive > 0:
                     self.trait_results[this_trait.name].append(-float(qtl.lrs))
                 else:
-                    self.trait_results[this_trait.name].append(float(qtl.lrs))
-            #for lrs in lrs_values:
-            #    if
-            #    self.trait_results[this_trait.name].append(lrs)
-
-
-            #this_db_samples = self.dataset.group.samplelist
-            #this_sample_data = this_trait.data
-            ##print("this_sample_data", this_sample_data)
-            #this_trait_vals = []
-            #for index, sample in enumerate(this_db_samples):
-            #    if sample in this_sample_data:
-            #        sample_value = this_sample_data[sample].value
-            #        this_trait_vals.append(sample_value)
-            #    else:
-            #        this_trait_vals.append("x")
-
-            #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals])
-
-            #key = "pylmm:input:" + str(self.temp_uuid)
-            #print("key is:", pf(key))
-
-            #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-
-            #no_val_samples = self.identify_empty_samples(this_trait_vals)
-            #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
-            #genotype_matrix = np.array(trimmed_genotype_data).T
-
-            #print("genotype_matrix:", str(genotype_matrix.tolist()))
-            #print("pheno_vector:", str(pheno_vector.tolist()))
-
-            #params = dict(pheno_vector = pheno_vector.tolist(),
-            #            genotype_matrix = genotype_matrix.tolist(),
-            #            restricted_max_likelihood = True,
-            #            refit = False,
-            #            temp_uuid = str(self.temp_uuid),
-            #
-            #            # meta data
-            #            timestamp = datetime.datetime.now().isoformat(),
-            #            )
-            #
-            #json_params = json.dumps(params)
-            ##print("json_params:", json_params)
-            #Redis.set(key, json_params)
-            #Redis.expire(key, 60*60)
-            #print("before printing command")
-            #
-            #command = 'python lmm.py --key {} --species {}'.format(key,
-            #                                                                                                        "other")
-            #print("command is:", command)
-            #print("after printing command")
-            #
-            #os.system(command)
-            #
-            #json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60)
-
-    def gen_pylmm_results(self):
-        # This function is NOT used. If it is, we should use a shared function with marker_regression.py
-        self.trait_results = {}
-        for trait_db in self.trait_list:
-            this_trait = trait_db[0]
-            #this_db = trait_db[1]
-            self.dataset.group.get_markers()
-
-            this_db_samples = self.dataset.group.samplelist
-            this_sample_data = this_trait.data
-            #print("this_sample_data", this_sample_data)
-            this_trait_vals = []
-            for index, sample in enumerate(this_db_samples):
-                if sample in this_sample_data:
-                    sample_value = this_sample_data[sample].value
-                    this_trait_vals.append(sample_value)
-                else:
-                    this_trait_vals.append("x")
-
-            pheno_vector = np.array([val == "x" and np.nan or float(val) for val in this_trait_vals])
-
-            key = "pylmm:input:" + str(self.temp_uuid)
-            #print("key is:", pf(key))
-
-            genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-
-            no_val_samples = self.identify_empty_samples(this_trait_vals)
-            trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
-            genotype_matrix = np.array(trimmed_genotype_data).T
-
-            #print("genotype_matrix:", str(genotype_matrix.tolist()))
-            #print("pheno_vector:", str(pheno_vector.tolist()))
-
-            params = dict(pheno_vector = pheno_vector.tolist(),
-                        genotype_matrix = genotype_matrix.tolist(),
-                        restricted_max_likelihood = True,
-                        refit = False,
-                        temp_uuid = str(self.temp_uuid),
-
-                        # meta data
-                        timestamp = datetime.datetime.now().isoformat(),
-                        )
-
-            json_params = json.dumps(params)
-            #print("json_params:", json_params)
-            Redis.set(key, json_params)
-            Redis.expire(key, 60*60)
-            print("before printing command")
-
-            command = PYLMM_COMMAND+' --key {} --species {}'.format(key,
-                                                                                                                    "other")
-            print("command is:", command)
-            print("after printing command")
-
-            os.system(command)
-
-            json_results = Redis.blpop("pylmm:results:" + str(self.temp_uuid), 45*60)
-            results = json.loads(json_results[1])
-            p_values = [float(result) for result in results['p_values']]
-            #print("p_values:", p_values)
-            self.dataset.group.markers.add_pvalues(p_values)
-
-            self.trait_results[this_trait.name] = []
-            for marker in self.dataset.group.markers.markers:
-                self.trait_results[this_trait.name].append(marker['lod_score'])
-
-
-    def identify_empty_samples(self, values):
-        no_val_samples = []
-        for sample_count, val in enumerate(values):
-            if val == "x":
-                no_val_samples.append(sample_count)
-        return no_val_samples
-
-    def trim_genotypes(self, genotype_data, no_value_samples):
-        trimmed_genotype_data = []
-        for marker in genotype_data:
-            new_genotypes = []
-            for item_count, genotype in enumerate(marker):
-                if item_count in no_value_samples:
-                    continue
-                try:
-                    genotype = float(genotype)
-                except ValueError:
-                    genotype = np.nan
-                    pass
-                new_genotypes.append(genotype)
-            trimmed_genotype_data.append(new_genotypes)
-        return trimmed_genotype_data
-
-
+                    self.trait_results[this_trait.name].append(float(qtl.lrs))
\ No newline at end of file
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index fda7773f..2c60dd70 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -6,7 +6,7 @@ from flask import Flask, g
 
 #Just return a list of dictionaries
 #each dictionary contains sub-dictionary
-def loadGenes(chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse'):
+def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
 	fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
 	'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
 	'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 3ec61e55..bfb63995 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -16,7 +16,6 @@ import uuid
 
 import rpy2.robjects as ro
 import numpy as np
-from scipy import linalg
 
 import cPickle as pickle
 import itertools
@@ -84,7 +83,6 @@ class MarkerRegression(object):
             self.geno_db_exists = start_vars['geno_db_exists']
         else:
           try:
-            geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno")
             self.geno_db_exists = "True"
           except:
             self.geno_db_exists = "False"
@@ -278,7 +276,6 @@ class MarkerRegression(object):
             )
 
         else:
-            self.cutoff = 2
             self.qtl_results = []
             highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
             for marker in results:
@@ -426,7 +423,6 @@ class MarkerRegression(object):
 
         if self.dataset.group.species == "human":
             p_values, t_stats = self.gen_human_results(pheno_vector, key, temp_uuid)
-            #p_values = self.trim_results(p_values)
 
         else:
             logger.debug("NOW CWD IS:", os.getcwd())
@@ -478,8 +474,6 @@ class MarkerRegression(object):
             json_results = Redis.blpop("pylmm:results:" + temp_uuid, 45*60)
             results = json.loads(json_results[1])
             p_values = [float(result) for result in results['p_values']]
-            #logger.debug("p_values:", p_values[:10])
-            #p_values = self.trim_results(p_values)
             t_stats = results['t_stats']
 
             #t_stats, p_values = lmm.run(
@@ -493,19 +487,8 @@ class MarkerRegression(object):
 
         self.dataset.group.markers.add_pvalues(p_values)
 
-        #self.get_lod_score_cutoff()
-
         return self.dataset.group.markers.markers
 
-    def trim_results(self, p_values):
-        logger.debug("len_p_values:", len(p_values))
-        if len(p_values) > 500:
-            p_values.sort(reverse=True)
-            trimmed_values = p_values[:500]
-
-        return trimmed_values
-
-    #def gen_human_results(self, pheno_vector, tempdata):
     def gen_human_results(self, pheno_vector, key, temp_uuid):
         file_base = locate(self.dataset.group.name,"mapping")
 
@@ -562,18 +545,6 @@ class MarkerRegression(object):
 
         return p_values, t_stats
 
-    def get_lod_score_cutoff(self):
-        logger.debug("INSIDE GET LOD CUTOFF")
-        high_qtl_count = 0
-        for marker in self.dataset.group.markers.markers:
-            if marker['lod_score'] > 1:
-                high_qtl_count += 1
-
-        if high_qtl_count > 1000:
-            return 1
-        else:
-            return 0
-
     def identify_empty_samples(self):
         no_val_samples = []
         for sample_count, val in enumerate(self.vals):
@@ -597,28 +568,6 @@ class MarkerRegression(object):
             trimmed_genotype_data.append(new_genotypes)
         return trimmed_genotype_data
 
-def create_snp_iterator_file(group):
-    """
-    This function is only called by main below
-    """
-    raise Exception("Paths are undefined here")
-    plink_file_base = os.path.join(TMPDIR, group)
-    plink_input = input.plink(plink_file_base, type='b')
-
-    data = dict(plink_input = list(plink_input),
-                numSNPs = plink_input.numSNPs)
-
-    #input_dict = {}
-    #
-    #input_dict['plink_input'] = list(plink_input)
-    #input_dict['numSNPs'] = plink_input.numSNPs
-    #
-
-    snp_file_base = os.path.join(webqtlConfig.SNP_PATH, group + ".snps.gz")
-
-    with gzip.open(snp_file_base, "wb") as fh:
-        pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)
-
 def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type):
     with open(results_path, "w+") as output_file:
         output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
@@ -652,8 +601,6 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
                 output_file.write("\n")
 
 def trim_markers_for_table(markers):
-    num_markers = len(markers)
-
     if 'lod_score' in markers[0].keys():
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
     else:
@@ -664,8 +611,4 @@ def trim_markers_for_table(markers):
         trimmed_sorted_markers = sorted_markers[:200]
         return trimmed_sorted_markers
     else:
-        return sorted_markers
-
-
-if __name__ == '__main__':
-    import cPickle as pickle
+        return sorted_markers
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 81da8976..da713325 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -30,7 +30,7 @@ from math import *
 import piddle as pid
 import sys,os
 import cPickle
-import httplib, urllib
+import httplib
 
 from flask import Flask, g
 
@@ -52,7 +52,6 @@ logger = utility.logger.getLogger(__name__ )
 #########################################
 class MarkerRegression(object):
     cMGraphInterval = 5
-    maxBootStrap = 50
     GRAPH_MIN_WIDTH = 900
     GRAPH_MAX_WIDTH = 10000 # Don't set this too high
     GRAPH_DEFAULT_WIDTH = 1280
@@ -81,8 +80,6 @@ class MarkerRegression(object):
     DRAW_DETAIL_MB = 4
     DRAW_UTR_LABELS_MB = 4
 
-    MIN_PIXELS_BETWEEN_LABELS = 50
-
     qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
     # Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
     # like the ones on the image, though, which is why we don't use it here.
@@ -93,11 +90,8 @@ class MarkerRegression(object):
     NR_INDIVIDUALS = 0
     ## END HaplotypeAnalyst
 
-    ALEX_DEBUG_BOOL_COLORIZE_GENES = 1 # 0=don't colorize, 1=colorize
     ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1
 
-    kWIDTH_DEFAULT=1
-
     kONE_MILLION = 1000000
 
     LODFACTOR = 4.61
@@ -105,18 +99,14 @@ class MarkerRegression(object):
     SNP_COLOR           = pid.orange # Color for the SNP "seismograph"
     TRANSCRIPT_LOCATION_COLOR = pid.mediumpurple
 
-    GENE_FILL_COLOR     = pid.HexColor(0x6666FF)
-    GENE_OUTLINE_COLOR  = pid.HexColor(0x000077)
     BOOTSTRAP_BOX_COLOR = pid.yellow
     LRS_COLOR           = pid.HexColor(0x0000FF)
-    LRS_LINE_WIDTH = 2
     SIGNIFICANT_COLOR   = pid.HexColor(0xEBC7C7)
     SUGGESTIVE_COLOR    = pid.gainsboro
     SIGNIFICANT_WIDTH = 5
     SUGGESTIVE_WIDTH = 5
     ADDITIVE_COLOR_POSITIVE = pid.green
     ADDITIVE_COLOR_NEGATIVE = pid.orange
-    ADDITIVE_COLOR = ADDITIVE_COLOR_POSITIVE
     DOMINANCE_COLOR_POSITIVE = pid.darkviolet
     DOMINANCE_COLOR_NEGATIVE = pid.red
 
@@ -127,15 +117,7 @@ class MarkerRegression(object):
     HAPLOTYPE_RECOMBINATION = pid.darkgray
     ## END HaplotypeAnalyst
 
-    QMARK_EDGE_COLOR    = pid.HexColor(0x718118)
-    QMARK_FILL_COLOR    = pid.HexColor(0xDEE3BB)
-
     TOP_RIGHT_INFO_COLOR = pid.black
-    X_AXIS_LABEL_COLOR  = pid.black #HexColor(0x505050)
-
-    MINI_VIEW_MAGNIFIED_REGION_COLOR = pid.HexColor(0xCC0000)
-    MINI_VIEW_OUTSIDE_REGION_COLOR   = pid.HexColor(0xEEEEEE)
-    MINI_VIEW_BORDER_COLOR           = pid.black
 
     CLICKABLE_WEBQTL_REGION_COLOR     = pid.HexColor(0xF5D3D3)
     CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
@@ -154,18 +136,9 @@ class MarkerRegression(object):
 
     HELP_PAGE_REF = '/glossary.html'
 
-    DRAW_UTR_LABELS=0
-
     def __init__(self, start_vars):
-
-        #templatePage.__init__(self, fd)
-
-        #if not self.openMysql():
-        #    return
         logger.info("Running qtlreaper")
 
-        #helper_functions.get_species_dataset_trait(self, start_vars)
-
         self.temp_uuid = start_vars['temp_uuid']
 
         self.dataset = start_vars['dataset']
@@ -249,17 +222,7 @@ class MarkerRegression(object):
         if 'use_loco' in start_vars.keys():
             self.use_loco = start_vars['use_loco']
 
-        #try:
         self.selectedChr = int(start_vars['selected_chr'])
-        #except:
-        #    self.selectedChr = -1
-
-        #whether include parents and F1 for InbredSet
-        #fd.parentsf14regression = fd.formdata.getvalue('parentsf14regression')
-        #if ((fd.parentsf14regression == 'on') and fd.genotype_2):
-        #    fd.genotype = fd.genotype_2
-        #else:
-        #    fd.genotype = fd.genotype_1
 
         self.strainlist = self.dataset.group.samplelist
         self.genotype = self.dataset.group.read_genotype_file()
@@ -279,7 +242,6 @@ class MarkerRegression(object):
                self.graphWidth  = self.MULT_GRAPH_DEFAULT_WIDTH
 
 ## BEGIN HaplotypeAnalyst
-        #self.haplotypeAnalystChecked = fd.formdata.getvalue('haplotypeAnalystCheck')
         if 'haplotypeAnalystCheck' in start_vars.keys():
             self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck']
         else:
@@ -292,7 +254,6 @@ class MarkerRegression(object):
             self.LRS_LOD = start_vars['LRSCheck']
         else:
             self.LRS_LOD = start_vars['score_type']
-        self.cutoff = start_vars['cutoff']
         self.intervalAnalystChecked = True
         self.draw2X = False
         if 'additiveCheck' in start_vars.keys():
@@ -324,34 +285,8 @@ class MarkerRegression(object):
         except:
             self.lrsMax = 0
 
-        #self.additiveChecked = fd.formdata.getvalue('additiveCheck')
-        #self.dominanceChecked = fd.formdata.getvalue('dominanceCheck')
-        #self.LRS_LOD = fd.formdata.getvalue('LRSCheck', 'LRS')
-        #self.intervalAnalystChecked = fd.formdata.getvalue('intervalAnalystCheck')
-        #self.legendChecked = fd.formdata.getvalue('viewLegend')
-        #self.geneChecked = fd.formdata.getvalue('showGenes')
-        #self.SNPChecked  = fd.formdata.getvalue('showSNP')
-        #self.draw2X = fd.formdata.getvalue('draw2X')
-        #self.lrsMax = float(fd.formdata.getvalue('lrsMax', 0))
-        #self.startMb = fd.formdata.getvalue('startMb', "-1")
-        #self.endMb = fd.formdata.getvalue('endMb', "-1")
-
-        #try:
-        #    self.startMb = float(self.startMb)
-        #    self.endMb = float(self.endMb)
-        #    if self.startMb > self.endMb:
-        #        temp = self.startMb
-        #        self.startMb = self.endMb
-        #        self.endMb = temp
-        #    #minimal distance 10bp
-        #    if self.endMb - self.startMb < 0.00001:
-        #        self.endMb = self.startMb + 0.00001
-        #except:
-        #    self.startMb = self.endMb = -1
-
         #Trait Infos
         self.identification = ""
-        #self.identification = fd.formdata.getvalue('identification', "")
 
         ################################################################
         # Generate Chr list and Retrieve Length Information
@@ -390,7 +325,6 @@ class MarkerRegression(object):
         else:
             self.GraphInterval = self.cMGraphInterval #cM
 
-        self.dataSource = 'editingPage'
         self.traitList = []
         thisTrait = start_vars['this_trait']
         self.traitList.append(thisTrait)
@@ -412,8 +346,6 @@ class MarkerRegression(object):
                        self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
 # default:
            self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
-## for paper:
-        #    #self.graphHeight = self.graphHeight + 1 * self.NR_INDIVIDUALS * self.EACH_GENE_HEIGHT - 180
 ## END HaplotypeAnalyst
 
         ################################################################
@@ -421,12 +353,6 @@ class MarkerRegression(object):
         ################################################################
         self.multipleInterval = len(self.traitList) > 1
         self.qtlresults = start_vars['qtl_results']
-        #errorMessage = self.calculateAllResult(fd)
-        #if errorMessage:
-        #    heading = "Mapping"
-        #    detail = ['%s' % errorMessage]
-        #    self.error(heading=heading,detail=detail)
-        #    return
 
         if self.multipleInterval:
             self.colorCollection = Plot.colorSpectrum(len(self.qtlresults))
@@ -455,9 +381,6 @@ class MarkerRegression(object):
 
         for i, strain in enumerate(self.diffCol):
             self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0]
-            #self.cursor.execute("select Id from Strain where Symbol = %s", strain)
-            #self.diffCol[i] = self.cursor.fetchone()[0]
-        #print self.diffCol
 
         ################################################################
         # GeneCollection goes here
@@ -480,13 +403,13 @@ class MarkerRegression(object):
                     chrName = "X"
                 else:
                     chrName = self.selectedChr
-                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "mouse")
+                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "mouse")
             elif self.dataset.group.species == "rat":
                 if self.selectedChr == 21:
                     chrName = "X"
                 else:
                     chrName = self.selectedChr
-                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, webqtldatabase, "rat")
+                self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "rat")
 
             if self.geneCol and self.intervalAnalystChecked:
                #######################################################################
@@ -495,26 +418,13 @@ class MarkerRegression(object):
                #through set GENEID is None                                           #
                #######################################################################
 
-               #GENEID = fd.formdata.getvalue('GeneId') or None
                GENEID = None
 
-               geneTableContainer = HT.Div(Id="sortable") #Div to hold table
                self.geneTable(self.geneCol, GENEID)
-               #geneTable = self.geneTable(self.geneCol, GENEID)
-               #geneTableContainer.append(geneTable)
-
-               #mainfmName = webqtlUtil.genRandStr("fm_")
-               #tableForm = HT.Form(cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=mainfmName, submit=HT.Input(type='hidden'))
-               #tableForm.append(HT.Input(name='FormID', value='', type='hidden'))
-               #tableForm.append(geneTableContainer)
-
 
         ################################################################
         # Plots goes here
         ################################################################
-        #if self.plotScale != 'physic' or self.multipleInterval:
-        #    showLocusForm =  webqtlUtil.genRandStr("fm_")
-        #else:
         showLocusForm = ""
         intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
         gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
@@ -530,23 +440,6 @@ class MarkerRegression(object):
             intCanvasX2 = pid.PILCanvas(size=(self.graphWidth*2,self.graphHeight*2))
             gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
             intCanvasX2.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename+"X2"), format='png')
-            #DLintImgX2=HT.Href(text='Download',url = '/image/'+self.filename+'X2.png', Class='smallsize', target='_blank')
-
-        #textUrl = self.writeQTL2Text(fd, self.filename)
-
-        ################################################################
-        # Info tables goes here
-        ################################################################
-        #traitInfoTD = self.traitInfoTD(fd)
-
-        #if self.draw2X:
-        #    traitInfoTD.append(HT.P(), DLintImgX2, ' a higher resolution 2X image. ')
-        #else:
-        #    traitInfoTD.append(HT.P())
-        #if textUrl:
-        #    traitInfoTD.append(HT.BR(), textUrl, ' results in tab-delimited text format.')
-        #traitRemapTD = self.traitRemapTD(self.cursor, fd)
-        #topTable = HT.TableLite(HT.TR(traitInfoTD, HT.TD("&nbsp;", width=25), traitRemapTD), border=0, cellspacing=0, cellpadding=0)
 
         ################################################################
         # Outputs goes here
@@ -564,158 +457,15 @@ class MarkerRegression(object):
 
         if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm):
             self.perm_filename = self.drawPermutationHistogram()
-            #perm_text_file = self.permutationTextFile()
 
         ################################################################
         # footnote goes here
         ################################################################
         btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
 
-        #if (self.additiveChecked):
-        #    btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar)
-
         if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
             btminfo.append(HT.BR(), 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
 
-        #if self.permChecked and not self.multipleInterval and 0 < self.nperm:
-        #    TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
-        #    #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
-        #else:
-        TD_LR = HT.TD(HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo), bgColor='#eeeeee', height = 200)
-        #TD_LR = HT.TD(HT.Blockquote(topTable), HT.Blockquote(gifmap, showLocusForm, HT.P(), btminfo, HT.P(), perm_histogram, HT.P(), perm_text_file), bgColor='#eeeeee', height = 200)
-
-
-        if geneTable:
-            iaForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, "main.py?FormID=intervalAnalyst"), enctype='multipart/form-data',
-                name="iaForm", submit=HT.Input(type='hidden'))
-            hddn = {'chromosome':self.genotype[0].name, 'species':self.species,'startMb':self.startMb,'endMb':self.endMb}
-            if self.diffCol:
-                hddn['s1'] = self.diffCol[0]
-                hddn['s2'] = self.diffCol[1]
-            for key in hddn.keys():
-                iaForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
-            iaForm.append(HT.Paragraph("Interval Analyst : Chr %s from %2.6f to %2.6f Mb" % (self.genotype[0].name, self.startMb, self.endMb),
-                HT.Input(name='customize', value='Customize', onClick= "formInNewWindow(this.form);", type='button', Class="button"), Class="subtitle"))
-            TD_LR.append(HT.Blockquote(iaForm))
-            # optionsTable
-            selectall = HT.Href(url="#redirect", onClick="checkAll(document.getElementsByName('%s')[0]);" % mainfmName)
-            selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
-            selectall.append(selectall_img)
-            reset = HT.Href(url="#redirect", onClick="checkNone(document.getElementsByName('%s')[0]); return false;" % mainfmName)
-            reset_img = HT.Image("/images/select_none2_final.jpg", alt="Select None", title="Select None", style="border:none;")
-            reset.append(reset_img)
-            selectinvert = HT.Href(url="#redirect", onClick = "checkInvert(document.getElementsByName('%s')[0]);" % mainfmName)
-            selectinvert_img = HT.Image("/images/invert_selection2_final.jpg", name="selectinvert", alt="Invert Selection", title="Invert Selection", style="border:none;")
-            selectinvert.append(selectinvert_img)
-            addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (RISet, mainfmName))
-            addselect_img = HT.Image("/images/add_collection1_final.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
-            addselect.append(addselect_img)
-            geneweaver = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'ODEIM');" % mainfmName)
-            geneweaver_img = HT.Image("/images/ODE_logo_final.jpg", name="GeneWeaver", alt="Gene Weaver", title="Gene Weaver", style="border:none")
-            geneweaver.append(geneweaver_img)
-            optionsTable = HT.TableLite()
-            optionsTable.append(HT.TR(
-                HT.TD(selectall, width="77", style="text-align:center"),
-                HT.TD(reset, width="77", style="text-align:center"),
-                HT.TD(selectinvert, width="77", style="text-align:center"),
-                HT.TD(geneweaver, width="77", style="text-align:center"),
-                ))
-            optionsTable.append(HT.TR(
-                HT.TD("Select", style="text-align:center"),
-                HT.TD("Deselect", style="text-align:center"),
-                HT.TD("Invert", style="text-align:center"),
-                HT.TD("Gene Weaver", style="text-align:center"),
-                ))
-            TD_LR.append(HT.Blockquote(optionsTable))
-            # geneTableContainer
-            TD_LR.append(HT.Blockquote(tableForm))
-
-        self.body = TD_LR
-
-        #self.dict['body'] = TD_LR
-        #self.dict['title'] = "Mapping"
-
-
-    def writeQTL2Text(self, filename):
-        if self.multipleInterval:
-            return ""
-        #_dominance = (self.genotype.type == 'intercross')
-        _Mb = self.genotype.Mbmap
-
-        ###Write to text file
-        fpText = open(os.path.join(webqtlConfig.TMPDIR, filename) + '.txt','wb')
-
-        fpText.write("Source: WebQTL, The GeneNetwork (%s)\n" % webqtlConfig.PORTADDR)
-        #
-        fpText.write("Site: GN\n")
-        fpText.write("Page: Map Viewer\n")
-        fpText.write(time.strftime("Date and Time (US Center): %b %d, %Y at %I.%M %p\n", time.localtime()))
-        fpText.write("Trait ID: %s\n" % self.this_trait.name)
-        fpText.write("Suggestive LRS = %0.2f\n" % self.suggestive)
-        fpText.write("Significant LRS = %0.2f\n" % self.significant)
-        """
-        if self.this_trait.symbol and self.this_trait.chr and self.this_trait.mb:
-                writeSymbol, writeChromosome, writeMb = self.this_trait.symbol, self.this_trait.chr, self.this_trait.mb
-        else:
-                writeSymbol, writeChromosome, writeMb = (" ", " ", " ")
-        fpText.write("Gene Symbol: %s\n" % writeSymbol)
-        fpText.write("Location: Chr %s @ %s Mb\n" % (writeChromosome, writeMb))
-        #selectedChr = self.indexToChrName(int(fd.formdata.getvalue('chromosomes', -1)))
-        #fpText.write("Chromosome: %s\n" % selectedChr)
-        fpText.write("Region: %0.6f-%0.6f Mb\n\n" % (self.startMb, self.endMb))
-        """
-
-        if hasattr(self, 'LRSArray'):
-            if _dominance:
-                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\tDominance\n')
-            else:
-                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tP-value\tAdditive\n')
-        else:
-            if _dominance:
-                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\tDominance\n')
-            else:
-                fpText.write('Chr\tLocus\tcM\tMb\tLRS\tAdditive\n')
-
-        i = 0
-        for marker in self.qtlresults:
-            if _Mb:
-                locusMb = '%2.3f' % marker['Mb']
-            else:
-                locusMb = 'N/A'
-
-            if hasattr(self, 'LRSArray'):
-                if start_vars['score_type'] == "LRS":
-                    lrs_lod = marker['lrs_value']
-                else:
-                    lrs_lod = marker['lod_score']
-
-                P_value = self.calculatePValue(lrs_lod, self.perm_output)
-
-                #if _dominance:
-                #    fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
-                #            qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, P_value,  qtlresult.additive, qtlresult.dominance))
-                #else:
-                if P_value:
-                    fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\n" %(marker['chr'], \
-                        marker['name'], marker['cM'], locusMb, lrs_lod, P_value))
-                else:
-                    fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%s\n" %(marker['chr'], \
-                        marker['name'], marker['cM'], locusMb , lrs_lod, '-'))
-            else:
-                #if _dominance:
-                #    fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\t%2.3f\t%2.3f\n" %(qtlresult.locus.chr, \
-                #            qtlresult.locus.name, qtlresult.locus.cM, locusMb , qtlresult.lrs, qtlresult.additive, qtlresult.dominance))
-                #else:
-                fpText.write("%s\t%s\t%2.3f\t%s\t%2.3f\n" %(marker['chr'], \
-                        marker['name'], marker['cM'], locusMb , lrs_lod))
-
-            i += 1
-
-        fpText.close()
-        textUrl = '/tmp/'+filename+'.txt'
-        #textUrl = HT.Href(text = 'Download', url= '/tmp/'+filename+'.txt', target = "_blank", Class='smallsize')
-        return textUrl
-
     def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
         #calculating margins
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -742,8 +492,6 @@ class MarkerRegression(object):
         cHeight = canvas.size[1]
         plotWidth = cWidth - xLeftOffset - xRightOffset
         plotHeight = cHeight - yTopOffset - yBottomOffset
-        startPixelX = xLeftOffset
-        endPixelX   = (xLeftOffset + plotWidth)
 
         #Drawing Area Height
         drawAreaHeight = plotHeight
@@ -767,7 +515,6 @@ class MarkerRegression(object):
 
         #Image map
         gifmap = HT.Map(name = "WebQTLImageMap")
-        #gifmap = None
 
         newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
         # Draw the alternating-color background first and get plotXScale
@@ -946,15 +693,6 @@ class MarkerRegression(object):
             this_chr = str(self.ChrList[self.selectedChr][0])
         else:
             this_chr = str(self.ChrList[self.selectedChr][1]+1)
-        # for i, qtlresult in enumerate(self.qtlresults):
-            # if Chr == this_chr:
-                # if Mb < self.startMb or Mb > self.endMb:
-                    # return
-                # else:
-                    # locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
-                    # break
-            # elif self.selectedChr == -1: 
-                # if str(qtlresult['chr']) != Chr:
 
         if self.plotScale == 'physic':
             if self.selectedChr > -1:
@@ -1012,7 +750,6 @@ class MarkerRegression(object):
             canvas.drawPolygon(((leftOffset+6, startPosY-6), (leftOffset, startPosY+6), (leftOffset+12, startPosY+6)), edgeColor=pid.black, fillColor=self.TRANSCRIPT_LOCATION_COLOR, closed=1)
             canvas.drawString("Sequence Site", (leftOffset+15), (startPosY+5), smallLabelFont, self.TOP_RIGHT_INFO_COLOR)
 
-
     def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
             return
@@ -1052,7 +789,7 @@ class MarkerRegression(object):
                     snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
                     canvas.drawLine(i, drawSNPLocationY+(snpDensity)*zoom, i, drawSNPLocationY-(snpDensity)*zoom, color=self.SNP_COLOR, width=1)
 
-    def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
+    def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
         nameWidths = []
         yPaddingTop = 10
         colorFont=pid.Font(ttf="trebuc",size=12,bold=1)
@@ -1080,14 +817,12 @@ class MarkerRegression(object):
             canvas.drawRect(rightShift,yPaddingTop+kstep*15, rectWidth+rightShift,yPaddingTop+10+kstep*15, fillColor=thisLRSColor)
             canvas.drawString(name,rectWidth+2+rightShift,yPaddingTop+10+kstep*15,font=colorFont,color=pid.black)
             if thisTrait.db:
-
                 COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
                 HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
                 Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
                 gifmap.areas.append(Areas)
 
-
-    def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1, locLocation= None):
+    def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
         plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
         plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
@@ -1131,9 +866,6 @@ class MarkerRegression(object):
             startPosX = xLeftOffset
             canvas.drawLine(startPosX, startPosY, startPosX + 32, startPosY, color=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
             canvas.drawLine(startPosX, startPosY + stepPosY, startPosX + 32, startPosY + stepPosY, color=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
-            lod = 1
-            if self.LRS_LOD == 'LOD':
-                lod = self.LODFACTOR
             canvas.drawString('Significant %s = %2.2f' % (self.LRS_LOD, self.significant),xLeftOffset+42,startPosY +5,font=labelFont,color=pid.black)
             canvas.drawString('Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),xLeftOffset+42,startPosY + 5 +stepPosY,font=labelFont,color=pid.black)
 
@@ -1156,7 +888,6 @@ class MarkerRegression(object):
                 string3 = cofactor_names
             else:
                 string2 += 'no cofactors'
-                string3 = ''
         elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
             string2 = 'Using R/qtl mapping method with '
             if self.controlLocus and self.doControl != "false":
@@ -1198,9 +929,6 @@ class MarkerRegression(object):
 
         yPaddingTop = yTopOffset
 
-        displayStartInBases = startMb*self.kONE_MILLION
-        displayEndInBases = endMb*self.kONE_MILLION
-
         for gIndex, theGO in enumerate(self.geneCol):
             geneNCBILink = 'http://www.ncbi.nlm.nih.gov/gene?term=%s'
             if self.dataset.group.species == "mouse":
@@ -1215,7 +943,6 @@ class MarkerRegression(object):
                 cdsStart = theGO['cdsStart']
                 cdsEnd = theGO['cdsEnd']
                 accession = theGO['NM_ID']
-                geneId = theGO['GeneID']
                 geneSymbol = theGO["GeneSymbol"]
                 strand = theGO["Strand"]
                 exonCount = theGO["exonCount"]
@@ -1233,10 +960,7 @@ class MarkerRegression(object):
                     geneStartPix = xLeftOffset; # clip the first in-range gene
 
                 #color the gene based on SNP density
-
-
                 #found earlier, needs to be recomputed as snps are added
-
                 #always apply colors now, even if SNP Track not checked - Zach 11/24/2010
 
                 densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
@@ -1269,7 +993,6 @@ class MarkerRegression(object):
                 txEnd = theGO["TxEnd"]
                 cdsStart = theGO["TxStart"]
                 cdsEnd = theGO["TxEnd"]
-                geneId = theGO["GeneID"]
                 geneSymbol = theGO["GeneSymbol"]
                 strand = theGO["Strand"]
                 exonCount = 0
@@ -1298,11 +1021,7 @@ class MarkerRegression(object):
 
             #Draw Genes
             geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
-
-            if 1:#drawClickableRegions:
-                geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
-            else:
-                geneYLocation += self.BAND_SPACING
+            geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
 
             #draw the detail view
             if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
@@ -1310,7 +1029,6 @@ class MarkerRegression(object):
                 arrowColor = pid.Color(0.7, 0.7, 0.7)
 
                 #draw the line that runs the entire length of the gene
-                #canvas.drawString(str(geneStartPix), 300, 400)
                 canvas.drawLine(geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom, color=outlineColor, width=1)
 
                 #draw the arrows
@@ -1360,7 +1078,6 @@ class MarkerRegression(object):
                         utrStartPix = xLeftOffset + plotWidth
                     #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
 
-                    #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
                     if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
                         if strand == "-":
                             labelText = "3'"
@@ -1382,7 +1099,6 @@ class MarkerRegression(object):
                         utrStartPix = xLeftOffset + plotWidth
                     #canvas.drawRect(utrStartPix, geneYLocation, utrEndPix, (geneYLocation+self.EACH_GENE_HEIGHT*zoom), edgeColor=utrColor, fillColor =utrColor)
 
-                    #if self.DRAW_UTR_LABELS and self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
                     if self.endMb - self.startMb <= self.DRAW_UTR_LABELS_MB:
                         if strand == "-":
                             labelText = "5'"
@@ -1403,8 +1119,6 @@ class MarkerRegression(object):
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
             return
 
-        fpText = open(os.path.join(webqtlConfig.TMPDIR, "hallo") + '.txt','wb')
-
         clickableRegionLabelFont=pid.Font(ttf="verdana", size=9, bold=0)
 
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -1412,13 +1126,9 @@ class MarkerRegression(object):
         plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
         yZero = canvas.size[1] - yBottomOffset
         fontZoom = zoom
-        widthMultiplier = 1
 
         yPaddingTop = yTopOffset
 
-        exprdrawn = 0
-
-        #thisTrait = self.traitList[0]
         thisTrait = self.this_trait
         _strains, _vals, _vars, _aliases = thisTrait.export_informative()
 
@@ -1428,7 +1138,6 @@ class MarkerRegression(object):
                 temp = GeneralObject(name=_strains[ii], value=_val)
                 smd.append(temp)
 
-
         smd.sort(lambda A, B: cmp(A.value, B.value))
         smd.reverse()
 
@@ -1453,13 +1162,9 @@ class MarkerRegression(object):
                 drawit = 0;
 
             if drawit == 1:
-
                 if self.genotype[0][i].name != " - " :
-
                     plotRight = geneEndPix + 4
 
-
-
 #### end find out PlotRight
 
         firstGene = 1
@@ -1514,11 +1219,7 @@ class MarkerRegression(object):
                 #Draw Genes
 
                 geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
-
-                if 1:#drawClickableRegions:
-                    geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
-                else:
-                    geneYLocation += self.BAND_SPACING
+                geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
 
                 if self.genotype[0][i].name != " - " :
 
@@ -1605,8 +1306,6 @@ class MarkerRegression(object):
                 canvas.drawString("%s" % (samplelist[j]), (xLeftOffset + plotWidth + 10) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
                 canvas.drawString("%2.2f" % (expr), (xLeftOffset + plotWidth + 60) , geneYLocation+8+2*ind*self.EACH_GENE_HEIGHT*zoom, font=pid.Font(ttf="verdana", size=12, bold=0), color=pid.black)
 
-        fpText.close()
-
 ## END HaplotypeAnalyst
 
     def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1650,7 +1349,6 @@ class MarkerRegression(object):
                 xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
 
                 WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
-                bandWidth = xBrowse2 - xBrowse1
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
@@ -1688,7 +1386,6 @@ class MarkerRegression(object):
             traitFont = pid.Font(ttf="verdana", size=14, bold=0)
             chrX = xLeftOffset + plotWidth - 2 - canvas.stringWidth("Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)
             canvas.drawString("Chr %s" % self.ChrList[self.selectedChr][0], chrX, ensemblPaddingTop-5, font=chrFont, color=pid.gray)
-            traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
             # end of drawBrowserClickableRegions
         else:
             #draw the gray text
@@ -1696,7 +1393,6 @@ class MarkerRegression(object):
             traitFont = pid.Font(ttf="verdana", size=14, bold=0)
             chrX = xLeftOffset + (plotWidth - canvas.stringWidth("Chr %s" % currentChromosome, font=chrFont))/2
             canvas.drawString("Chr %s" % currentChromosome, chrX, 32, font=chrFont, color=pid.gray)
-            traitX = chrX - 28 - canvas.stringWidth("database", font=traitFont)
             # end of drawBrowserClickableRegions
         pass
 
@@ -1723,13 +1419,11 @@ class MarkerRegression(object):
         xAxisLabelColor = pid.black
         fontHeight = 12*fontZoom # How tall the font that we're using is
         spacingFromLabelToAxis = 5
-        spacingFromLineToLabel = 3
 
         if self.plotScale == 'physic':
             strYLoc = yZero + spacingFromLabelToAxis + canvas.fontHeight(MBLabelFont)
             ###Physical single chromosome view
             if self.selectedChr > -1:
-                graphMbWidth  = endMb - startMb
                 XScale = Plot.detScale(startMb, endMb)
                 XStart, XEnd, XStep = XScale
                 if XStep < 8:
@@ -1755,7 +1449,6 @@ class MarkerRegression(object):
                         canvas.drawString(labelStr, drawStringXc, strYLoc, font=MBLabelFont, color=xAxisLabelColor, angle=0)
                     else:
                         canvas.drawLine(Xc, yZero, Xc, yZero+xMinorTickHeight, color=xAxisTickMarkColor, width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
-                    # end else
 
             ###Physical genome wide view
             else:
@@ -1785,7 +1478,6 @@ class MarkerRegression(object):
             preLpos = -1
             distinctCount = 0.0
 
-            #if len(self.genotype) > 1:
             if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
                 for i, _chr in enumerate(self.genotype):
                     thisChr = []
@@ -1894,12 +1586,6 @@ class MarkerRegression(object):
         #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment.
         #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter.
 
-        #ZS: I'm not sure what this if statement is supposed to do. It appears to work correctly for both LOD and LRS if I just set lodm to 1.0
-        # if self.LRS_LOD == 'LRS':
-            # lodm = self.LODFACTOR
-        # else:
-            # lodm = 1.0
-
         #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
         if self.lrsMax <= 0:  #sliding scale
             if "lrs_value" in self.qtlresults[0]:
@@ -2016,10 +1702,6 @@ class MarkerRegression(object):
         else:
             if self.additiveChecked:
                 additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults))
-            #if INTERCROSS:
-            #    dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
-            #else:
-            #    dominanceMax = -1
             lrsEdgeWidth = 2
 
         if zoom == 2:
@@ -2038,7 +1720,6 @@ class MarkerRegression(object):
         startPosX = xLeftOffset
         for i, qtlresult in enumerate(self.qtlresults):
             m = 0
-            #startPosX = xLeftOffset
             thisLRSColor = self.colorCollection[0]
 
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
@@ -2085,25 +1766,13 @@ class MarkerRegression(object):
                     startPosX += newStartPosX
                     oldStartPosX = newStartPosX
 
-            #startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
-
-            #for j, _chr in enumerate(self.genotype):
             #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
             if self.plotScale == "physic":
                 this_chr = str(self.ChrList[self.selectedChr][0])
             else:
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
-                #AdditiveCoordXY = []
-                #DominanceCoordXY = []
-                #for k, _locus in enumerate(_chr):
                 Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-                #if self.plotScale == 'physic':
-                    #Xc = startPosX + (_locus.Mb-startMb)*plotXScale
-                    #Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-                #else:
-                    #Xc = startPosX + (_locus.cM-_chr[0].cM)*plotXScale
-                    #Xc = startPosX + (qtlresult['cM']-qtlresult[0]['cM'])*plotXScale
 
                 # updated by NL 06-18-2011:
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
@@ -2127,11 +1796,6 @@ class MarkerRegression(object):
                             Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max
                         else:
                             Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
-                #if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
-                #if self.qtlresults[j]['lrs_value'] > 460 or self.qtlresults[j]['lrs_value']=='inf':
-                #    Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
-                #else:
-                #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
 
                 if self.manhattan_plot == True:
                     point_color = pid.black
@@ -2144,11 +1808,8 @@ class MarkerRegression(object):
                        additiveMax = 0.000001
                    Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax
                    AdditiveCoordXY.append((Xc, Yc))
-                # if not self.multipleInterval and INTERCROSS and self.additiveChecked:
-                   # Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax
-                   # DominanceCoordXY.append((Xc, Yc))
+
                 m += 1
-                #canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
         if self.manhattan_plot != True:
             canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
@@ -2220,7 +1881,6 @@ class MarkerRegression(object):
             additiveScale = Plot.detScaleOld(0,additiveMax)
             additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
             additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
-            maxAdd =  additiveScale[1]
             addPlotScale = AdditiveHeightThresh/additiveMax
 
             additiveAxisList.append(additiveScale[1])
@@ -2312,298 +1972,6 @@ class MarkerRegression(object):
 
         return plotXScale
 
-    def calculateAllResult(self, fd):
-
-        weightedRegression = fd.formdata.getvalue('applyVarianceSE')
-
-        self.genotype = self.genotype.addinterval()
-        resultSlice = []
-        controlGeno = []
-
-        if self.multipleInterval:
-            self.suggestive = 0
-            self.significant = 0
-            if self.selectedChr > -1:
-                self.genotype.chromosome = [self.genotype[self.selectedChr]]
-        else:
-            #single interval mapping
-            try:
-                self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
-                self.significant = float(fd.formdata.getvalue('permSignificance'))
-            except:
-                self.suggestive = None
-                self.significant = None
-
-            _strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
-
-            if webqtlUtil.ListNotNull(_vars):
-                pass
-            else:
-                weightedRegression = 0
-                _strains, _vals, _vars = self.traitList[0].exportInformative()
-
-            ##locate genotype of control Locus
-            if self.controlLocus:
-                controlGeno2 = []
-                _FIND = 0
-                for _chr in self.genotype:
-                    for _locus in _chr:
-                        if _locus.name == self.controlLocus:
-                            controlGeno2 = _locus.genotype
-                            _FIND = 1
-                            break
-                    if _FIND:
-                        break
-                if controlGeno2:
-                    _prgy = list(self.genotype.prgy)
-                    for _strain in _strains:
-                        _idx = _prgy.index(_strain)
-                        controlGeno.append(controlGeno2[_idx])
-                else:
-                    return "The control marker you selected is not in the genofile."
-
-            if weightedRegression:
-                self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals,
-                        variance = _vars, nperm=self.nperm)
-            else:
-                self.perm_output = self.genotype.permutation(strains = _strains, trait = _vals,
-                        nperm=self.nperm)
-
-            if self.significant and self.suggestive:
-                pass
-            else:
-                if self.nperm < 100:
-                    self.suggestive = 0
-                    self.significant = 0
-                else:
-                    self.suggestive = self.perm_output[int(self.nperm*0.37-1)]
-                    self.significant = self.perm_output[int(self.nperm*0.95-1)]
-
-            #calculating bootstrap
-            #from now on, genotype could only contain a single chromosome
-            #permutation need to be performed genome wide, this is not the case for bootstrap
-
-            #due to the design of qtlreaper, composite regression need to be performed genome wide
-            if not self.controlLocus and self.selectedChr > -1:
-                self.genotype.chromosome = [self.genotype[self.selectedChr]]
-            elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
-                lociPerChr = map(len, self.genotype)
-                resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
-                resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
-            else:
-                pass
-
-        #calculate QTL for each trait
-        self.qtlresults = []
-
-        for thisTrait in self.traitList:
-            _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
-            if self.controlLocus:
-                if weightedRegression:
-                    qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
-                                    variance = _vars, control = self.controlLocus)
-                else:
-                    qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
-                            control = self.controlLocus)
-                if resultSlice:
-                    qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
-            else:
-                if weightedRegression:
-                    qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
-                                    variance = _vars)
-                else:
-                    qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
-
-            self.qtlresults.append(qtlresult)
-
-        if not self.multipleInterval:
-            if self.controlLocus and self.selectedChr > -1:
-                self.genotype.chromosome = [self.genotype[self.selectedChr]]
-
-            if self.bootChecked:
-                if controlGeno:
-                    self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
-                            control = controlGeno, nboot=fd.nboot)
-                elif weightedRegression:
-                    self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
-                            variance = _vars, nboot=fd.nboot)
-                else:
-                    self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
-                            nboot=fd.nboot)
-            else:
-                self.bootResult = []
-
-    def calculatePValue (self, query_LRS, permutation_LRS_array):
-        query_index = len(permutation_LRS_array)
-        for i, one_permutation_LRS in enumerate(permutation_LRS_array):
-            if one_permutation_LRS >= query_LRS:
-                query_index = i
-                break
-        try:
-            P_value = float(len(permutation_LRS_array) - query_index) / len(permutation_LRS_array)
-        except:
-            P_value = ''
-        return P_value
-
-    def helpButton(self, anchor):
-        return HT.Href(self.HELP_PAGE_REF + '#%s' % anchor, self.qmarkImg, target=self.HELP_WINDOW_NAME)
-
-
-    def traitRemapTD(self, cursor, fd):
-        chrList = HT.Select(name="chromosomes", data=self.ChrList, selected=[self.selectedChr],
-                onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
-
-        physicOnly = HT.Span(' *', Class="cr")
-
-        showSNPCheck   = HT.Input(type='checkbox', Class='checkbox', name='showSNP', value='ON', checked=self.SNPChecked)
-        showSNPText    = HT.Span('SNP Track ', self.helpButton("snpSeismograph"), Class="fs12 fwn")
-
-        showGenesCheck = HT.Input(type='checkbox', Class='checkbox', name='showGenes', value='ON', checked=self.geneChecked)
-        showGenesText  = HT.Span('Gene Track', Class="fs12 fwn")
-
-        showIntervalAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='intervalAnalystCheck', value='ON', checked=self.intervalAnalystChecked)
-        showIntervalAnalystText = HT.Span('Interval Analyst', Class="fs12 fwn")
-## BEGIN HaplotypeAnalyst
-
-        showHaplotypeAnalystCheck = HT.Input(type='checkbox', Class='checkbox', name='haplotypeAnalystCheck', value='ON', checked=self.haplotypeAnalystChecked)
-        showHaplotypeAnalystText = HT.Span('Haplotype Analyst', Class="fs12 fwn")
-## END HaplotypeAnalyst
-
-        leftBox = HT.Input(type="text", name="startMb", size=10)
-        rightBox = HT.Input(type="text", name="endMb", size=10)
-        if self.selectedChr > -1 and self.plotScale=='physic':
-            leftBox.value = self.startMb
-            rightBox.value = self.endMb
-
-        scaleBox = HT.Select(name="scale", onChange="chrLength(this.form.chromosomes.value, this.form.scale.value, this.form, self.ChrLengthMbList);")
-        scaleBox.append(("Genetic", "morgan"))
-        if fd.genotype.Mbmap:
-            scaleBox.append(("Physical", "physic"))
-        scaleBox.selected.append(self.plotScale)
-
-        permBox = HT.Input(type="checkbox", name="permCheck", value='ON', checked=self.permChecked, Class="checkbox")
-        permText = HT.Span("Permutation Test ", self.helpButton("Permutation"), Class="fs12 fwn")
-        bootBox = HT.Input(type="checkbox", name="bootCheck", value='ON', checked=self.bootChecked, Class="checkbox")
-        bootText = HT.Span("Bootstrap Test ", self.helpButton("bootstrap"), Class="fs12 fwn")
-        additiveBox = HT.Input(type="checkbox", name="additiveCheck", value='ON', checked=self.additiveChecked, Class="checkbox")
-        additiveText = HT.Span("Allele Effects ", self.helpButton("additive"), Class="fs12 fwn")
-        dominanceBox = HT.Input(type="checkbox", name="dominanceCheck", value='ON', checked=self.dominanceChecked, Class="checkbox")
-        dominanceText = HT.Span("Dominance Effects ", self.helpButton("Dominance"), Class="fs12 fwn")
-
-        lrsRadio = HT.Input(type="radio", name="LRSCheck", value='LRS', checked = (self.LRS_LOD == "LRS"))
-        lodRadio = HT.Input(type="radio", name="LRSCheck", value='LOD', checked = (self.LRS_LOD != "LRS"))
-        lrsMaxBox = HT.Input(type="text", name="lrsMax", value=self.lrsMax, size=3)
-        widthBox = HT.Input(type="text", name="graphWidth", size=5, value=str(self.graphWidth))
-        legendBox = HT.Input(type="checkbox", name="viewLegend", value='ON', checked=self.legendChecked, Class="checkbox")
-        legendText = HT.Span("Legend", Class="fs12 fwn")
-
-        draw2XBox = HT.Input(type="checkbox", name="draw2X", value='ON', Class="checkbox")
-        draw2XText = HT.Span("2X Plot", Class="fs12 fwn")
-
-        regraphButton = HT.Input(type="button", Class="button", onClick="javascript:databaseFunc(this.form,'showIntMap');", value="Remap")
-        controlsForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype="multipart/form-data", name="changeViewForm", submit=HT.Input(type='hidden'))
-        controlsTable = HT.TableLite(border=0)
-        innerControlsTable = HT.TableLite(border=0)
-        if self.selectedChr == -1:
-            minimumGraphWidth = self.MULT_GRAPH_MIN_WIDTH
-        else:
-            minimumGraphWidth = self.GRAPH_MIN_WIDTH
-        innerControlsTable.append(
-                HT.TR(HT.TD("Chr: ", Class="fs12 fwb ffl"),HT.TD(chrList, scaleBox, regraphButton)),
-                HT.TR(HT.TD("View: ", Class="fs12 fwb ffl"),HT.TD(leftBox, " to ", rightBox, "Mb", physicOnly, NOWRAP="on")),
-                HT.TR(HT.TD("Units: ", Class="fs12 fwb ffl"), HT.TD(lrsRadio, "LRS ", lodRadio, "LOD ", self.helpButton("LOD"))),
-                HT.TR(HT.TD(" ", Class="fs12 fwb ffl"), HT.TD(lrsMaxBox, "units on Y-axis (0 for default)", Class="fs11 fwn")),
-                HT.TR(HT.TD("Width: ", Class="fs12 fwb ffl"), HT.TD(widthBox, "pixels (minimum=%d)" % minimumGraphWidth, Class="fs11 fwn "))
-        )
-        #whether SNP
-        # comment this, because this will make caculation very slow.
-        #cursor.execute("Select Species.Id from SnpAll, Species where SnpAll.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
-        #SNPorNot = cursor.fetchall()
-        SNPorNot = True
-        #Whether Gene
-        cursor.execute("Select Species.Id from GeneList, Species where GeneList.SpeciesId = Species.Id and Species.Name = %s limit 1", self.species)
-        GeneorNot = cursor.fetchall()
-
-        if self.multipleInterval:
-            optionPanel = HT.TD(valign="top", NOWRAP="on")
-        else:
-            optionPanel = HT.TD(permBox, permText, HT.BR(), bootBox, bootText, HT.BR(), additiveBox, additiveText, HT.BR(), valign="top", NOWRAP="on")
-		#whether dominance
-        if self.genotype.type == 'intercross':
-            optionPanel.append(dominanceBox, dominanceText, HT.BR())
-        if SNPorNot:
-            optionPanel.append(showSNPCheck, showSNPText, physicOnly, HT.BR())
-        if GeneorNot:
-            optionPanel.append(showGenesCheck, showGenesText, physicOnly, HT.BR(),
-                    showIntervalAnalystCheck, showIntervalAnalystText, physicOnly, HT.BR())
-## BEGIN HaplotypeAnalyst
-        optionPanel.append(showHaplotypeAnalystCheck, showHaplotypeAnalystText, physicOnly, HT.BR())
-## END HaplotypeAnalyst
-        optionPanel.append(legendBox, legendText, HT.BR(),draw2XBox, draw2XText)
-        controlsTable.append(
-                HT.TR(HT.TD(innerControlsTable, valign="top"),
-                        HT.TD("&nbsp;", width=15), optionPanel),
-                HT.TR(HT.TD(physicOnly, " only apply to single chromosome physical mapping", align="Center", colspan=3, Class="fs11 fwn"))
-                        )
-        controlsForm.append(controlsTable)
-
-        controlsForm.append(HT.Input(name="permSuggestive", value=self.suggestive, type="hidden"))
-        controlsForm.append(HT.Input(name="permSignificance", value=self.significant, type="hidden"))
-
-## BEGIN HaplotypeAnalyst #### haplotypeAnalystCheck added below
-## END HaplotypeAnalyst
-
-        for key in fd.formdata.keys():
-            if key == "searchResult" and type([]) == type(fd.formdata.getvalue(key)):
-                controlsForm.append(HT.Input(name=key, value=string.join(fd.formdata.getvalue(key), "\t"), type="hidden"))
-            elif key not in ("endMb",  "startMb",  "chromosomes", "scale", "permCheck", "bootCheck",  "additiveCheck", "dominanceCheck",
-                    "LRSCheck", "intervalAnalystCheck", "haplotypeAnalystCheck", "lrsMax", "graphWidth", "viewLegend", 'showGenes', 'showSNP', 'draw2X',
-                    'permSuggestive', "permSignificance"):
-                controlsForm.append(HT.Input(name=key, value=fd.formdata.getvalue(key), type="hidden"))
-            else:
-                pass
-
-        # updated by NL, move function changeView(i) to webqtl.js and change it to function changeView(i, Chr_Mb_list)
-        #                move function chrLength(a, b, c) to webqtl.js and change it to function chrLength(a, b, c, Chr_Mb_list)
-        self.dict['js1'] = '<script src="/javascript/sorttable.js"></script>'
-        return HT.TD(controlsForm, Class="doubleBorder", width=400)
-
-    def traitInfoTD(self, fd):
-        if self.selectedChr == -1:
-            intMapHeading = HT.Paragraph('Map Viewer: Whole Genome', Class="title")
-        else:
-            intMapHeading = HT.Paragraph('Map Viewer: Chr %s' % self.genotype[0].name, Class="title")
-
-        heading2 = HT.Paragraph(HT.Strong('Population: '), "%s %s" % (self.species.title(), fd.RISet) , HT.BR())
-        #Trait is from an database
-        if self.traitList and self.traitList[0] and self.traitList[0].db:
-            #single trait
-            if len(self.traitList) == 1:
-                thisTrait = self.traitList[0]
-                trait_url = HT.Href(text=thisTrait.name, url = os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + \
-                        "?FormID=showDatabase&incparentsf1=1&database=%s&ProbeSetID=%s" % (thisTrait.db.name, thisTrait.name), \
-                        target='_blank', Class="normalsize")
-                heading2.append(HT.Strong("Database: "), HT.Href(text=thisTrait.db.fullname, url = webqtlConfig.INFOPAGEHREF % thisTrait.db.name ,\
-                        target='_blank',Class="normalsize"),HT.BR())
-                if thisTrait.db.type == 'ProbeSet':
-                    heading2.append(HT.Strong('Trait ID: '), trait_url, HT.BR(),
-                            HT.Strong("Gene Symbol: "), HT.Italic('%s' % thisTrait.symbol,id="green"),HT.BR())
-                    if thisTrait.chr and thisTrait.mb:
-                        heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
-                elif thisTrait.db.type == 'Geno':
-                    heading2.append(HT.Strong('Locus : '), trait_url, HT.BR())
-                    if thisTrait.chr and thisTrait.mb:
-                        heading2.append(HT.Strong("Location: "), 'Chr %s @ %s Mb' % (thisTrait.chr, thisTrait.mb))
-                elif thisTrait.db.type == 'Publish':
-                    heading2.append(HT.Strong('Record ID: '), trait_url, HT.BR())
-                else:
-                    pass
-            else:
-                heading2.append(HT.Strong("Traits: "), "Multiple Traits")
-        else:
-            heading2.append(HT.Strong("Trait Name: "), fd.identification)
-        return HT.TD(intMapHeading, heading2, valign="top")
-
     def drawPermutationHistogram(self):
         #########################################
         #      Permutation Graph
@@ -2622,78 +1990,18 @@ class MarkerRegression(object):
 
         return filename
 
-        # img=HT.Image('/image/'+filename+'.gif',border=0,alt='Histogram of Permutation Test')
-
-        # self.suggestive = self.perm_output[int(self.nperm*0.37-1)]
-        # self.significant = self.perm_output[int(self.nperm*0.95-1)]
-        # self.highlysignificant = self.perm_output[int(self.nperm*0.99-1)]
-
-        # permutationHeading = HT.Paragraph('Histogram of Permutation Test')
-        # permutationHeading.__setattr__("class","title")
-
-        # permutation = HT.TableLite()
-        # permutation.append(HT.TR(HT.TD(img)),
-                           # HT.TR(HT.TD('')),
-                           # HT.TR(HT.TD('Total of %d permutations'%self.nperm)))
-
-        # return permutation
-
-    def permutationTextFile(self):
-        filename= webqtlUtil.genRandStr("Reg_")
-        fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb')
-        fpText.write('Suggestive LRS (p = 0.63) = %3.2f\n'%self.suggestive)
-        fpText.write('Significant LRS (p = 0.05) = %3.2f\n'%self.significant)
-        fpText.write('Highly Significant LRS (p = 0.01) = %3.2f\n\n'%self.highlysignificant)
-        fpText.write('%s Permutations\n\n' % str(len(self.perm_output)))
-        LRSInfo =HT.Paragraph('&nbsp;&nbsp;&nbsp;&nbsp;Suggestive LRS = %3.2f\n'%self.suggestive,
-                              HT.BR(),
-                              '&nbsp;&nbsp;&nbsp;&nbsp;Significant LRS =%3.2f\n'%self.significant,
-                              HT.BR(),
-                              '&nbsp;&nbsp;&nbsp;&nbsp;Highly Significant LRS =%3.2f\n' % self.highlysignificant)
-
-        for lrs_value in self.perm_output:
-            fpText.write(str(lrs_value) + "\n")
-
-        textUrl = HT.Href(text = 'Download Permutation Results', url= '/tmp/'+filename+'.txt', target = "_blank", Class='fs12 fwn')
-
-        return textUrl
-
     def geneTable(self, geneCol, refGene=None):
-        #SNPLink = 0 #Not sure what this is used for
-
         if self.dataset.group.species == 'mouse' or self.dataset.group.species == 'rat':
-            #gene_tblobj = {}
-            self.gene_table_header = self.getGeneTableHeader(refGene=None)
+            self.gene_table_header = self.getGeneTableHeaderList(refGene=None)
             self.gene_table_body = self.getGeneTableBody(geneCol, refGene=None)
-            #gene_tblobj["header"] = self.getGeneTableHeader(refGene=None)
-            #gene_tblobj["body"] = self.getGeneTableBody(geneCol, refGene=None)
-
-            #sortby = self.getSortByValue()
-
-            #filename= webqtlUtil.genRandStr("Mapping_")
-
-            #objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
-            #cPickle.dump(gene_tblobj, objfile)
-            #objfile.close()
-
-            #gene_table = webqtlUtil.genTableObj(tblobj=gene_tblobj, file=filename, sortby=sortby, tableID="sortable", addIndex="0")
         else:
             self.gene_table_header = None
             self.gene_table_body = None
-            #gene_table = ""
-
-        #return gene_table
-
-    def getGeneTableHeader(self, refGene=None):
 
-        gene_tblobj_header = []
+    def getGeneTableHeaderList(self, refGene=None):
 
         gene_table_header_list = []
-
-        col_class = "fs14 fwb ffl b1 cw cbrb"
-
         if self.dataset.group.species == "mouse":
-
             if refGene:
                 gene_table_header_list = ["Index",
                                                "Symbol",
@@ -2706,25 +2014,6 @@ class MarkerRegression(object):
                                                "Mb Start (hg19)",
                                                "Literature Correlation",
                                                "Gene Description"]
-                                               #"PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(),
-                                               #"Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()]
-
-                # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0),
-                        # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1),
-                        # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2),
-                        # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3),
-                        # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4),
-                        # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5),
-                        # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6),
-                        # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7),
-                        # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8),
-                        # THCell(HT.TD('Literature',HT.BR(),'Correlation', align='left', width=100, Class=col_class), text="lit_corr", idx=9),
-                        # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=10),
-                        # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"),
-                                        # align='left', width=100, Class=col_class), sort=0, idx=11),
-                        # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"),
-                                        # align='left', width=110, Class=col_class), sort=0, idx=12),
-                                        # ]]
             else:
                 gene_table_header_list = ["",
                                           "Index",
@@ -2737,27 +2026,7 @@ class MarkerRegression(object):
                                           "Human Chr",
                                           "Mb Start (hg19)",
                                           "Gene Description"]
-                                          #"PolymiRTS Database" + HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank").__str__(),
-                                          #"Gene Weaver Info Content" + HT.Href(url='http://geneweaver.org/', text='>>', target="_blank").__str__()]
-
-                # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0),
-                        # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1),
-                        # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=2),
-                        # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3),
-                        # THCell(HT.TD('SNP',HT.BR(),'Count', align='left', width=47, Class=col_class), text="snp_count", idx=4),
-                        # THCell(HT.TD('SNP',HT.BR(),'Density', align='left', width=78, Class=col_class), text="snp_density", idx=5),
-                        # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=6),
-                        # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7),
-                        # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8),
-                        # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', width=290, Class=col_class), text="description", idx=9),
-                        # THCell(HT.TD('PolymiRTS',HT.BR(),'Database', HT.BR(), HT.Href(url='http://compbio.uthsc.edu/miRSNP/', text='>>', target="_blank", Class="normalsize"),
-                                        # align='left', width=100, Class=col_class), sort=0, idx=10),
-                        # THCell(HT.TD('Gene Weaver', HT.BR(), 'Info Content', HT.BR(), HT.Href(url='http://geneweaver.org/', text='>>', target="_blank", Class="normalsize"),
-                                        # align='left', width=110, Class=col_class), sort=0, idx=11),
-                                        # ]]
-
         elif self.dataset.group.species == "rat":
-
             gene_table_header_list = ["",
                                       "Index",
                                       "Symbol",
@@ -2770,52 +2039,13 @@ class MarkerRegression(object):
                                       "Mb Start (hg19)",
                                       "Gene Description"]
 
-            # gene_tblobj_header = [[THCell(HT.TD('Index', HT.BR(), HT.BR(), align='left', width=50, Class=col_class), text="index", idx=0),
-                    # THCell(HT.TD('Symbol', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="symbol", idx=1),
-                    # THCell(HT.TD('Mb Start',HT.BR(),'(rn3)', align='left', width=100, Class=col_class), text="mb_start_rn3", idx=2),
-                    # THCell(HT.TD('Length (Kb)', HT.BR(), HT.BR(), align='left', width=100, Class=col_class), text="length", idx=3),
-                    # THCell(HT.TD('Avg',HT.BR(),'Expr', HT.BR(), HT.BR(), align='left', width=44, Class=col_class), sort=0, idx=4),
-                    # THCell(HT.TD('Mouse',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="mouse_chr", idx=5),
-                    # THCell(HT.TD('Mb Start',HT.BR(),'(mm9)', align='left', width=100, Class=col_class), text="mb_start_mm9", idx=6),
-                    # THCell(HT.TD('Human',HT.BR(),'Chr', align='left', width=60, Class=col_class), text="human_chr", idx=7),
-                    # THCell(HT.TD('Mb Start',HT.BR(),'(hg19)', align='left', width=100, Class=col_class), text="mb_start_hg19", idx=8),
-                    # THCell(HT.TD('Gene Description', HT.BR(), HT.BR(), align='left', Class=col_class), text="description", idx=9)]]
-
-        else:
-            pass
-
         return gene_table_header_list
-        #return gene_tblobj_header
 
     def getGeneTableBody(self, geneCol, refGene=None):
-
-        tblobj_body = [] #contains table rows
-        className = "fs13 b1 c222"
-
         gene_table_body = []
 
         tableIterationsCnt = 0
         if self.dataset.group.species == "mouse":
-
-            # polymiRTS
-            # http://lily.uthsc.edu:8080/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=2&chrom_from=115&chrom_to=125
-            #XZ: We can NOT assume their web service is always on. We must put this block of code in try except.
-            try:
-                conn = httplib.HTTPConnection("lily.uthsc.edu:8080")
-                conn.request("GET", "/20090422_UTHSC_cuiyan/PolymiRTS_CLS?chrom=%s&chrom_from=%s&chrom_to=%s" % (self.genotype[0].name, self.startMb, self.endMb))
-                response = conn.getresponse()
-                data = response.read()
-                data = data.split()
-                conn.close()
-                dic = {}
-                index = 0
-                for i in data:
-                    if index%3==0:
-                        dic[data[index]] = HT.Href(url=data[index+2], text=data[index+1], target="_blank", Class="normalsize")
-                    index = index+1
-            except Exception:
-                dic={}
-
             for gIndex, theGO in enumerate(geneCol):
 
                 tableIterationsCnt = tableIterationsCnt + 1
@@ -2829,7 +2059,6 @@ class MarkerRegression(object):
                 txEnd = theGO["TxEnd"]
                 theGO["snpDensity"] = theGO["snpCount"]/geneLength
                 if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST:
-                    #accessionString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Display&DB=gene&term=%s'  % theGO["NM_ID"]
                     geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
 
                     allProbeString = '%s?cmd=sch&gene=%s&alias=1' % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), theGO["GeneSymbol"])
@@ -2842,10 +2071,6 @@ class MarkerRegression(object):
 
                     mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0))  + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit"
 
-                    #Used for sorting
-                    mouseStartValue = int(theGO["TxStart"])
-
-
                     #the chromosomes for human 1 are 1qXX.XX
                     if theGO['humanGene']:
                         if theGO['humanGene']["TxStart"] == '':
@@ -2854,20 +2079,11 @@ class MarkerRegression(object):
                             humanStartDisplay = "%0.6f" % theGO['humanGene']["TxStart"]
 
                         humanChr = theGO['humanGene']["Chromosome"]
-                        if humanChr.find('q'):
-                            humanChrSort = humanChr[:humanChr.find("q")].join(humanChr[(humanChr.find("q")+1):]) #value used when sorting table
-                        elif humanChr.find('p'):
-                            humanChrSort = humanChr[:humanChr.find("p")].join(humanChr[(humanChr.find("p")+1):]) #value used when sorting table
-                        else:
-                            humanChrSort = humanChr
                         humanTxStart = theGO['humanGene']["TxStart"]
 
-                        #Used for sorting
-                        humanStartValue = float(theGO['humanGene']["TxStart"])
-
                         humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" %  (humanChr, int(1000000*theGO['humanGene']["TxStart"]), int(1000000*theGO['humanGene']["TxEnd"]))
                     else:
-                        humanStartString = humanChr = humanChrSort = humanStartDisplay = humanStartValue = "--"
+                        humanStartString = humanChr = humanStartDisplay = "--"
 
                     geneDescription = theGO["GeneDescription"]
                     if len(geneDescription) > 26:
@@ -2885,22 +2101,12 @@ class MarkerRegression(object):
                     else:
                         avgExpr = "%0.6f" % avgExpr
 
-                    # polymiRTS
-                    polymiRTS = ' '
-                    if dic.has_key(theGO["GeneID"]):
-                        polymiRTS = dic[theGO["GeneID"]]
-
                     # If we have a referenceGene then we will show the Literature Correlation
                     if theGO["Chromosome"] == "X":
                         chr_as_int = 19
                     else:
                         chr_as_int = int(theGO["Chromosome"]) - 1
                     if refGene:
-                        try:
-                            literatureCorrelation = self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID'])
-                        except:
-                            literatureCorrelation = "N/A"
-
                         literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
 
                         this_row = [selectCheck.__str__(),
@@ -2915,25 +2121,7 @@ class MarkerRegression(object):
                                     HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
                                     literatureCorrelationString,
                                     geneDescription]
-                                    #polymiRTS,
-
-
-                        # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt))
-                        # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), "&nbsp;", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"]))
-                        # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue))
-                        # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength))
-                        # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"]))
-                        # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"]))
-                        # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--"))
-                        # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort))
-                        # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue))
-                        # this_row.append(TDCell(HT.TD(literatureCorrelationString, align='right', Class=className), literatureCorrelationString, literatureCorrelation))
-                        # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription))
-                        # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", ""))
-                        # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", ""))
-
                     else:
-
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
                                     HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__() +  "&nbsp;" + probeSetSearch.__str__(),
@@ -2945,29 +2133,11 @@ class MarkerRegression(object):
                                     humanChr,
                                     HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
                                     geneDescription]
-                                    #polymiRTS,
-
-
-                        # this_row.append(TDCell(HT.TD(tableIterationsCnt, selectCheck, width=30, align='right', Class=className), tableIterationsCnt, tableIterationsCnt))
-                        # this_row.append(TDCell(HT.TD(HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank"), "&nbsp;", probeSetSearch, align='right', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"]))
-                        # this_row.append(TDCell(HT.TD(HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank"), align='right', Class=className), str(mouseStartValue), mouseStartValue))
-                        # this_row.append(TDCell(HT.TD(HT.Href("javascript:centerIntervalMapOnRange2('%s', " % theGO["Chromosome"]+str(txStart-tenPercentLength) + ", " + str(txEnd+tenPercentLength) + ", document.changeViewForm)", "%0.3f" % geneLength), align='right', Class=className), "%0.3f" % geneLength, geneLength))
-                        # this_row.append(TDCell(HT.TD(snpString, align='right', Class=className), str(theGO["snpCount"]), theGO["snpCount"]))
-                        # this_row.append(TDCell(HT.TD(snpDensityStr, align='right', Class=className), snpDensityStr, theGO["snpDensity"]))
-                        # this_row.append(TDCell(HT.TD(avgExpr, align='right', Class=className), "--", "--"))
-                        # this_row.append(TDCell(HT.TD(humanChr, align='right', Class=className), humanChr, humanChrSort))
-                        # this_row.append(TDCell(HT.TD(HT.Href(humanStartString, humanStartDisplay, target="_blank"), align='right', Class=className), humanStartDisplay, humanStartValue))
-                        # this_row.append(TDCell(HT.TD(geneDescription, align='right', Class=className), geneDescription, geneDescription))
-                        # this_row.append(TDCell(HT.TD(polymiRTS, align='right', Class=className), "", ""))
-                        # this_row.append(TDCell(HT.TD("", align='right', Class=className), "", ""))
 
                 gene_table_body.append(this_row)
-                #tblobj_body.append(this_row)
 
         elif self.dataset.group.species == 'rat':
-
             for gIndex, theGO in enumerate(geneCol):
-
                 this_row = [] #container for the cells of each row
                 selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
 
@@ -2984,7 +2154,6 @@ class MarkerRegression(object):
                     chr_as_int = int(theGO["Chromosome"]) - 1
 
                 geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
-                #geneLengthURL = "javascript:centerIntervalMapOnRange2('%s', %f, %f, document.changeViewForm)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
                 geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
 
                 avgExprVal = []
@@ -3003,15 +2172,9 @@ class MarkerRegression(object):
                 #the chromosomes for human 1 are 1qXX.XX
                 if theGO['humanGene']:
                     humanChr = theGO['humanGene']["Chromosome"]
-                    if 'q' in humanChr:
-                        humanChrSort = humanChr[:humanChr.find("q")].join(humanChr[(humanChr.find("q")+1):]) #value used when sorting table
-                    elif 'p' in humanChr:
-                        humanChrSort = humanChr[:humanChr.find("p")].join(humanChr[(humanChr.find("p")+1):]) #value used when sorting table
-                    else:
-                        humanChrSort = humanChr
                     humanTxStart = theGO['humanGene']["TxStart"]
                 else:
-                    humanChr = humanTxStart = humanChrSort = ""
+                    humanChr = humanTxStart = ""
 
                 geneDesc = theGO["GeneDescription"]
                 if geneDesc == "---":
@@ -3029,26 +2192,9 @@ class MarkerRegression(object):
                             humanTxStart,
                             geneDesc]
 
-
-                #this_row.append(TDCell(HT.TD(gIndex + 1, selectCheck, align='left', Class=className), str(gIndex+1), gIndex+1))
-                #this_row.append(TDCell(HT.TD(webqtlSearch, geneSymbolNCBI, align='left', Class=className), theGO["GeneSymbol"], theGO["GeneSymbol"]))
-                #this_row.append(TDCell(HT.TD(theGO["TxStart"], align='left', Class=className), theGO["TxStart"], theGO["TxStart"]))
-                #this_row.append(TDCell(HT.TD(HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)), align='left', Class=className), "%0.3f" % (geneLength*1000.0), (geneLength*1000.0)))
-                #this_row.append(TDCell(HT.TD(avgExprVal, align='left', Class=className), "", ""))
-                #this_row.append(TDCell(HT.TD(mouseChr, align='left', Class=className), mouseChr, mouseChr))
-                #this_row.append(TDCell(HT.TD(mouseTxStart, align='left', Class=className), mouseTxStart, mouseTxStart))
-                #this_row.append(TDCell(HT.TD(humanChr, align='left', Class=className), humanChr, humanChrSort))
-                #this_row.append(TDCell(HT.TD(humanTxStart, align='left', Class=className), humanTxStart, humanTxStart))
-                #this_row.append(TDCell(HT.TD(geneDesc, align='left', Class=className), geneDesc, geneDesc))
-
                 gene_table_body.append(this_row)
-                #tblobj_body.append(this_row)
-
-        else:
-            pass
 
         return gene_table_body
-        #return tblobj_body
 
     def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None):
         if not geneId1 or not geneId2:
@@ -3067,10 +2213,4 @@ class MarkerRegression(object):
                     lCorr = lCorr[0]
                     break
         except: raise #lCorr = None
-        return lCorr
-
-    def getSortByValue(self):
-
-        sortby = ("", "")
-
-        return sortby
+        return lCorr
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index b7ebb9ed..d00b52b8 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1527,6 +1527,36 @@
          }
       },
       "mouse": {
+         "AIL": {
+            "Hippocampus mRNA": [
+               [
+                  "844",
+                  "UCSD_AIL_HIP_RNA-Seq_0418",
+                  "UCSD AIL Hippocampus (Apr18) RNA-Seq"
+               ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "AILPublish",
+                  "AIL Published Phenotypes"
+               ]
+            ],
+            "Prefrontal Cortex mRNA": [
+               [
+                  "846",
+                  "UCSD_AIL_PFC_RNA-Seq_0418",
+                  "UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq"
+               ]
+            ],
+            "Striatum mRNA": [
+               [
+                  "845",
+                  "UCSD_AIL_STR_RNA-Seq_0418",
+                  "UCSD AIL Striatum (Apr18) RNA-Seq"
+               ]
+            ]
+         },
          "AKXD": {
             "Genotypes": [
                [
@@ -2968,7 +2998,7 @@
          "BXD-Bone": {
             "Phenotypes": [
                [
-                  "None",
+                  "650",
                   "BXD-BonePublish",
                   "BXD-Bone Published Phenotypes"
                ]
@@ -3156,6 +3186,13 @@
             ]
          },
          "CIE-RMA": {
+            "Hippocampus mRNA": [
+               [
+                  "831",
+                  "INIA_UTHSC_Hip_AffyMTA1_May17",
+                  "INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) RMA"
+               ]
+            ],
             "Midbrain mRNA": [
                [
                   "830",
@@ -3825,6 +3862,10 @@
          ]
       ],
       "mouse": [
+         [
+            "AIL",
+            "AIL Advanced Intercross Line"
+         ],
          [
             "AKXD",
             "AKXD"
@@ -3875,7 +3916,7 @@
          ],
          [
             "BXD-Bone",
-            "BXD Bone"
+            "BXD Bone Individual Data"
          ],
          [
             "BXD-Harvested",
@@ -4727,6 +4768,24 @@
          ]
       },
       "mouse": {
+         "AIL": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
+               "Hippocampus mRNA",
+               "Hippocampus mRNA"
+            ],
+            [
+               "Prefrontal Cortex mRNA",
+               "Prefrontal Cortex mRNA"
+            ],
+            [
+               "Striatum mRNA",
+               "Striatum mRNA"
+            ]
+         ],
          "AKXD": [
             [
                "Genotypes",
@@ -5110,6 +5169,10 @@
                "Phenotypes",
                "Phenotypes"
             ],
+            [
+               "Hippocampus mRNA",
+               "Hippocampus mRNA"
+            ],
             [
                "Midbrain mRNA",
                "Midbrain mRNA"
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 49d7f962..68880829 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -39,7 +39,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lodheatmap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/curvechart.js"></script>
-<!--    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_heatmap.js"></script>-->
     <script language="javascript" type="text/javascript" src="/static/new/javascript/iplotMScanone_noeff.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
-- 
cgit v1.2.3


From 8abe2be79c7b3e89cf1d245cff64d0bda7730b45 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Apr 2018 21:57:13 +0000
Subject: Removed file tracer.py that wasn't being used

Removed some unused code from the other files listed
---
 wqflask/wqflask/marker_regression/plink_mapping.py | 16 +--------
 .../wqflask/marker_regression/qtlreaper_mapping.py |  2 +-
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 38 +++++++-------------
 wqflask/wqflask/model.py                           | 33 ++---------------
 wqflask/wqflask/network_graph/network_graph.py     | 32 ++++++-----------
 wqflask/wqflask/show_trait/export_trait_data.py    |  2 --
 wqflask/wqflask/show_trait/show_trait.py           | 39 +-------------------
 .../templates/show_trait_mapping_tools.html        | 17 ---------
 wqflask/wqflask/tracer.py                          | 41 ----------------------
 wqflask/wqflask/views.py                           |  5 ---
 10 files changed, 29 insertions(+), 196 deletions(-)
 delete mode 100644 wqflask/wqflask/tracer.py

diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 4de88f00..2f327faf 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -10,9 +10,7 @@ logger = utility.logger.getLogger(__name__ )
 
 def run_plink(this_trait, dataset, species, vals, maf):
     plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name))
-
     gen_pheno_txt_file(dataset, vals)
-    #gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
 
     plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % (
         flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename)
@@ -22,12 +20,6 @@ def run_plink(this_trait, dataset, species, vals, maf):
 
     count, p_values = parse_plink_output(plink_output_filename, species)
 
-    #for marker in self.dataset.group.markers.markers:
-    #    if marker['name'] not in included_markers:
-    #        logger.debug("marker:", marker)
-    #        self.dataset.group.markers.markers.remove(marker)
-    #        #del self.dataset.group.markers.markers[marker]
-
     logger.debug("p_values:", p_values)
     dataset.group.markers.add_pvalues(p_values)
 
@@ -108,7 +100,6 @@ def parse_plink_output(output_filename, species):
 
     result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb")
 
-    header_line = result_fp.readline()# read header line
     line = result_fp.readline()
 
     value_list = [] # initialize value list, this list will include snp, bp and pvalue info
@@ -156,11 +147,6 @@ def parse_plink_output(output_filename, species):
         else:
             line = result_fp.readline()
 
-    #if p_value_list:
-    #    min_p_value = min(p_value_list)
-    #else:
-    #    min_p_value = 0
-
     return count, p_value_dict
 
 ######################################################
@@ -173,4 +159,4 @@ def build_line_list(line=None):
     line_list = [item for item in line_list if item <>'']
     line_list = map(string.strip, line_list)
 
-    return line_list
+    return line_list
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 6b58190f..ffbfb5c5 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -26,7 +26,7 @@ def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_dat
         perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=num_perm)
         suggestive = perm_output[int(num_perm*0.37-1)]
         significant = perm_output[int(num_perm*0.95-1)]
-        highly_significant = perm_output[int(num_perm*0.99-1)]
+        #highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
 
     json_data['suggestive'] = suggestive
     json_data['significant'] = significant
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index f3694f0b..41d67012 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -5,15 +5,16 @@ from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
 from utility.tools import locate, TEMPDIR
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control, control_marker, manhattan_plot, pair_scan):
     geno_to_rqtl_function(dataset)
 
     ## Get pointers to some common R functions
     r_library     = ro.r["library"]                 # Map the library function
     r_c           = ro.r["c"]                       # Map the c function
-    r_sum         = ro.r["sum"]                     # Map the sum function
     plot          = ro.r["plot"]                    # Map the plot function
-    postscript    = ro.r["postscript"]              # Map the postscript function
     png           = ro.r["png"]                     # Map the png function
     dev_off       = ro.r["dev.off"]                 # Map the device off function
 
@@ -23,17 +24,13 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
     scanone         = ro.r["scanone"]               # Map the scanone function
     scantwo         = ro.r["scantwo"]               # Map the scantwo function
     calc_genoprob   = ro.r["calc.genoprob"]         # Map the calc.genoprob function
-    read_cross      = ro.r["read.cross"]            # Map the read.cross function
-    write_cross     = ro.r["write.cross"]           # Map the write.cross function
     GENOtoCSVR      = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
 
     crossname = dataset.group.name
     genofilelocation  = locate(crossname + ".geno", "genotype")
     crossfilelocation = TMPDIR + crossname + ".cross"
 
-    #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation)
-
-    cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                                  # TODO: Add the SEX if that is available
+    cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)                            # TODO: Add the SEX if that is available
 
     if manhattan_plot:
         cross_object = calc_genoprob(cross_object)
@@ -42,18 +39,14 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
 
     cross_object = add_phenotype(cross_object, sanitize_rqtl_phenotype(vals))                 # Add the phenotype
 
-    # for debug: write_cross(cross_object, "csvr", "test.csvr")
-
     # Scan for QTLs
-    covar = create_covariates(control_marker, cross_object)                                                    # Create the additive covariate matrix
+    covar = create_covariates(control_marker, cross_object)                                   # Create the additive covariate matrix
 
     if pair_scan:
-        if do_control == "true":                                                # If sum(covar) > 0 we have a covariate matrix
-            print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
+        if do_control == "true":
+            logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method, n_cluster = 16)
         else:
-            print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
-
-        #print("Pair scan results:", result_data_frame)
+            logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
 
         pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
         png(file=TEMPDIR+pair_scan_filename)
@@ -63,9 +56,9 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
         return process_pair_scan_results(result_data_frame)
     else:
         if do_control == "true":
-            print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
+            logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=model, method=method)
         else:
-            print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+            logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
 
         if num_perm > 0 and permCheck == "ON":                                                                   # Do permutation (if requested by user)
             if do_control == "true":
@@ -79,7 +72,6 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
             return process_rqtl_results(result_data_frame)
 
 def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
-
     ro.r("""
        trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
 
@@ -117,15 +109,13 @@ def add_phenotype(cross, pheno_as_string):
 def create_covariates(control_marker, cross):
     ro.globalenv["the_cross"] = cross
     ro.r('genotypes <- pull.geno(the_cross)')                             # Get the genotype matrix
-    userinputS = control_marker.replace(" ", "").split(",")                 # TODO: sanitize user input, Never Ever trust a user
+    userinputS = control_marker.replace(" ", "").split(",")               # TODO: sanitize user input, Never Ever trust a user
     covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
-    #print("Marker names of selected covariates:", covariate_names)
     ro.r('covnames <- c(' + covariate_names + ')')
     ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
     ro.r('covnames <- covnames[covInGeno]')
     ro.r("cat('covnames (purged): ', covnames,'\n')")
     ro.r('covariates <- genotypes[,covnames]')                            # Get the covariate matrix by using the marker name as index to the genotype file
-    #print("R/qtl matrix of covariates:", ro.r["covariates"])
     return ro.r["covariates"]
 
 def sanitize_rqtl_phenotype(vals):
@@ -149,7 +139,6 @@ def process_pair_scan_results(result):
 
     result = result[1]
     output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-    #print("R/qtl scantwo output:", output)
 
     for i, line in enumerate(result.iter_row()):
         marker = {}
@@ -175,9 +164,7 @@ def process_rqtl_perm_results(num_perm, results):
 
 def process_rqtl_results(result):        # TODO: how to make this a one liner and not copy the stuff in a loop
     qtl_results = []
-
     output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-    #print("R/qtl scanone output:", output)
 
     for i, line in enumerate(result.iter_row()):
         marker = {}
@@ -187,5 +174,4 @@ def process_rqtl_results(result):        # TODO: how to make this a one liner an
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results
-
+    return qtl_results
\ No newline at end of file
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 5321e420..38117a8e 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -6,31 +6,16 @@ import datetime
 import simplejson as json
 
 from flask import request
-from flask.ext.sqlalchemy import SQLAlchemy
 
 from wqflask import app
 
 import sqlalchemy
-
-from sqlalchemy import (Column, Integer, String, Table, ForeignKey, Unicode, Boolean, DateTime,
+from sqlalchemy import (Column, ForeignKey, Unicode, Boolean, DateTime,
                         Text, Index)
-from sqlalchemy.orm import relationship, backref
+from sqlalchemy.orm import relationship
 
 from wqflask.database import Base, init_db
 
-
-
-# Define models
-#roles_users = Table('roles_users',
-#        Column('user_id', Integer(), ForeignKey('user.the_id')),
-#        Column('role_id', Integer(), ForeignKey('role.the_id')))
-
-#class Role(Base):
-#    __tablename__ = "role"
-#    id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
-#    name = Column(Unicode(80), unique=True, nullable=False)
-#    description = Column(Unicode(255))
-
 class User(Base):
     __tablename__ = "user"
     id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
@@ -133,11 +118,6 @@ class User(Base):
         except IndexError:
             return None
 
-
-    #roles = relationship('Role', secondary=roles_users,
-    #                        backref=backref('users', lazy='dynamic'))
-
-
 class Login(Base):
     __tablename__ = "login"
     id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
@@ -177,22 +157,15 @@ class UserCollection(Base):
         except:
             return 0
 
-    #@property
-    #def display_num_members(self):
-    #    return display_collapsible(self.num_members)
-
     def members_as_set(self):
         return set(json.loads(self.members))
 
-
 def display_collapsible(number):
     if number:
         return number
     else:
         return ""
 
-
 def user_uuid():
     """Unique cookie for a user"""
-    user_uuid = request.cookies.get('user_uuid')
-
+    user_uuid = request.cookies.get('user_uuid')
\ No newline at end of file
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index b42904a4..63273a29 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -21,9 +21,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-# sys.path.append(".")   Never do this in a webserver!
 
-import gc
 import string
 import cPickle
 import os
@@ -95,7 +93,6 @@ class NetworkGraph(object):
 
         self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
 
-        self.network_data = {}
         self.nodes_list = []
         self.edges_list = []
         for trait_db in self.trait_list:
@@ -107,9 +104,9 @@ class NetworkGraph(object):
 
             corr_result_row = []
             is_spearman = False #ZS: To determine if it's above or below the diagonal
-            
+
             max_corr = 0 #ZS: Used to determine whether node should be hidden when correlation coefficient slider is used
-            
+
             for target in self.trait_list:
                 target_trait = target[0]
                 target_db = target[1]
@@ -141,7 +138,7 @@ class NetworkGraph(object):
                             continue
                     else:
                         sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
- 
+
                     if -1 <= sample_r < -0.7:
                         color = "#0000ff"
                         width = 3
@@ -163,10 +160,10 @@ class NetworkGraph(object):
                     else:
                         color = "#000000"
                         width = 0                      
- 
+
                     if abs(sample_r) > max_corr:
                         max_corr = abs(sample_r)
- 
+
                     edge_data = {'id' : str(this_trait.name) + '_to_' + str(target_trait.name),
                                  'source' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
                                  'target' : str(target_trait.name) + ":" + str(target_trait.dataset.name),
@@ -176,11 +173,11 @@ class NetworkGraph(object):
                                  'overlap' : num_overlap,
                                  'color' : color,
                                  'width' : width }
-                                 
+
                     edge_dict = { 'data' : edge_data }
-                                 
+
                     self.edges_list.append(edge_dict)
-      
+
             if trait_db[1].type == "ProbeSet":
                 node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
                                         'label' : this_trait.symbol,
@@ -197,19 +194,13 @@ class NetworkGraph(object):
                                         'label' : this_trait.name,
                                         'max_corr' : max_corr } }
             self.nodes_list.append(node_dict)
-      
-        #self.network_data['dataSchema'] = {'nodes' : [{'name' : "label" , 'type' : "string"}],
-        #                                   'edges' : [{'name' : "label" , 'type' : "string"}] }
-        
-        #self.network_data['data'] = {'nodes' : self.nodes_list,
-        #                             'edges' : self.edges_list }
 
         self.elements = json.dumps(self.nodes_list + self.edges_list)
-        
+
         groups = []
         for sample in self.all_sample_list:
             groups.append(1)
-            
+
         self.js_data = dict(traits = [trait.name for trait in self.traits],
                             groups = groups,
                             cols = range(len(self.traits)),
@@ -217,7 +208,6 @@ class NetworkGraph(object):
                             samples = self.all_sample_list,
                             sample_data = self.sample_data,
                             elements = self.elements,)
-        #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
 
     def get_trait_db_obs(self, trait_db_list):
         self.trait_list = []
@@ -229,4 +219,4 @@ class NetworkGraph(object):
             trait_ob = GeneralTrait(dataset=dataset_ob,
                                    name=trait_name,
                                    cellid=None)
-            self.trait_list.append((trait_ob, dataset_ob))
+            self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index ac3cd366..558372bb 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,7 +1,5 @@
 from __future__ import print_function, division
 
-import operator
-
 import simplejson as json
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 1f000564..8b801396 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -6,7 +6,6 @@ import datetime
 import cPickle
 import uuid
 import json as json
-#import pyXLWriter as xl
 
 from collections import OrderedDict
 
@@ -73,14 +72,6 @@ class ShowTrait(object):
                                            cellid=None)
             self.trait_vals = Redis.get(self.trait_id).split()
 
-        #self.dataset.group.read_genotype_file()
-
-        #if this_trait:
-        #    if this_trait.dataset and this_trait.dataset.type and this_trait.dataset.type == 'ProbeSet':
-        #            self.cursor.execute("SELECT h2 from ProbeSetXRef WHERE DataId = %d" %
-        #                                this_trait.mysqlid)
-        #            heritability = self.cursor.fetchone()
-
         #ZS: Get verify/rna-seq link URLs
         try:
             blatsequence = self.this_trait.blatseq
@@ -192,7 +183,7 @@ class ShowTrait(object):
             self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
 
-        self.get_mapping_methods()
+        self.genofiles = get_genofiles(self.dataset)
 
         self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups)
 
@@ -211,28 +202,6 @@ class ShowTrait(object):
                        temp_uuid = self.temp_uuid)
         self.js_data = js_data
 
-    def get_mapping_methods(self):
-        '''Only display mapping methods when the dataset group's genotype file exists'''
-        def check_plink_gemma():
-            if flat_file_exists("mapping"):
-                MAPPING_PATH = flat_files("mapping")+"/"
-                if (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bed") and
-                    (os.path.isfile(MAPPING_PATH+self.dataset.group.name+".map") or
-                     os.path.isfile(MAPPING_PATH+self.dataset.group.name+".bim"))):
-                    return True
-            return False
-
-        def check_pylmm_rqtl():
-            if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.JSON_GENODIR+self.dataset.group.name+".json") > 0):
-                return True
-            else:
-                return False
-
-        self.genofiles = get_genofiles(self.dataset)
-        self.use_plink_gemma = check_plink_gemma()
-        self.use_pylmm_rqtl = check_pylmm_rqtl()
-
-
     def build_correlation_tools(self):
         if self.temp_trait == True:
             this_group = self.temp_group
@@ -245,7 +214,6 @@ class ShowTrait(object):
             this_group = 'BXD'
 
         if this_group:
-            #dataset_menu = self.dataset.group.datasets()
             if self.temp_trait == True:
                 dataset_menu = data_set.datasets(this_group)
             else:
@@ -263,7 +231,6 @@ class ShowTrait(object):
                                           return_results_menu = return_results_menu,
                                           return_results_menu_selected = return_results_menu_selected,)
 
-
     def make_sample_lists(self):
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         
@@ -315,10 +282,6 @@ class ShowTrait(object):
                                             sample_group_type='primary',
                                             header="%s Only" % (self.dataset.group.name))
             self.sample_groups = (primary_samples,)
-        #TODO: Figure out why this if statement is written this way - Zach
-        #if (other_sample_names or (fd.f1list and this_trait.data.has_key(fd.f1list[0]))
-        #        or (fd.f1list and this_trait.data.has_key(fd.f1list[1]))):
-        #    logger.debug("hjs")
         self.dataset.group.allsamples = all_samples_ordered
 
 def get_nearest_marker(this_trait, this_db):
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 03590c2c..0ecf1eb9 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,6 @@
             </ul>
 
             <div class="tab-content">
-                {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
                 {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane active" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
@@ -70,10 +69,6 @@
                                </label>
                             </div>
                         </div>
-                    <!--
-                    </div>
-                    <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
-                    -->
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
@@ -99,18 +94,6 @@
                           </div>
                         </div>
                     </div>
-<!--
-                    <div class="form-group">
-                        <div class="col-xs-4 controls">
-                            <label class="col-xs-2 control-label"></label>
-                            <div class="col-xs-4">
-                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                            </div>
-                        </div>
-                    </div>
--->
                 </div>
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
diff --git a/wqflask/wqflask/tracer.py b/wqflask/wqflask/tracer.py
deleted file mode 100644
index a1043d28..00000000
--- a/wqflask/wqflask/tracer.py
+++ /dev/null
@@ -1,41 +0,0 @@
-from __future__ import absolute_import, division, print_function
-
-print("At top of tracer")
-
-import sys
-
-####################################################################################
-
-# Originally based on http://stackoverflow.com/a/8315566
-def tracefunc(frame, event, arg, indent=[0]):
-
-    func = dict(funcname = frame.f_code.co_name,
-                     filename = frame.f_code.co_filename,
-                     lineno = frame.f_lineno)
-
-    #These are too common to bother printing...
-    too_common = (
-        '/home/sam/ve27/local/lib/python2.7/site-packages/werkzeug/',
-        '/home/sam/ve27/local/lib/python2.7/site-packages/jinja2/',
-    )
-
-
-    if func['filename'].startswith(too_common):
-        return tracefunc
-
-    info = "{funcname} [{filename}: {lineno}]".format(**func)
-
-    if event == "call":
-        indent[0] += 2
-        #print("-" * indent[0] + "> call function", frame.f_code.co_name)
-        print("-" * indent[0] + "> call function:", info)
-    elif event == "return":
-        print("<" + "-" * indent[0], "exit function:", info)
-        indent[0] -= 2
-    return tracefunc
-
-def turn_on():
-    sys.settrace(tracefunc)
-    print("Tracing turned on!!!!")
-####################################################################################
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 8ff359a7..49b47123 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -89,11 +89,6 @@ def shutdown_session(exception=None):
         db_session.remove()
         g.db = None
 
-#@app.before_request
-#def trace_it():
-#    from wqflask import tracer
-#    tracer.turn_on()
-
 @app.errorhandler(Exception)
 def handle_bad_request(e):
     err_msg = str(e)
-- 
cgit v1.2.3


From 273b79a0c2096a2eae5ce9aa2800917437459f68 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Apr 2018 22:15:24 +0000
Subject: Removed some unused code from collect.py and user_manager.py

---
 wqflask/wqflask/collect.py      |  4 ---
 wqflask/wqflask/user_manager.py | 64 ++---------------------------------------
 2 files changed, 2 insertions(+), 66 deletions(-)

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 04035e96..2bd4b721 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -123,10 +123,6 @@ class AnonCollection(object):
             collections_list.append(collection_dict)
 
         Redis.set(self.key, json.dumps(collections_list))
-        #Redis.sadd(self.key, *list(traits))
-        #Redis.expire(self.key, 60 * 60 * 24 * 5)
-        #len_now = len(Redis.smembers(self.key))
-        #report_change(len_before, len_now)
 
     def remove_traits(self, params):
         traits_to_remove = [(":").join(trait.split(":")[:2]) for trait in params.getlist('traits[]')]
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5f6c818e..0e56ebd3 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -13,7 +13,6 @@ import urlparse
 
 import simplejson as json
 
-#from redis import StrictRedis
 import redis # used for collections
 Redis = redis.StrictRedis()
 
@@ -42,7 +41,6 @@ from smtplib import SMTP
 from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
 
 THREE_DAYS = 60 * 60 * 24 * 3
-#THREE_DAYS = 45
 
 def timestamp():
     return datetime.datetime.utcnow().isoformat()
@@ -66,16 +64,6 @@ class AnonUser(object):
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
 
-    def add_collection(self, new_collection):
-        collection_dict = dict(name = new_collection.name,
-                               created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
-                               changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
-                               num_members = new_collection.num_members,
-                               members = new_collection.get_members())
-
-        Redis.set(self.key, json.dumps(collection_dict))
-        Redis.expire(self.key, 60 * 60 * 24 * 5)
-
     def delete_collection(self, collection_name):
         existing_collections = self.get_collections()
         updated_collections = []
@@ -171,19 +159,11 @@ class UserSession(object):
             self.session_id = session_id
             self.record = Redis.hgetall(self.redis_key)
 
-
             if not self.record:
                 # This will occur, for example, when the browser has been left open over a long
                 # weekend and the site hasn't been visited by the user
                 self.logged_in = False
 
-                ########### Grrr...this won't work because of the way flask handles cookies
-                # Delete the cookie
-                #response = make_response(redirect(url_for('login')))
-                #response.set_cookie(self.cookie_name, '', expires=0)
-                #flash(
-                #   "Due to inactivity your session has expired. If you'd like please login again.")
-                #return response
                 return
 
             if Redis.ttl(self.redis_key) < THREE_DAYS:
@@ -218,7 +198,6 @@ class UserSession(object):
             self.db_object = model.User.query.get(self.user_id)
             return self.db_object
 
-
     def delete_session(self):
         # And more importantly delete the redis record
         Redis.delete(self.cookie_name)
@@ -234,12 +213,10 @@ class UsersManager(object):
         self.users = model.User.query.all()
         logger.debug("Users are:", self.users)
 
-
 class UserManager(object):
     def __init__(self, kw):
         self.user_id = kw['user_id']
         logger.debug("In UserManager locals are:", pf(locals()))
-        #self.user = model.User.get(user_id)
         #logger.debug("user is:", user)
         self.user = model.User.query.get(self.user_id)
         logger.debug("user is:", self.user)
@@ -253,10 +230,8 @@ class UserManager(object):
             logger.debug("  Confidential:", dataset.check_confidentiality())
         #logger.debug("   ---> self.datasets:", self.datasets)
 
-
 class RegisterUser(object):
     def __init__(self, kw):
-        self.thank_you_mode = False
         self.errors = []
         self.user = Bunch()
         es = kw.get('es_connection', None)
@@ -304,7 +279,6 @@ def set_password(password, user):
 
     pwfields.algorithm = "pbkdf2"
     pwfields.hashfunc = "sha256"
-    #hashfunc = getattr(hashlib, pwfields.hashfunc)
 
     # Encoding it to base64 makes storing it in json much easier
     pwfields.salt = base64.b64encode(os.urandom(32))
@@ -333,7 +307,6 @@ def set_password(password, user):
                                     sort_keys=True,
                                    )
 
-
 class VerificationEmail(object):
     template_name =  "email/verification.txt"
     key_prefix = "verification_code"
@@ -348,7 +321,6 @@ class VerificationEmail(object):
                           )
 
         Redis.set(key, data)
-        #two_days = 60 * 60 * 24 * 2
         Redis.expire(key, THREE_DAYS)
         to = user.email_address
         subject = self.subject
@@ -463,7 +435,6 @@ def password_reset_step2():
 
     logger.debug("locals are:", locals())
 
-
     user = Bunch()
     password = request.form['password']
     set_password(password, user)
@@ -489,8 +460,6 @@ class DecodeUser(object):
     def __init__(self, code_prefix):
         verify_url_hmac(request.url)
 
-        #params = urlparse.parse_qs(url)
-
         self.verification_code = request.args['code']
         self.user = self.actual_get_user(code_prefix, self.verification_code)
 
@@ -662,8 +631,6 @@ class LoginUser(object):
             else:
                 import_col = "false"
 
-            #g.cookie_session.import_traits_to_user()
-
             return self.actual_login(user, import_collections=import_col)
 
         else:
@@ -691,7 +658,6 @@ class LoginUser(object):
         login_rec.successful = True
         login_rec.session_id = str(uuid.uuid4())
         login_rec.assumed_by = assumed_by
-        #session_id = "session_id:{}".format(login_rec.session_id)
         session_id_signature = actual_hmac_creation(login_rec.session_id)
         session_id_signed = login_rec.session_id + ":" + session_id_signature
         logger.debug("session_id_signed:", session_id_signed)
@@ -726,7 +692,6 @@ def logout():
     response.set_cookie(UserSession.cookie_name, '', expires=0)
     return response
 
-
 @app.route("/n/forgot_password")
 def forgot_password():
     """Entry point for forgotten password"""
@@ -742,13 +707,7 @@ def forgot_password_submit():
     user_details = get_user_by_unique_column(es, "email_address", email_address)
     if user_details:
         ForgotPasswordEmail(user_details["email_address"])
-    # try:
-    #     user = model.User.query.filter_by(email_address=email_address).one()
-    # except orm.exc.NoResultFound:
-    #     flash("Couldn't find a user associated with the email address {}. Sorry.".format(
-    #         email_address))
-    #     return redirect(url_for("login"))
-    # ForgotPasswordEmail(user)
+
     return render_template("new_security/forgot_password_step2.html",
                             subject=ForgotPasswordEmail.subject)
 
@@ -765,8 +724,6 @@ def super_only():
         flash("You must be a superuser to access that page.", "alert-error")
         abort(401)
 
-
-
 @app.route("/manage/users")
 def manage_users():
     super_only()
@@ -807,13 +764,11 @@ def assume_identity():
     assumed_by = g.user_session.user_id
     return LoginUser().actual_login(user, assumed_by=assumed_by)
 
-
 @app.route("/n/register", methods=('GET', 'POST'))
 def register():
     params = None
     errors = None
 
-
     params = request.form if request.form else request.args
     params = params.to_dict(flat=True)
     es = get_elasticsearch_connection()
@@ -830,7 +785,6 @@ def register():
 
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
-
 ################################# Sign and unsign #####################################
 
 def url_for_hmac(endpoint, **values):
@@ -849,7 +803,6 @@ def data_hmac(stringy):
     """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
     return stringy + ":" + actual_hmac_creation(stringy)
 
-
 def verify_url_hmac(url):
     """Pass in a url that was created with url_hmac and this assures it hasn't been tampered with"""
     logger.debug("url passed in to verify is:", url)
@@ -884,13 +837,6 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 
 #######################################################################################
 
-# def send_email(to, subject, body):
-#     msg = json.dumps(dict(From="no-reply@genenetwork.org",
-#                      To=to,
-#                      Subject=subject,
-#                      Body=body))
-#     Redis.rpush("mail_queue", msg)
-
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
     """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
     'UNKNOWN' TLS is used
@@ -915,10 +861,4 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
 
 class GroupsManager(object):
     def __init__(self, kw):
-        self.datasets = create_datasets_list()
-
-
-class RolesManager(object):
-    def __init__(self):
-        self.roles = model.Role.query.all()
-        logger.debug("Roles are:", self.roles)
+        self.datasets = create_datasets_list()
\ No newline at end of file
-- 
cgit v1.2.3


From 6c50d1d26934d682ff0d3c8ee95caefa6c3393dd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 16 Apr 2018 22:52:35 +0000
Subject: Undoing changes to user_manager.py, because I think they may have
 caused some problem. Probably better to leave this file alone for the time
 being.

---
 wqflask/wqflask/user_manager.py | 60 ++++++++++++++++++++++++++++++++++++++---
 1 file changed, 57 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 15eaf8cc..d652f2e9 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -13,6 +13,7 @@ import urlparse
 
 import simplejson as json
 
+#from redis import StrictRedis
 import redis # used for collections
 Redis = redis.StrictRedis()
 
@@ -41,6 +42,7 @@ from smtplib import SMTP
 from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
 
 THREE_DAYS = 60 * 60 * 24 * 3
+#THREE_DAYS = 45
 
 def timestamp():
     return datetime.datetime.utcnow().isoformat()
@@ -64,6 +66,16 @@ class AnonUser(object):
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
 
+    def add_collection(self, new_collection):
+        collection_dict = dict(name = new_collection.name,
+                               created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+                               changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+                               num_members = new_collection.num_members,
+                               members = new_collection.get_members())
+
+        Redis.set(self.key, json.dumps(collection_dict))
+        Redis.expire(self.key, 60 * 60 * 24 * 5)
+
     def delete_collection(self, collection_name):
         existing_collections = self.get_collections()
         updated_collections = []
@@ -159,11 +171,19 @@ class UserSession(object):
             self.session_id = session_id
             self.record = Redis.hgetall(self.redis_key)
 
+
             if not self.record:
                 # This will occur, for example, when the browser has been left open over a long
                 # weekend and the site hasn't been visited by the user
                 self.logged_in = False
 
+                ########### Grrr...this won't work because of the way flask handles cookies
+                # Delete the cookie
+                #response = make_response(redirect(url_for('login')))
+                #response.set_cookie(self.cookie_name, '', expires=0)
+                #flash(
+                #   "Due to inactivity your session has expired. If you'd like please login again.")
+                #return response
                 return
 
             if Redis.ttl(self.redis_key) < THREE_DAYS:
@@ -198,6 +218,7 @@ class UserSession(object):
             self.db_object = model.User.query.get(self.user_id)
             return self.db_object
 
+
     def delete_session(self):
         # And more importantly delete the redis record
         Redis.delete(self.cookie_name)
@@ -213,10 +234,12 @@ class UsersManager(object):
         self.users = model.User.query.all()
         logger.debug("Users are:", self.users)
 
+
 class UserManager(object):
     def __init__(self, kw):
         self.user_id = kw['user_id']
         logger.debug("In UserManager locals are:", pf(locals()))
+        #self.user = model.User.get(user_id)
         #logger.debug("user is:", user)
         self.user = model.User.query.get(self.user_id)
         logger.debug("user is:", self.user)
@@ -230,8 +253,10 @@ class UserManager(object):
             logger.debug("  Confidential:", dataset.check_confidentiality())
         #logger.debug("   ---> self.datasets:", self.datasets)
 
+
 class RegisterUser(object):
     def __init__(self, kw):
+        self.thank_you_mode = False
         self.errors = []
         self.user = Bunch()
         es = kw.get('es_connection', None)
@@ -279,6 +304,7 @@ def set_password(password, user):
 
     pwfields.algorithm = "pbkdf2"
     pwfields.hashfunc = "sha256"
+    #hashfunc = getattr(hashlib, pwfields.hashfunc)
 
     # Encoding it to base64 makes storing it in json much easier
     pwfields.salt = base64.b64encode(os.urandom(32))
@@ -307,6 +333,7 @@ def set_password(password, user):
                                     sort_keys=True,
                                    )
 
+
 class VerificationEmail(object):
     template_name =  "email/verification.txt"
     key_prefix = "verification_code"
@@ -321,6 +348,7 @@ class VerificationEmail(object):
                           )
 
         Redis.set(key, data)
+        #two_days = 60 * 60 * 24 * 2
         Redis.expire(key, THREE_DAYS)
         to = user.email_address
         subject = self.subject
@@ -435,6 +463,7 @@ def password_reset_step2():
 
     logger.debug("locals are:", locals())
 
+
     user = Bunch()
     password = request.form['password']
     set_password(password, user)
@@ -460,6 +489,8 @@ class DecodeUser(object):
     def __init__(self, code_prefix):
         verify_url_hmac(request.url)
 
+        #params = urlparse.parse_qs(url)
+
         self.verification_code = request.args['code']
         self.user = self.actual_get_user(code_prefix, self.verification_code)
 
@@ -631,6 +662,8 @@ class LoginUser(object):
             else:
                 import_col = "false"
 
+            #g.cookie_session.import_traits_to_user()
+
             return self.actual_login(user, import_collections=import_col)
 
         else:
@@ -658,6 +691,7 @@ class LoginUser(object):
         login_rec.successful = True
         login_rec.session_id = str(uuid.uuid4())
         login_rec.assumed_by = assumed_by
+        #session_id = "session_id:{}".format(login_rec.session_id)
         session_id_signature = actual_hmac_creation(login_rec.session_id)
         session_id_signed = login_rec.session_id + ":" + session_id_signature
         logger.debug("session_id_signed:", session_id_signed)
@@ -692,12 +726,13 @@ def logout():
     response.set_cookie(UserSession.cookie_name, '', expires=0)
     return response
 
+
 @app.route("/n/forgot_password", methods=['GET'])
 def forgot_password():
     """Entry point for forgotten password"""
-    logger.debug("ARGS: ", request.args)
+    print("ARGS: ", request.args)
     errors = {"no-email": request.args.get("no-email")}
-    logger.debug("ERRORS: ", errors)
+    print("ERRORS: ", errors)
     return render_template("new_security/forgot_password.html", errors=errors)
 
 @app.route("/n/forgot_password_submit", methods=('POST',))
@@ -733,6 +768,8 @@ def super_only():
         flash("You must be a superuser to access that page.", "alert-error")
         abort(401)
 
+
+
 @app.route("/manage/users")
 def manage_users():
     super_only()
@@ -773,11 +810,13 @@ def assume_identity():
     assumed_by = g.user_session.user_id
     return LoginUser().actual_login(user, assumed_by=assumed_by)
 
+
 @app.route("/n/register", methods=('GET', 'POST'))
 def register():
     params = None
     errors = None
 
+
     params = request.form if request.form else request.args
     params = params.to_dict(flat=True)
     es = get_elasticsearch_connection()
@@ -794,6 +833,7 @@ def register():
 
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
+
 ################################# Sign and unsign #####################################
 
 def url_for_hmac(endpoint, **values):
@@ -812,6 +852,7 @@ def data_hmac(stringy):
     """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
     return stringy + ":" + actual_hmac_creation(stringy)
 
+
 def verify_url_hmac(url):
     """Pass in a url that was created with url_hmac and this assures it hasn't been tampered with"""
     logger.debug("url passed in to verify is:", url)
@@ -846,6 +887,13 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 
 #######################################################################################
 
+# def send_email(to, subject, body):
+#     msg = json.dumps(dict(From="no-reply@genenetwork.org",
+#                      To=to,
+#                      Subject=subject,
+#                      Body=body))
+#     Redis.rpush("mail_queue", msg)
+
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
     """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
     'UNKNOWN' TLS is used
@@ -870,4 +918,10 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
 
 class GroupsManager(object):
     def __init__(self, kw):
-        self.datasets = create_datasets_list()
\ No newline at end of file
+        self.datasets = create_datasets_list()
+
+
+class RolesManager(object):
+    def __init__(self):
+        self.roles = model.Role.query.all()
+        logger.debug("Roles are:", self.roles)
-- 
cgit v1.2.3


From f59c0c12415a23982e593f46b608fedab2367c03 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 18 Apr 2018 15:50:32 +0000
Subject: Removed a little more code in webqtlDatabaseFunction.py and do_search

---
 wqflask/db/webqtlDatabaseFunction.py |  8 --------
 wqflask/wqflask/do_search.py         | 28 +---------------------------
 wqflask/wqflask/views.py             |  1 -
 3 files changed, 1 insertion(+), 36 deletions(-)

diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index ba998e91..8a9dc79d 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -30,14 +30,6 @@ logger = getLogger(__name__ )
 #output: cursor instance
 #function: connect to database and return cursor instance
 ###########################################################################
-def getCursor():
-    try:
-        logger.warning("Creating new MySQLdb cursor (this method is OBSOLETE!)")
-        con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
-        cursor = con.cursor()
-        return cursor
-    except:
-        return None
 
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e2a0a479..c7dbc972 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -872,32 +872,6 @@ if __name__ == "__main__":
     dataset_name = "HC_M2_0606_P"
     dataset = create_dataset(db_conn, dataset_name)
 
-    #cursor.execute("""
-    #            SELECT ProbeSet.Name as TNAME, 0 as thistable,
-    #            ProbeSetXRef.Mean as TMEAN, ProbeSetXRef.LRS as TLRS,
-    #            ProbeSetXRef.PVALUE as TPVALUE, ProbeSet.Chr_num as TCHR_NUM,
-    #            ProbeSet.Mb as TMB, ProbeSet.Symbol as TSYMBOL,
-    #            ProbeSet.name_num as TNAME_NUM
-    #            FROM ProbeSetXRef, ProbeSet, Geno
-    #            WHERE ProbeSetXRef.LRS > 99.0 and
-    #            ABS(ProbeSet.Mb-Geno.Mb) < 5 and
-    #            ProbeSetXRef.Locus = Geno.name and
-    #            Geno.SpeciesId = 1 and
-    #            ProbeSet.Chr = Geno.Chr and
-    #            ProbeSet.Id = ProbeSetXRef.ProbeSetId and
-    #            ProbeSetXRef.ProbeSetFreezeId = 112""")
-
-    #logger.debug(pf(cursor.fetchall()))
-    #results = ProbeSetSearch("shh", None, dataset, cursor, db_conn).run()
     results = PvalueSearch(['0.005'], '<', dataset, cursor, db_conn).run()
-    #results = RifSearch("diabetes", dataset, cursor, db_conn).run()
-    #results = WikiSearch("nicotine", dataset, cursor, db_conn).run()
-    #results = CisLrsSearch(['99'], '>', dataset, cursor, db_conn).run() # cisLRS > 99
-    #results = LrsSearch('99', '>', dataset, cursor, db_conn).run()
-    #results = TransLrsSearch(['9', '999', '10'], dataset, cursor, db_conn).run()
-    #results = PhenotypeSearch("brain", dataset, cursor, db_conn).run()
-    #results = GenotypeSearch("rs13475699", dataset, cursor, db_conn).run()
-    #results = GoSearch("0045202", dataset, cursor, db_conn).run()
-
-    logger.debug("results are:", pf(results))
+
     db_conn.close()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 49b47123..2089f9de 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -72,7 +72,6 @@ import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
 
-
 @app.before_request
 def connect_db():
     db = getattr(g, '_database', None)
-- 
cgit v1.2.3


From 72db6b91baf15de4fbd64cd4aef022cf32067b0c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 19 Apr 2018 15:31:23 +0000
Subject: Changed width of top bar and a couple other html objects to 100%
 instead of set width

Changed to using BIMBAM files to build Marker objects in dataset.py
---
 wqflask/base/data_set.py                           | 23 +++++++++++++++++++---
 wqflask/wqflask/marker_regression/gemma_mapping.py |  4 ++--
 .../wqflask/marker_regression/marker_regression.py |  1 -
 wqflask/wqflask/templates/base.html                |  4 ++--
 wqflask/wqflask/templates/index_page_orig.html     |  2 +-
 5 files changed, 25 insertions(+), 9 deletions(-)

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 9ca880d0..4a422ee4 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -169,8 +169,27 @@ class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
         json_data_fh = open(locate(name + ".json",'genotype/json'))
+
         try:
-            markers = json.load(json_data_fh)
+            markers = []
+            with open(locate(name + "_snps.txt", 'r')) as bimbam_fh:
+                marker = {}
+                if len(bimbam_fh[0].split(", ")) > 2:
+                    delimiter = ", "
+                elif len(bimbam_fh[0].split(",")) > 2:
+                    delimiter = ","
+                elif len(bimbam_fh[0].split("\t")) > 2:
+                    delimiter = "\t"
+                else:
+                    delimiter = " "
+                for line in bimbam_fh:
+                    marker['name'] = line.split(delimiter)[0]
+                    marker['Mb']
+                    marker['chr'] = line.split(delimiter)[2]
+                    marker['cM']
+                    markers.append(marker)
+        #try:
+        #    markers = json.load(json_data_fh)
         except:
             markers = []
 
@@ -180,8 +199,6 @@ class Markers(object):
             marker['Mb'] = float(marker['Mb'])
 
         self.markers = markers
-        #logger.debug("self.markers:", self.markers)
-
 
     def add_pvalues(self, p_values):
         logger.debug("length of self.markers:", len(self.markers))
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 7563eb2c..157e4f33 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -32,7 +32,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     if covariates != "":
         gen_covariates_file(this_dataset, covariates)
 
-    if method == "gemma":
+    if method == "gemma_plink":
         gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
                                                                                         this_dataset.group.name,
                                                                                         flat_files('mapping'),
@@ -113,7 +113,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 def gen_pheno_txt_file(this_dataset, genofile_name, vals, method):
     """Generates phenotype file for GEMMA"""
 
-    if method == "gemma":
+    if method == "gemma_plink":
         current_file_data = []
         with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
             for i, line in enumerate(outfile):
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index bfb63995..50e673c4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -587,7 +587,6 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             output_file.write(",Dominance")
         output_file.write("\n")
         for i, marker in enumerate(markers):
-            logger.debug("THE MARKER:", marker)
             output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",")
             if "lod_score" in marker.keys():
                 output_file.write(str(marker['lod_score']))
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 64daa1cc..e8b51523 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -22,9 +22,9 @@
 <body style="width: 100% !important;">
     <!-- Navbar ================================================== -->
 
-    <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation">
+    <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%;">
 
-            <div class="container-fluid" style="width: 1500px !important;">
+            <div class="container-fluid" style="width: 100%;">
                 <!-- Brand and toggle get grouped for better mobile display -->
                 <div class="navbar-header">
                 <a class="navbar-brand" href="/">GeneNetwork</a>
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 72ced084..2a5556ea 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -21,7 +21,7 @@
 
         {{ flash_me() }}
 
-        <div class="row" style="width: 1400px !important;">
+        <div class="row" style="width: 100%;">
 
             <div class="col-xs-5">
                 <section id="search">
-- 
cgit v1.2.3


From 36ceda09d76c898c5f818236122f5d431261a5b1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 23 Apr 2018 16:19:24 +0000
Subject: Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a
 parameter instead of -lmm 1 (Wald test)

Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
---
 wqflask/maintenance/geno_to_json.py                | 195 +++++++++++++++++++++
 wqflask/wqflask/marker_regression/gemma_mapping.py |  10 +-
 .../marker_regression/marker_regression_gn1.py     |   8 +-
 .../templates/show_trait_mapping_tools.html        |  13 ++
 4 files changed, 214 insertions(+), 12 deletions(-)
 create mode 100644 wqflask/maintenance/geno_to_json.py

diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
new file mode 100644
index 00000000..789a1691
--- /dev/null
+++ b/wqflask/maintenance/geno_to_json.py
@@ -0,0 +1,195 @@
+#!/usr/bin/python
+
+"""
+Convert .geno files to json
+
+This file goes through all of the genofiles in the genofile directory (.geno)
+and converts them to json files that are used when running the marker regression
+code
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+import os
+import glob
+import traceback
+import gzip
+
+#import numpy as np
+#from pyLMM import lmm
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class EmptyConfigurations(Exception): pass
+
+        
+
+class Marker(object):
+    def __init__(self):
+        self.name = None
+        self.chr = None
+        self.cM = None
+        self.Mb = None
+        self.genotypes = []
+
+class ConvertGenoFile(object):
+
+    def __init__(self, input_file, output_file):
+        
+        self.input_file = input_file
+        self.output_file = output_file
+        
+        self.mb_exists = False
+        self.cm_exists = False
+        self.markers = []
+        
+        self.latest_row_pos = None
+        self.latest_col_pos = None
+        
+        self.latest_row_value = None
+        self.latest_col_value = None
+        
+    def convert(self):
+
+        self.haplotype_notation = {
+            '@mat': "1",
+            '@pat': "0",
+            '@het': "0.5",
+            '@unk': "NA"
+            }
+        
+        self.configurations = {}
+        #self.skipped_cols = 3
+        
+        #if self.input_file.endswith(".geno.gz"):
+        #    print("self.input_file: ", self.input_file)
+        #    self.input_fh = gzip.open(self.input_file)
+        #else:
+        self.input_fh = open(self.input_file)
+        
+        with open(self.output_file, "w") as self.output_fh:
+            #if self.file_type == "geno":
+            self.process_csv()
+            #elif self.file_type == "snps":
+            #    self.process_snps_file()
+
+
+    def process_csv(self):
+        for row_count, row in enumerate(self.process_rows()):
+            row_items = row.split("\t")
+
+            this_marker = Marker()
+            this_marker.name = row_items[1]
+            this_marker.chr = row_items[0]
+            if self.cm_exists and self.mb_exists:
+                this_marker.cM = row_items[2]
+                this_marker.Mb = row_items[3]
+                genotypes = row_items[4:]
+            elif self.cm_exists:
+                this_marker.cM = row_items[2]
+                genotypes = row_items[3:]
+            elif self.mb_exists:
+                this_marker.Mb = row_items[2]
+                genotypes = row_items[3:]
+            else:
+                genotypes = row_items[2:]
+            for item_count, genotype in enumerate(genotypes):
+                if genotype.upper() in self.configurations:
+                    this_marker.genotypes.append(self.configurations[genotype.upper()])
+                else:
+                    this_marker.genotypes.append("NA")
+                
+            #print("this_marker is:", pf(this_marker.__dict__))   
+            #if this_marker.chr == "14":
+            self.markers.append(this_marker.__dict__)
+
+        with open(self.output_file, 'w') as fh:
+            json.dump(self.markers, fh, indent="   ", sort_keys=True)
+                
+                # print('configurations:', str(configurations))
+                #self.latest_col_pos = item_count + self.skipped_cols
+                #self.latest_col_value = item
+                
+                #if item_count != 0:
+                #    self.output_fh.write(" ")
+                #self.output_fh.write(self.configurations[item.upper()])
+                    
+            #self.output_fh.write("\n")
+
+
+    def process_rows(self):
+        for self.latest_row_pos, row in enumerate(self.input_fh):
+            #if self.input_file.endswith(".geno.gz"):
+            #    print("row: ", row)
+            self.latest_row_value = row
+            # Take care of headers
+            if not row.strip():
+                continue
+            if row.startswith('#'):
+                continue
+            if row.startswith('Chr'):
+                if 'Mb' in row.split():
+                    self.mb_exists = True
+                if 'cM' in row.split():
+                    self.cm_exists = True
+                continue
+            if row.startswith('@'):
+                key, _separater, value = row.partition(':')
+                key = key.strip()
+                value = value.strip()
+                if key in self.haplotype_notation:
+                    self.configurations[value] = self.haplotype_notation[key]
+                continue
+            if not len(self.configurations):
+                raise EmptyConfigurations
+            yield row
+
+    @classmethod
+    def process_all(cls, old_directory, new_directory):
+        os.chdir(old_directory)
+        for input_file in glob.glob("*"):
+            if not input_file.endswith(('geno', '.geno.gz')):
+                continue
+            group_name = ".".join(input_file.split('.')[:-1])
+            output_file = os.path.join(new_directory, group_name + ".json")
+            print("%s -> %s" % (
+                os.path.join(old_directory, input_file), output_file))
+            convertob = ConvertGenoFile(input_file, output_file)
+            try:
+                convertob.convert()
+            except EmptyConfigurations as why:
+                print("  No config info? Continuing...")
+                #excepted = True
+                continue
+            except Exception as why:
+
+                print("  Exception:", why)
+                print(traceback.print_exc())
+                print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
+                                                                convertob.latest_col_pos))
+                print("    Column is:", convertob.latest_col_value)
+                print("    Row is:", convertob.latest_row_value)
+                break
+            
+    #def process_snps_file(cls, snps_file, new_directory):
+    #    output_file = os.path.join(new_directory, "mouse_families.json")
+    #    print("%s -> %s" % (snps_file, output_file))
+    #    convertob = ConvertGenoFile(input_file, output_file)
+        
+
+
+if __name__=="__main__":
+    Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
+    New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/"""
+    #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
+    #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
+    #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
+    #convertob.convert()
+    ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
+    #ConvertGenoFiles(Geno_Directory)
+    
+    #process_csv(Input_File, Output_File)
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 157e4f33..0e31e73e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -33,7 +33,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
         gen_covariates_file(this_dataset, covariates)
 
     if method == "gemma_plink":
-        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
+        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('mapping'),
                                                                                         this_dataset.group.name,
                                                                                         flat_files('mapping'),
                                                                                         this_dataset.group.name)
@@ -43,7 +43,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
                                                                                    webqtlConfig.GENERATED_IMAGE_DIR,
                                                                                    this_dataset.group.name)
         else:
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
+            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 2 -maf 0.1 -o %s_output' % (flat_files('mapping'),
             gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
                                                            this_dataset.group.name)
     else:
@@ -69,20 +69,20 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 
             gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
             if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
                                                                                                                                          this_dataset.group.name,
                                                                                                                                          flat_files('genotype/bimbam'),
                                                                                                                                          genofile_name,
                                                                                                                                          TEMPDIR,
                                                                                                                                          gwa_output_filename)
             else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
                                                                                                                  genofile_name,
                                                                                                                  TEMPDIR,
                                                                                                                  gwa_output_filename)
 
         else:
-            gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('genotype/bimbam'),
+            gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
                                                                                             genofile_name,
                                                                                             flat_files('genotype/bimbam'),
                                                                                             genofile_name,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index da713325..8e9c5b4c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1062,10 +1062,6 @@ class MarkerRegression(object):
 
                 #draw gray blocks for 3' and 5' UTR blocks
                 if cdsStart and cdsEnd:
-                    logger.debug("txStart:", txStart)
-                    logger.debug("cdsStart:", cdsStart)
-                    logger.debug("txEnd:", txEnd)
-                    logger.debug("cdsEnd:", cdsEnd)
                     utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
                     utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
                     if (utrStartPix < xLeftOffset):
@@ -1721,8 +1717,8 @@ class MarkerRegression(object):
         for i, qtlresult in enumerate(self.qtlresults):
             m = 0
             thisLRSColor = self.colorCollection[0]
-
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
+
                 if self.manhattan_plot != True:
                     canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
@@ -1760,7 +1756,6 @@ class MarkerRegression(object):
                 AdditiveCoordXY = []
                 previous_chr = qtlresult['chr']
                 previous_chr_as_int += 1
-
                 newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale
                 if newStartPosX != oldStartPosX:
                     startPosX += newStartPosX
@@ -1773,7 +1768,6 @@ class MarkerRegression(object):
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
                 Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-
                 # updated by NL 06-18-2011:
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                 # for any lrs is over than 460(LRS max in this system), it will be reset to 460
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 0ecf1eb9..d40a7bd6 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -342,6 +342,19 @@
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="True" checked="">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="False">
+                                    No
+                               </label>
+                            </div>
+                        </div>
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
-- 
cgit v1.2.3


From 1995c6018f5d5d93b97f85b908cb67112d3f01b6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 27 Apr 2018 16:07:17 +0000
Subject: Added marker filtering for data set groups with larger genotype files

Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 21 ++++-----
 .../wqflask/marker_regression/marker_regression.py | 55 ++++++++++++++++++++--
 .../marker_regression/marker_regression_gn1.py     |  4 +-
 3 files changed, 62 insertions(+), 18 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 0e31e73e..5242ec05 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -171,9 +171,7 @@ def parse_gemma_output(genofile_name):
     included_markers = []
     p_values = []
     marker_obs = []
-    previous_chr = 0
 
-    #with open("/home/zas1024/gene/wqflask/output/{}_output.assoc.txt".format(this_dataset.group.name)) as output_file:
     with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
         for line in output_file:
             if line.startswith("chr"):
@@ -185,14 +183,8 @@ def parse_gemma_output(genofile_name):
                     marker['chr'] = int(line.split("\t")[0])
                 else:
                     marker['chr'] = line.split("\t")[0]
-                # try:
-                    # marker['chr'] = int(line.split("\t")[0])
-                # except:
-                    # marker['chr'] = previous_chr + 1
-                # if marker['chr'] != previous_chr:
-                    # previous_chr = marker['chr']
                 marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                marker['p_value'] = float(line.split("\t")[11])
+                marker['p_value'] = float(line.split("\t")[9])
                 if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                     marker['lod_score'] = 0
                     #marker['lrs_value'] = 0
@@ -202,7 +194,7 @@ def parse_gemma_output(genofile_name):
                 marker_obs.append(marker)
 
                 included_markers.append(line.split("\t")[1])
-                p_values.append(float(line.split("\t")[11]))
+                p_values.append(float(line.split("\t")[9]))
 
     return marker_obs
 
@@ -222,7 +214,6 @@ def parse_loco_output(this_dataset, gwa_output_filename):
     previous_chr = 0
 
     for this_file in output_filelist:
-        #with open("/home/zas1024/gene/wqflask/output/{}_output.assoc.txt".format(this_dataset.group.name)) as output_file:
         with open(this_file) as output_file:
             for line in output_file:
                 if line.startswith("chr"):
@@ -232,10 +223,14 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     marker['name'] = line.split("\t")[1]
                     if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
                         marker['chr'] = int(line.split("\t")[0])
+                        if marker['chr'] > previous_chr:
+                            previous_chr = marker['chr']
+                        elif marker['chr'] < previous_chr:
+                            break
                     else:
                         marker['chr'] = line.split("\t")[0]
                     marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                    marker['p_value'] = float(line.split("\t")[11])
+                    marker['p_value'] = float(line.split("\t")[9])
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                         #marker['lrs_value'] = 0
@@ -245,6 +240,6 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     marker_obs.append(marker)
 
                     included_markers.append(line.split("\t")[1])
-                    p_values.append(float(line.split("\t")[11]))
+                    p_values.append(float(line.split("\t")[9]))
 
     return marker_obs
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 50e673c4..a3631462 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -285,9 +285,15 @@ class MarkerRegression(object):
                     if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                         self.qtl_results.append(marker)
 
-            export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
+            with Bench("Exporting Results"):
+                export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
-            self.trimmed_markers = trim_markers_for_table(results)
+            with Bench("Trimming Markers for Figure"):
+                if len(self.qtl_results) > 20000:
+                    self.qtl_results = trim_markers_for_figure(self.qtl_results)
+
+            with Bench("Trimming Markers for Table"):
+                self.trimmed_markers = trim_markers_for_table(results)
 
             if self.mapping_method != "gemma":
                 self.json_data['chr'] = []
@@ -321,8 +327,6 @@ class MarkerRegression(object):
                     self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
                     chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
 
-                # logger.debug("json_data:", self.json_data)
-
                 self.js_data = dict(
                     result_score_type = self.score_type,
                     json_data = self.json_data,
@@ -599,6 +603,49 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             if i < (len(markers) - 1):
                 output_file.write("\n")
 
+def trim_markers_for_figure(markers):
+    if 'lod_score' in markers[0].keys():
+        score_type = 'lod_score'
+    else:
+        score_type = 'lrs_value'
+
+    filtered_markers = []
+    low_counter = 0
+    med_counter = 0
+    high_counter = 0
+    for marker in markers:
+        if score_type == 'lod_score':
+            if marker[score_type] < 1:
+                if low_counter % 20 == 0:
+                    filtered_markers.append(marker)
+                low_counter += 1
+            elif 1 <= marker[score_type] < 2:
+                if med_counter % 10 == 0:
+                    filtered_markers.append(marker)
+                med_counter += 1
+            elif 2 <= marker[score_type] <= 3:
+                if high_counter % 2 == 0:
+                    filtered_markers.append(marker)
+                high_counter += 1
+            else:
+                filtered_markers.append(marker)
+        else:
+            if marker[score_type] < 4.16:
+                if low_counter % 20 == 0:
+                    filtered_markers.append(marker)
+                low_counter += 1
+            elif 4.16 <= marker[score_type] < (2*4.16):
+                if med_counter % 10 == 0:
+                    filtered_markers.append(marker)
+                med_counter += 1
+            elif (2*4.16) <= marker[score_type] <= (3*4.16):
+                if high_counter % 2 == 0:
+                    filtered_markers.append(marker)
+                high_counter += 1
+            else:
+                filtered_markers.append(marker)
+    return filtered_markers
+
 def trim_markers_for_table(markers):
     if 'lod_score' in markers[0].keys():
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 8e9c5b4c..40402597 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -41,6 +41,7 @@ from base.GeneralObject import GeneralObject
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot
+from utility.benchmark import Bench
 from wqflask.interval_analyst import GeneUtil
 from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
 
@@ -427,7 +428,8 @@ class MarkerRegression(object):
         ################################################################
         showLocusForm = ""
         intCanvas = pid.PILCanvas(size=(self.graphWidth, self.graphHeight))
-        gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
+        with Bench("Drawing Plot"):
+            gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
 
         self.gifmap = gifmap.__str__()
 
-- 
cgit v1.2.3


From ff20eff6ad7e86f890f7de7fb3779e313d9b66ee Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 1 May 2018 19:59:57 +0000
Subject: Removed all code related to using GEMMA with PLINK input files

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 144 ++++++++-------------
 .../wqflask/marker_regression/marker_regression.py |   6 +-
 .../new/javascript/show_trait_mapping_tools.js     |  32 -----
 .../templates/show_trait_mapping_tools.html        | 107 +--------------
 4 files changed, 64 insertions(+), 225 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 5242ec05..dc13afc3 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -8,7 +8,7 @@ from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMP
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
+def run_gemma(this_dataset, samples, vals, covariates, use_loco):
     """Generates p-values for each marker using GEMMA"""
 
     if this_dataset.group.genofile != None:
@@ -16,7 +16,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     else:
         genofile_name = this_dataset.group.name
 
-    gen_pheno_txt_file(this_dataset, genofile_name, vals, method)
+    gen_pheno_txt_file(this_dataset, genofile_name, vals)
 
     if not os.path.isfile("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)):
         open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name), "w+")
@@ -32,73 +32,58 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
     if covariates != "":
         gen_covariates_file(this_dataset, covariates)
 
-    if method == "gemma_plink":
-        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('mapping'),
-                                                                                        this_dataset.group.name,
-                                                                                        flat_files('mapping'),
-                                                                                        this_dataset.group.name)
+    if use_loco == "True":
+        k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+        generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        TEMPDIR,
+                                                                                        k_output_filename)
+        logger.debug("k_command:" + generate_k_command)
+        os.system(generate_k_command)
+
+        gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
+                                                                                        k_output_filename,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name)
+
+        gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
         if covariates != "":
-            gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
-                                                                                   this_dataset.group.name,
-                                                                                   webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                                   this_dataset.group.name)
+            gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+                                                                                                                                     this_dataset.group.name,
+                                                                                                                                     flat_files('genotype/bimbam'),
+                                                                                                                                     genofile_name,
+                                                                                                                                     TEMPDIR,
+                                                                                                                                     gwa_output_filename)
         else:
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 2 -maf 0.1 -o %s_output' % (flat_files('mapping'),
-            gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
-                                                           this_dataset.group.name)
+            gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                                                                                                             genofile_name,
+                                                                                                             TEMPDIR,
+                                                                                                             gwa_output_filename)
+
     else:
-        if use_loco == "True":
-            k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
-            generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            TEMPDIR,
-                                                                                            k_output_filename)
-            logger.debug("k_command:" + generate_k_command)
-            os.system(generate_k_command)
-
-            gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (TEMPDIR,
-                                                                                            k_output_filename,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name)
-
-            gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
-            if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
-                                                                                                                                         this_dataset.group.name,
-                                                                                                                                         flat_files('genotype/bimbam'),
-                                                                                                                                         genofile_name,
-                                                                                                                                         TEMPDIR,
-                                                                                                                                         gwa_output_filename)
-            else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-                                                                                                                 genofile_name,
-                                                                                                                 TEMPDIR,
-                                                                                                                 gwa_output_filename)
+        gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name,
+                                                                                        flat_files('genotype/bimbam'),
+                                                                                        genofile_name)
 
+        if covariates != "":
+            gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
+                                                                                                         this_dataset.group.name,
+                                                                                                         webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                                                         genofile_name)
         else:
-            gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name,
-                                                                                            flat_files('genotype/bimbam'),
-                                                                                            genofile_name)
-
-            if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
-                                                                                                             this_dataset.group.name,
-                                                                                                             webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                                                             genofile_name)
-            else:
-                gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
-                                                                      genofile_name)
+            gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+                                                                  genofile_name)
 
     logger.debug("gemma_command:" + gemma_command)
     os.system(gemma_command)
@@ -110,31 +95,16 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 
     return marker_obs
 
-def gen_pheno_txt_file(this_dataset, genofile_name, vals, method):
+def gen_pheno_txt_file(this_dataset, genofile_name, vals):
     """Generates phenotype file for GEMMA"""
 
-    if method == "gemma_plink":
-        current_file_data = []
-        with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile:
-            for i, line in enumerate(outfile):
-                split_line = line.split()
-                current_file_data.append(split_line)
-
-        with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile:
-            for i, line in enumerate(current_file_data):
-                if vals[i] == "x":
-                    this_val = -9
-                else:
-                    this_val = vals[i]
-                outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
-    else:
-        current_file_data = []
-        with open("{}/{}_pheno.txt".format(flat_files('genotype/bimbam'), genofile_name), "w") as outfile:
-            for value in vals:
-                if value == "x":
-                    outfile.write("NA\n")
-                else:
-                    outfile.write(value + "\n")
+    current_file_data = []
+    with open("{}/{}_pheno.txt".format(flat_files('genotype/bimbam'), genofile_name), "w") as outfile:
+        for value in vals:
+            if value == "x":
+                outfile.write("NA\n")
+            else:
+                outfile.write(value + "\n")
 
 def gen_covariates_file(this_dataset, covariates):
     covariate_list = covariates.split(",")
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a3631462..033fa2a4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -174,11 +174,11 @@ class MarkerRegression(object):
             self.genofile_string = start_vars['genofile']
             self.dataset.group.genofile = self.genofile_string.split(":")[0]
         self.dataset.group.get_markers()
-        if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
+        if self.mapping_method == "gemma":
             self.score_type = "-log(p)"
             self.manhattan_plot = True
             with Bench("Running GEMMA"):
-                marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.mapping_method, self.use_loco)
+                marker_obs = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals, self.covariates, self.use_loco)
             results = marker_obs
         elif self.mapping_method == "rqtl_plink":
             results = self.run_rqtl_plink()
@@ -289,7 +289,7 @@ class MarkerRegression(object):
                 export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
             with Bench("Trimming Markers for Figure"):
-                if len(self.qtl_results) > 20000:
+                if len(self.qtl_results) > 30000:
                     self.qtl_results = trim_markers_for_figure(self.qtl_results)
 
             with Bench("Trimming Markers for Table"):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 4d98f5d8..81123de7 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -208,41 +208,10 @@
     };
   })(this));
 
-  $("#plink_compute").on("click", (function(_this) {
-    return function() {
-      var form_data, url;
-      //$("#static_progress_bar_container").modal();
-      url = "/loading";
-      $('input[name=method]').val("plink");
-      $('input[name=maf]').val($('input[name=maf_plink]').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
-    };
-  })(this));
-
   $("#gemma_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
       console.log("RUNNING GEMMA");
-      //$("#static_progress_bar_container").modal();
-      url = "/loading";
-      $('input[name=method]').val("gemma");
-      $('input[name=genofile]').val($('#genofile_gemma').val());
-      $('input[name=maf]').val($('input[name=maf_gemma]').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
-    };
-  })(this));
-
-  $("#gemma_bimbam_compute").on("click", (function(_this) {
-    return function() {
-      var form_data, url;
-      console.log("RUNNING GEMMA");
-      //$("#static_progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("gemma_bimbam");
       $('input[name=num_perm]').val(0);
@@ -251,7 +220,6 @@
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       return submit_special(url);
-      //return do_ajax_post(url, form_data);
     };
   })(this));
 
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index d40a7bd6..3d31797a 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -35,7 +35,6 @@
             </ul>
 
             <div class="tab-content">
-                {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane active" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
@@ -88,13 +87,14 @@
                         <div class="mapping_method_fields form-group">
                           <label class="col-xs-3 control-label"></label>
                           <div style="margin-left:20px;" class="col-xs-6">
-                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+                            <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
                           </div>
                         </div>
                     </div>
                 </div>
+                {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
@@ -164,8 +164,6 @@
                             </div>
                         </div>
 -->
-
-
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
@@ -187,11 +185,9 @@
                               </button>
                             </div>
                         </div>
-                        <!--<div id="alert_placeholder"></div>-->
                     </div>
                 </div>
                 <div class="tab-pane" id="rqtl_geno">
-
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
@@ -320,117 +316,22 @@
                     </div>
                 </div>
                 {% endif %}
-                {% for mapping_method in dataset.group.mapping_names %}
-                {% if mapping_method == "GEMMA" %}
-                <div class="tab-pane active" id="gemma_plink">
-                    <div style="padding-top: 10px;" class="form-horizontal">
-                        {% if genofiles and genofiles|length>0 %}
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <select id="genofile_gemma" class="form-control">
-                                    {% for item in genofiles %}
-                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
-                                    {% endfor %}
-                                </select>
-                            </div>
-                        </div>
-                        {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="maf_gemma" value="0.01" type="text" class="form-control">
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="True" checked="">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="False">
-                                    No
-                               </label>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
-                            <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
-                              No collections available. Please add traits to a collection to use them as covariates.
-                              {% elif g.cookie_session.display_num_collections() == "" %}
-                              No collections available. Please add traits to a collection to use them as covariates.
-                              {% else %}
-                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
-                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
-                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
-                              </div>
-                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
-                              {% endif %}
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                          <label class="col-xs-3 control-label"></label>
-                          <div style="margin-left:20px;" class="col-xs-6">
-                            <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                          </div>
-                        </div>
-                    </div>
-                </div>
-                {% elif mapping_method == "PLINK" %}
-                <div class="tab-pane" id="plink">
-                    <div style="padding: 20px" class="form-horizontal">
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">MAF</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                <input name="maf_plink" value="0.01" type="text" class="form-control">
-                            </div>
-                        </div>
-                    </div>
-
-                    <div class="form-group">
-                        <label style="text-align: right;" class="col-xs-3 control-label"></label>
-                        <div style="margin-left:20px;" class="col-xs-6 controls">
-                            <button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
-                        </div>
-                    </div>
-                </div>
-                {% endif %}
-                {% endfor %}
             </div>
         </div>
     </div>
     <div class="col-xs-5">
-        {% if dataset.group.mapping_id == "1" %}
         <dl>
              <dt>GEMMA</dt>
              <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd>
+             {% if dataset.group.mapping_id == "1" %}
              <dt>Interval Mapping</dt>
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
              <dt>pyLMM</dt>
              <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+             {% endif %}
         </dl>
-        {% else %}
-        <dl>
-            {% if mapping_method == "GEMMA" %}
-            <dt>GEMMA</dt>
-            <dd>
-                GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br>
-            </dd>
-            {% elif mapping_method == "PLINK" %}
-            <dt>PLINK</dt>
-            <dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
-            {% endif %}
-        </dl>
-        {% endif %}
     </div>
     <div id="mapping_result_holder_wrapper" style="display:none;">
         <div id="mapping_result_holder"></div>
-- 
cgit v1.2.3


From 67e8f12e103f48329d8b3e38125c0e84b9dc089d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 May 2018 16:32:44 +0000
Subject: Added script to quantile normalize a data set and enter its
 normalized sample data into ElasticSearch

Added option to replace trait page sample/strain values with normalized ones

Began editing Lei's scatterplot code

Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
---
 wqflask/base/anon_collection.py                    |  22 -
 wqflask/base/trait_collection.py                   |  53 ---
 wqflask/maintenance/quantile_normalize.py          | 129 ++++++
 wqflask/utility/elasticsearch_tools.py             |   5 +-
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  53 +--
 wqflask/wqflask/show_trait/SampleList.py           |  77 ++--
 wqflask/wqflask/show_trait/show_trait.py           |   4 -
 .../wqflask/static/new/css/corr_scatter_plot.css   |  40 +-
 .../static/new/javascript/draw_corr_scatterplot.js |  71 ++-
 .../wqflask/static/new/javascript/show_trait.js    |  13 +
 .../new/javascript/show_trait_mapping_tools.js     |   2 +-
 wqflask/wqflask/templates/corr_scatterplot.html    | 476 +++++++++++----------
 .../wqflask/templates/show_trait_edit_data.html    |   6 +-
 13 files changed, 567 insertions(+), 384 deletions(-)
 delete mode 100644 wqflask/base/anon_collection.py
 delete mode 100644 wqflask/base/trait_collection.py
 create mode 100644 wqflask/maintenance/quantile_normalize.py

diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
deleted file mode 100644
index dd1aa27f..00000000
--- a/wqflask/base/anon_collection.py
+++ /dev/null
@@ -1,22 +0,0 @@
-class AnonCollection(TraitCollection):
-    
-    def __init__(self, anon_id):
-        self.anon_id = anon_id
-        self.collection_members = Redis.smembers(self.anon_id)
-        print("self.collection_members is:", self.collection_members)
-        self.num_members = len(self.collection_members)
-        
-
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits(traits_to_remove):
-        print("traits_to_remove:", traits_to_remove)
-        for trait in traits_to_remove:
-            Redis.srem(self.anon_id, trait)
-
-        members_now = self.collection_members - traits_to_remove
-        print("members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py
deleted file mode 100644
index d388a3af..00000000
--- a/wqflask/base/trait_collection.py
+++ /dev/null
@@ -1,53 +0,0 @@
-class TraitCollection(object):
-    
-    def __init__(self, is_anon=False):
-        self.is_anon = is_anon
-        
-        
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits():
-        if is_anon:
-            AnonCollection.remove_traits()
-        else:
-            UserCollection.remove_traits()
-            
-        params = request.form
-        print("params are:", params)
-        uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
-        traits_to_remove = params.getlist('traits[]')
-        print("traits_to_remove are:", traits_to_remove)
-        traits_to_remove = process_traits(traits_to_remove)
-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)
-        all_traits = uc.members_as_set()
-        print("  all_traits:", all_traits)
-        members_now = all_traits - traits_to_remove
-        print("  members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
-        uc.members = json.dumps(list(members_now))
-        uc.changed_timestamp = datetime.datetime.utcnow()
-        db_session.commit()
-    
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
-
-    def __init__(self, anon_id)
-        self.anon_key = anon_key
-        self.collection_members = Redis.smembers(self.anon_id)
-        print("self.collection_members is:", self.collection_members)
-        self.num_members = len(self.collection_members)
-        
-
-    @app.route("/collections/remove", methods=('POST',))
-    def remove_traits(traits_to_remove):
-        print("traits_to_remove:", traits_to_remove)
-        for trait in traits_to_remove:
-            Redis.srem(self.anon_id, trait)
-        members_now = self.collection_members - traits_to_remove
-        print("members_now:", members_now)
-        print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
-        # We need to return something so we'll return this...maybe in the future
-        # we can use it to check the results
-        return str(len(members_now))
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
new file mode 100644
index 00000000..c11073fb
--- /dev/null
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -0,0 +1,129 @@
+from __future__ import absolute_import, print_function, division
+
+import sys
+sys.path.insert(0,'./')
+
+from itertools import izip
+
+import MySQLdb
+import urlparse
+
+import numpy as np
+import pandas as pd
+from elasticsearch import Elasticsearch, TransportError
+from elasticsearch.helpers import bulk
+
+from flask import Flask, g, request
+
+from wqflask import app
+from utility.elasticsearch_tools import get_elasticsearch_connection
+from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
+
+def parse_db_uri():
+    """Converts a database URI to the db name, host name, user name, and password"""
+
+    parsed_uri = urlparse.urlparse(SQL_URI)
+
+    db_conn_info = dict(
+                        db = parsed_uri.path[1:],
+                        host = parsed_uri.hostname,
+                        user = parsed_uri.username,
+                        passwd = parsed_uri.password)
+
+    print(db_conn_info)
+    return db_conn_info
+
+def create_dataframe(input_file):
+    with open(input_file) as f:
+        ncols = len(f.readline().split("\t"))
+
+    input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=range(1, ncols))
+    return pd.DataFrame(input_array)
+
+#This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+def quantileNormalize(df_input):
+    df = df_input.copy()
+    #compute rank
+    dic = {}
+    for col in df:
+        dic.update({col : sorted(df[col])})
+    sorted_df = pd.DataFrame(dic)
+    rank = sorted_df.mean(axis = 1).tolist()
+    #sort
+    for col in df:
+        t = np.searchsorted(np.sort(df[col]), df[col])
+        df[col] = [rank[i] for i in t]
+    return df
+
+def set_data(dataset_name):
+    orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
+
+    sample_list = []
+    with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh:
+        for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)):
+            trait_dict = {}
+            sample_list = []
+            if i == 0:
+                sample_names = line1.split('\t')[1:]
+            else:
+                trait_name = line1.split('\t')[0]
+                for i, sample in enumerate(sample_names):
+                    this_sample = {
+                                    "name": sample,
+                                    "value": line1.split('\t')[i+1],
+                                    "qnorm": line2.split('\t')[i+1]
+                                  }
+                    sample_list.append(this_sample)
+                query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
+                           FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet
+                           WHERE Species.Id = InbredSet.SpeciesId and
+                                 InbredSet.Id = ProbeFreeze.InbredSetId and
+                                 ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId and
+                                 ProbeSetFreeze.Name = '%s' and
+                                 ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId and
+                                 ProbeSetXRef.ProbeSetId = ProbeSet.Id and
+                                 ProbeSet.Name = '%s'""" % (dataset_name, line1.split('\t')[0])
+                Cursor.execute(query)
+                result_info = Cursor.fetchone()
+
+                yield {
+                    "_index": "traits",
+                    "_type": "trait",
+                    "_source": {
+                        "name": trait_name,
+                        "species": result_info[0],
+                        "group": result_info[1],
+                        "dataset": dataset_name,
+                        "dataset_fullname": result_info[2],
+                        "samples": sample_list,
+                        "transform_types": "qnorm"
+                    }
+                }
+
+if __name__ == '__main__':
+    Conn = MySQLdb.Connect(**parse_db_uri())
+    Cursor = Conn.cursor()
+
+    #es = Elasticsearch([{
+    #    "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
+    #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+
+    es = get_elasticsearch_connection(for_user=False)
+
+    #input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
+    #input_df = create_dataframe(input_filename)
+    #output_df = quantileNormalize(input_df)
+
+    #output_df.to_csv('quant_norm.csv', sep='\t')
+
+    #out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
+
+    #success, _ = bulk(es, set_data(sys.argv[1]))
+
+    response = es.search(
+        index = "traits", doc_type = "trait", body = {
+            "query": { "match": { "name": "ENSMUSG00000028982" } }
+        }
+    )
+
+    print(response)
\ No newline at end of file
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index cce210c3..293a9ae6 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -52,7 +52,7 @@ def test_elasticsearch_connection():
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
-def get_elasticsearch_connection():
+def get_elasticsearch_connection(for_user=True):
     """Return a connection to ES. Returns None on failure"""
     logger.info("get_elasticsearch_connection")
     es = None
@@ -65,7 +65,8 @@ def get_elasticsearch_connection():
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
         }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
-        setup_users_index(es)
+        if for_user:
+            setup_users_index(es)
 
         es_logger = logging.getLogger("elasticsearch")
         es_logger.setLevel(logging.INFO)
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 94711c67..831baf7e 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -6,44 +6,19 @@ from utility import corr_result_helpers
 from scipy import stats
 import numpy as np
 
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
 class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
         self.data_set_1 = data_set.create_dataset(params['dataset_1'])
         self.data_set_2 = data_set.create_dataset(params['dataset_2'])
+        #self.data_set_3 = data_set.create_dataset(params['dataset_3'])
         self.trait_1 = GeneralTrait(name=params['trait_1'], dataset=self.data_set_1)
         self.trait_2 = GeneralTrait(name=params['trait_2'], dataset=self.data_set_2)
-
-        try:
-            width = int(params['width'])
-        except:
-            width = 800
-
-        try:
-            height = int(params['height'])
-        except:
-            height = 600
-
-        try:
-            circle_color = params['circle_color']
-        except:
-            circle_color = '#3D85C6'
-
-        try:
-            circle_radius = int(params['circle_radius'])
-        except:
-            circle_radius = 5
-
-        try:
-            line_color = params['line_color']
-        except:
-            line_color = '#FF0000'
-
-        try:
-            line_width = int(params['line_width'])
-        except:
-            line_width = 1
+        #self.trait_3 = GeneralTrait(name=params['trait_3'], dataset=self.data_set_3)
 
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
@@ -60,14 +35,18 @@ class CorrScatterPlot(object):
 
         x = np.array(vals_1)
         y = np.array(vals_2)
-        slope, intercept, r_value, p_value, _std_err = stats.linregress(x, y)
+        slope, intercept, r_value, p_value, std_err = stats.linregress(x, y)
         
         rx = stats.rankdata(x)
         ry = stats.rankdata(y)        
         self.rdata = []
         self.rdata.append(rx.tolist())
         self.rdata.append(ry.tolist())        
-        srslope, srintercept, srr_value, srp_value, _srstd_err = stats.linregress(rx, ry)
+        srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry)
+
+        #vals_3 = []
+        #for sample in self.trait_3.data:
+        #    vals_3.append(self.trait_3.data[sample].value)
 
         self.js_data = dict(
             data = self.data,
@@ -89,13 +68,9 @@ class CorrScatterPlot(object):
             srslope = srslope,
             srintercept = srintercept,
             srr_value = srr_value,
-            srp_value = srp_value,
+            srp_value = srp_value
 
-            width = width,
-            height = height,
-            circle_color = circle_color,
-            circle_radius = circle_radius,
-            line_color = line_color,
-            line_width = line_width
+            #trait3 = self.trait_3.data,
+            #vals_3 = vals_3
         )
         self.jsdata = self.js_data
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6d84a960..78bb3b42 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -10,8 +10,12 @@ import numpy as np
 from scipy import stats
 from pprint import pformat as pf
 
+import simplejson as json
+
 import itertools
 
+from utility.elasticsearch_tools import get_elasticsearch_connection
+
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -33,6 +37,8 @@ class SampleList(object):
 
         self.get_attributes()
 
+        self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
+
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
 
@@ -152,36 +158,47 @@ class SampleList(object):
 
         return any(sample.variance for sample in self.sample_list)
 
-#def z_score(vals):
-#    vals_array = np.array(vals)
-#    mean = np.mean(vals_array)
-#    stdv = np.std(vals_array)
-#
-#    z_scores = []
-#    for val in vals_array:
-#        z_score = (val - mean)/stdv
-#        z_scores.append(z_score)
-#
-#
-#
-#    return z_scores
-
-
-#def z_score(row):
-#    L = [n for n in row if not np.isnan(n)]
-#    m = np.mean(L)
-#    s = np.std(L)
-#    zL = [1.0 * (n - m) / s for n in L]
-#    if len(L) == len(row):  return zL
-#    # deal with nan
-#    retL = list()
-#    for n in row:
-#        if np.isnan(n):
-#            retL.append(nan)
-#        else:
-#            retL.append(zL.pop(0))
-#    assert len(zL) == 0
-#    return retL
+def get_transform_vals(dataset, trait):
+    es = get_elasticsearch_connection(for_user=False)
+
+    logger.info("DATASET NAME:", dataset.name)
+
+    query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
+
+    es_body = {
+          "query": {
+            "bool": {
+              "must": [
+                {
+                  "match": {
+                    "name": "%s" % (trait.name)
+                  }
+                },
+                {
+                  "match": {
+                    "dataset": "%s" % (dataset.name)
+                  }
+                }
+              ]
+            }
+          }
+    }
+
+    response = es.search( index = "traits", doc_type = "trait", body = es_body )
+    logger.info("THE RESPONSE:", response)
+    results = response['hits']['hits']
+
+    if len(results) > 0:
+        samples = results[0]['_source']['samples']
+
+        sample_dict = {}
+        for sample in samples:
+            sample_dict[sample['name']] = sample['qnorm']
+
+        logger.info("SAMPLE DICT:", sample_dict)
+        return sample_dict
+    else:
+        return None
 
 def natural_sort_key(x):
     """Get expected results when using as a key for sort - ints or strings are sorted properly"""
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 8b801396..d6d83c02 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -26,9 +26,6 @@ from db import webqtlDatabaseFunction
 
 from pprint import pformat as pf
 
-from utility.tools import flat_files, flat_file_exists
-from utility.tools import get_setting
-
 from utility.logger import getLogger
 logger = getLogger(__name__ )
 
@@ -306,7 +303,6 @@ def get_nearest_marker(this_trait, this_db):
         #return "", ""
     else:
         return result[0][0]
-        #return result[0][0], result[1][0]
 
 def get_genofiles(this_dataset):
     jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, this_dataset.group.name)
diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot.css b/wqflask/wqflask/static/new/css/corr_scatter_plot.css
index c62d4c9a..a2ebb252 100644
--- a/wqflask/wqflask/static/new/css/corr_scatter_plot.css
+++ b/wqflask/wqflask/static/new/css/corr_scatter_plot.css
@@ -1,13 +1,41 @@
-.chart {
+.nvd3 .nv-axis.nv-x text {
+  font-size: 16px;
+  font-weight: normal;
+  fill: black;
+}
 
+.nvd3 .nv-axis.nv-y text {
+  font-size: 16px;
+  font-weight: normal;
+  fill: black;
 }
 
-.main text {
-    font: 10px sans-serif;	
+.nv-x .nv-axis g path.domain {
+    stroke: black;
+    stroke-width: 2;
 }
 
-.axis line, .axis path {
-    shape-rendering: crispEdges;
+.nv-y .nv-axis g path.domain {
     stroke: black;
-    fill: none;
+    stroke-width: 2;
+}
+
+.nvd3 .nv-axis.nv-x path.domain {
+    stroke-opacity: 1;
+}
+
+.nvd3 .nv-axis.nv-y path.domain {
+    stroke-opacity: 1;
+}
+
+line.nv-regLine {
+    stroke: red;
+    stroke-width: 1;
+}
+
+.nv-axisMin-x,
+.nv-axisMax-x,
+.nv-axisMin-y,
+.nv-axisMax-y {
+    display: none;
 }
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index cfde6f09..c290cdfe 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,3 +1,5 @@
+// http://gn2-lei.genenetwork.org/corr_scatter_plot2?dataset_1=HC_M2_0606_P&dataset_2=HC_M2_0606_P&dataset_3=HC_M2_0606_P&trait_1=1427571_at&trait_2=1457022_at&trait_3=1427571_at
+
 var chart;
 var srchart;
 
@@ -7,7 +9,7 @@ function drawg() {
     //
     chart.showLegend(false);
     chart.duration(300);
-    chart.color(d3.scale.category10().range());
+    //chart.color(d3.scale.category10().range());
     chart.pointRange([0, 400]);
     chart.pointDomain([0, 10]);
     //
@@ -74,18 +76,47 @@ function getdata(size, shape) {
             slope: js_data.slope,
             intercept: js_data.intercept
         });
+
+    sizemin = 1;
+    sizemax = 50;
+    if ('vals_3' in js_data) {
+        datamin = d3.min(js_data.vals_3);
+        datamax = d3.max(js_data.vals_3);
+        colormin = $("#cocolorfrom").val();
+        colormax = $("#cocolorto").val();
+        compute = d3.interpolate(colormin, colormax);
+        linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+    }
+
     for (j = 0; j < js_data.data[0].length; j++) {
+        if ('trait3' in js_data) {
+          if (js_data.indIDs[j] in js_data.trait3) {
+            datav = js_data.trait3[js_data.indIDs[j]].value;
+            // size = (sizemax - sizemin) * (datav - datamin) / (datamax - datamin) + sizemin;
+            sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
+          }
+        } else {
+            datav = 0;
+            sizev = sizemin;
+        }
         data[0].values.push({
             x: js_data.data[0][j],
             y: js_data.data[1][j],
             name: js_data.indIDs[j],
-            size: size,
-            shape: shape
+            size: sizev,
+            shape: shape,
+            v3: datav
         });
     }
+    console.log(data);
     return data;
 }
 
+function map1to2 (min1, max1, min2, max2, v1) {
+    v2 = (v1 - min1) * (max2 - min2) / (max1 - min1) + min2;
+    return v2;
+}
+
 function srgetdata(size, shape) {
     var data = [];
     data.push({
@@ -94,6 +125,12 @@ function srgetdata(size, shape) {
             intercept: js_data.srintercept
         });
     for (j = 0; j < js_data.rdata[0].length; j++) {
+        if (js_data.indIDs[j] in js_data.trait3) {
+            size = js_data.trait3[js_data.indIDs[j]].value;
+            //console.log("yes "+js_data.indIDs[j]+", "+size);
+        } else {
+            //console.log("no "+js_data.indIDs[j]);
+        }
         data[0].values.push({
             x: js_data.rdata[0][j],
             y: js_data.rdata[1][j],
@@ -163,13 +200,39 @@ function chartupdatewh() {
     window.dispatchEvent(new Event('resize'));
 }
 
+ function colorer(d) {
+    datamin = d3.min(js_data.vals_3);
+    datamax = d3.max(js_data.vals_3);
+    //colormin = d3.rgb(255,0,0);
+    //colormax = d3.rgb(0,255,0);
+    colormin = $("#cocolorfrom").val();
+    colormax = $("#cocolorto").val();
+
+    console.log("colormin: "+colormin);
+    console.log("colormax: "+colormax);
+
+    compute = d3.interpolate(colormin, colormax);
+    linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+    //console.log(d[0].x);
+          c= compute(linear(d[0].x));
+          //console.log(c);
+          return c;
+  }
+
 function chartupdatedata() {
     //
     var size = $("#marksize").val();
     var shape = $("#markshape").val();
     //
-    d3.select('#scatterplot2 svg').datum(nv.log(getdata(size, shape))).call(chart);
+    d3.select('#scatterplot2 svg').datum(getdata(size, shape)).call(chart);
     d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
+    //
+    d3.selectAll('.nv-point')
+      .attr({
+          'stroke': colorer,
+          'fill':   colorer
+      });
+    //
     nv.utils.windowResize(chart.update);
     nv.utils.windowResize(srchart.update);
 }
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index dfdafaf0..17afc814 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -559,6 +559,18 @@
       })(this));
     };
     $('#reset').click(reset_samples_table);
+    switch_qnorm_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          transform_val = $(element).data('transform')
+          if (transform_val != "") {
+              $(element).val(transform_val.toFixed(3));
+          }
+          return transform_val
+        };
+      })(this));
+    };
+    $('#qnorm').click(switch_qnorm_data);
     get_sample_table_data = function(table_name) {
       var samples;
       samples = [];
@@ -871,6 +883,7 @@
     $('#exclude_group').click(edit_data_change);
     $('#block_outliers').click(edit_data_change);
     $('#reset').click(edit_data_change);
+    $('#qnorm').click(edit_data_change);
     return console.log("end");
   });
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 81123de7..daa5b3f2 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -213,7 +213,7 @@
       var form_data, url;
       console.log("RUNNING GEMMA");
       url = "/loading";
-      $('input[name=method]').val("gemma_bimbam");
+      $('input[name=method]').val("gemma");
       $('input[name=num_perm]').val(0);
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 87588534..e0f017c2 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -1,222 +1,254 @@
-{% extends "base.html" %}
-
-{% block css %}
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
-	<link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
-	<link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot2.css" />
-{% endblock %}
-
-{% block content %}
-
-<div class="container-fluid">
-
-<h2>Correlation Scatterplot</h2>
-
-<div style="margin-left: 0px;">
-
-    {% if trait_1.dataset.type == "ProbeSet" %}
-		<div>
-			X axis:
-			<a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-				{{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
-			</a>
-		</div>
-		<div>
-			[{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
-			{{trait_1.description_display}}
-		</div>
-    {% elif trait_1.dataset.type == "Publish" %}
-		<div>
-			X axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-                {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
-            </a>
-		</div>
-		<div>
-			<a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
-			{{trait_1.description_display}}	
-		</div>
-    {% endif %}
-
-	<br/>
-
-    {% if trait_2.dataset.type == "ProbeSet" %}
-		<div>
-			Y axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-                {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
-            </a>
-        </div>
-        <div>
-			[{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
-			{{trait_2.description_display}}
-		</div>
-    {% elif trait_2.dataset.type == "Publish" %}
-        <div>
-			Y axis:
-            <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-                {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
-            </a>
-        </div>
-        <div>
-			<a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
-			{{trait_2.description_display}}
-		</div>
-    {% endif %}
-	
-</div>
-
-<br>
-
-<table class="table">
-	<tr>
-        <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
-        <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
-    </tr>
-</table>
-
-<table class="table">
-    <tr>
-		<td style="vertical-align: middle;">Mark
-            <input class="chartupdate" id="markcolor" type="color" value="#8fbbda">
-            <select class="chartupdatedata" id="marksize" style="width: 44px; height: 22px;">
-                <option value="0">0</option>
-                <option value="1">1</option>
-                <option value="2">2</option>
-                <option value="3">3</option>
-                <option value="4">4</option>
-                <option value="5" selected>5</option>
-                <option value="6">6</option>
-                <option value="7">7</option>
-                <option value="8">8</option>
-                <option value="9">9</option>
-                <option value="10">10</option>
-                <option value="15">15</option>
-                <option value="20">20</option>
-                <option value="25">25</option>
-                <option value="30">30</option>
-            </select>
-            <select class="chartupdatedata" id="markshape" style="width: 100px; height: 22px;">
-                <option value="circle" selected>Circle</option>
-                <option value="cross">Cross</option>
-                <option value="triangle-up">Triangle-up</option>
-                <option value="triangle-down">Triangle-down</option>
-                <option value="diamond">Diamond</option>
-                <option value="square">Square</option>
-            </select>
-        </td>
-    </tr>
-</table>
-
-<table class="table">    
-    <tr>
-        <td style="vertical-align: middle;">Label
-            <input class="chartupdate" id="labelcolor" type="color" value="#000000">
-            <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Number
-            <input class="chartupdate" id="numbercolor" type="color" value="#000000">
-            <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Axis
-            <input class="chartupdate" id="axiscolor" type="color" value="#000000">
-            <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
-        </td>
-        <td style="vertical-align: middle;">Line
-            <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
-            <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
-        </td>
-    </tr>
-</table>
-
-<br>
-
-<ul class="nav nav-tabs">
-    <li class="active"><a href="#tp1" data-toggle="tab">Pearson</a></li>
-    <li>               <a href="#tp2" data-toggle="tab">Spearman Rank</a></li>
-</ul>
-
-<div class="tab-content">
-    <div class="tab-pane active" id="tp1">
-
-<br>
-
-<div><a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a></div>
-
-<div style="width: 1000px; text-align: center;"><h2>Pearson Correlation Scatterplot</h2></div>
-
-<div id="scatterplot2"><svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
-
-<br>
-
-<table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-    <thead>
-        <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-    </thead>
-	<tbody>
-		<tr><td>Number</td>		<td>{{jsdata.num_overlap}}</td></tr>
-		<tr><td>Slope</td>		<td>{{'%0.3f' % jsdata.slope}}</td></tr>
-		<tr><td>Intercept</td>	<td>{{'%0.3f' % jsdata.intercept}}</td></tr>
-		<tr><td>r value</td>	<td>{{'%0.3f' % jsdata.r_value}}</td></tr>
-   		<tr><td>P value</td>	<td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td></tr>
-        <tr>
-            <td style="text-align: left;" colspan="2">
-                Regression Line
-                <br>
-                y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
-            </td>
-        </tr>
-	</tbody>
-</table>
-
-    </div>
-    
-    <div class="tab-pane" id="tp2">
-    
-<br>
-
-<div><a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a></div>
-
-<div style="width: 1000px; text-align: center;"><h2>Spearman Rank Correlation Scatterplot</h2></div>
-
-<div id="srscatterplot2"><svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg></div>
-
-<br>
-
-<table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-    <thead>
-        <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-    </thead>
-	<tbody>
-		<tr><td>Number</td>		<td>{{jsdata.num_overlap}}</td></tr>
-		<tr><td>Slope</td>		<td>{{'%0.3f' % jsdata.srslope}}</td></tr>
-		<tr><td>Intercept</td>	<td>{{'%0.3f' % jsdata.srintercept}}</td></tr>
-		<tr><td>r value</td>	<td>{{'%0.3f' % jsdata.srr_value}}</td></tr>
-		<tr><td>P value</td>	<td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td></tr>
-	</tbody>
-</table>
-
-    </div>
-    
-</div>
-
-</div>
-
-{% endblock %}
-
-{% block js %}
-    <script>
-       js_data = {{ js_data | safe }};
-    </script>
-    <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
-	<script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2.js"></script>
-{% endblock %}
+{% extends "base.html" %}
+
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+    <link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot.css" />
+{% endblock %}
+
+{% block content %}
+
+<div class="container-fluid">
+
+  <h2>Correlation Scatterplot</h2>
+
+  <div style="margin-left: 0px;">
+    {% if trait_1.dataset.type == "ProbeSet" %}
+    <div>
+      X axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+      {{trait_1.description_display}}
+    </div>
+    {% elif trait_1.dataset.type == "Publish" %}
+    <div>
+      X axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+        {{trait_1.description_display}}
+    </div>
+    {% endif %}
+
+    <br/>
+
+    {% if trait_2.dataset.type == "ProbeSet" %}
+    <div>
+      Y axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+      {{trait_2.description_display}}
+    </div>
+    {% elif trait_2.dataset.type == "Publish" %}
+    <div>
+      Y axis:
+      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+        {{trait_2.description_display}}
+    </div>
+    {% endif %}
+
+    <br/>
+
+    {% if trait_3 %}
+    {% if trait_3.dataset.type == "ProbeSet" %}
+    <div>
+      Cofactor:
+      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
+        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.tissue + " "  + trait_3.dataset.name + ": " + trait_3.name|string}}
+      </a>
+    </div>
+    <div>
+      [{{trait_3.symbol}} on {{trait_3.location_repr}} Mb]
+      {{trait_3.description_display}}
+    </div>
+    {% elif trait_3.dataset.type == "Publish" %}
+    <div>
+      Cofactor:
+      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
+        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.name + ": " + trait_3.name|string}}
+      </a>
+    </div>
+    <div>
+      <a href="{{trait_3.pubmed_link}}">PubMed: {{trait_3.pubmed_text}}</a>
+        {{trait_3.description_display}}
+    </div>
+    {% endif %}
+    {% endif %}
+
+    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#000000">
+    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
+
+  </div>
+
+  <br>
+
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
+      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+    </tr>
+  </table>
+
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Label
+        <input class="chartupdate" id="labelcolor" type="color" value="#000000">
+        <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Number
+        <input class="chartupdate" id="numbercolor" type="color" value="#000000">
+        <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Axis
+        <input class="chartupdate" id="axiscolor" type="color" value="#000000">
+        <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
+      </td>
+      <td style="vertical-align: middle;">Line
+        <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
+        <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
+      </td>
+    </tr>
+  </table>
+
+  <br>
+
+  <ul class="nav nav-tabs">
+    <li class="active">
+      <a href="#tp1" data-toggle="tab">Pearson</a>
+    </li>
+    <li>
+      <a href="#tp2" data-toggle="tab">Spearman Rank</a>
+    </li>
+  </ul>
+
+  <div class="tab-content">
+
+    <div class="tab-pane active" id="tp1">
+      <br>
+      <div>
+        <a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a>
+      </div>
+      <div style="width: 1000px; text-align: center;">
+        <h2>Pearson Correlation Scatterplot</h2>
+      </div>
+      <div id="scatterplot2">
+        <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
+      </div>
+      <br>
+      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+        <thead>
+          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+        </thead>
+        <tbody>
+          <tr>
+            <td>Number</td>
+            <td>{{jsdata.num_overlap}}</td>
+          </tr>
+          <tr>
+            <td>Slope</td>
+            <td>{{'%0.3f' % jsdata.slope}}</td>
+          </tr>
+          <tr>
+            <td>Intercept</td>
+            <td>{{'%0.3f' % jsdata.intercept}}</td>
+          </tr>
+          <tr>
+            <td>r value</td>
+            <td>{{'%0.3f' % jsdata.r_value}}</td>
+          </tr>
+          <tr>
+            <td>P value</td>
+            <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td>
+          </tr>
+          <tr>
+            <td style="text-align: left;" colspan="2">
+              Regression Line
+              <br>
+              y = {{'%0.3f' % jsdata.slope}} * x + {{'%0.3f' % jsdata.intercept}}
+            </td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+
+    <div class="tab-pane" id="tp2">
+
+      <br>
+
+      <div>
+        <a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a>
+      </div>
+      <div style="width: 1000px; text-align: center;">
+        <h2>Spearman Rank Correlation Scatterplot</h2>
+      </div>
+      <div id="srscatterplot2">
+        <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
+      </div>
+
+      <br>
+
+      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+        <thead>
+          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+        </thead>
+        <tbody>
+          <tr>
+            <td>Number</td>
+            <td>{{jsdata.num_overlap}}</td>
+          </tr>
+          <tr>
+            <td>Slope</td>
+            <td>{{'%0.3f' % jsdata.srslope}}</td>
+          </tr>
+          <tr>
+            <td>Intercept</td>
+            <td>{{'%0.3f' % jsdata.srintercept}}</td>
+          </tr>
+          <tr>
+            <td>r value</td>
+            <td>{{'%0.3f' % jsdata.srr_value}}</td>
+          </tr>
+	  <tr>
+            <td>P value</td>
+            <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+          </tr>
+        </tbody>
+      </table>
+    </div>
+
+  </div>
+
+</div>
+
+{% endblock %}
+
+{% block js %}
+    <script>
+       js_data = {{ js_data | safe }};
+    </script>
+    <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script>
+	<script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index a431821e..1402db47 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -54,6 +54,10 @@
                   <option value="csv">CSV</option>
                 </select>
               </span>
+              <br>
+              {% if sample_groups[0].sample_qnorm is not none %}
+              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+              {% endif %}
             </div>
         </fieldset>
         <br>
@@ -111,7 +115,7 @@
         
                         {# Todo: Add IDs #}
                         <td class="column_name-Value" align="right">
-                          <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}"
+                          <input type="text" data-value="{{ sample.display_value }}" data-transform="{{ sample_type.sample_qnorm[sample.name] }}" name="{{ 'value:' + sample.name }}"
                                  style="text-align:right;"
                                  class="trait_value_input edit_sample_value"
                                  value="{{ sample.display_value }}"
-- 
cgit v1.2.3


From 9bb60bb18ae5ac70fe480095554796b7c18f1b6c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 25 May 2018 15:52:40 +0000
Subject: Fixed issue causing anonymous collections to not work on my branch
 and staging, though still not sure why it's working on production without
 that change

Added script to convert the dryad format genotype files to BIMBAM

removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
---
 wqflask/maintenance/convert_dryad_to_bimbam.py     | 70 ++++++++++++++++++++++
 wqflask/maintenance/gen_select_dataset.py          |  2 +-
 wqflask/maintenance/quantile_normalize.py          |  4 +-
 .../new/javascript/dataset_menu_structure.json     | 34 +++++++++++
 wqflask/wqflask/user_manager.py                    | 10 +++-
 5 files changed, 116 insertions(+), 4 deletions(-)
 create mode 100644 wqflask/maintenance/convert_dryad_to_bimbam.py

diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
new file mode 100644
index 00000000..e833b395
--- /dev/null
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+"""
+Convert data dryad files to a BIMBAM _geno and _snps file
+
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+
+
+def read_dryad_file(filename):
+    exclude_count = 0
+    marker_list = []
+    sample_dict = {}
+    sample_list = []
+    geno_rows = []
+    with open(filename, 'r') as the_file:
+        for i, line in enumerate(the_file):
+            if i > 0:
+                if line.split(" ")[1] == "no":
+                    sample_name = line.split(" ")[0]
+                    sample_list.append(sample_name)
+                    sample_dict[sample_name] = line.split(" ")[2:]
+                else:
+                    exclude_count += 1
+            else:
+                marker_list = line.split(" ")[2:]
+
+    for i, marker in enumerate(marker_list):
+        this_row = []
+        this_row.append(marker)
+        this_row.append("X")
+        this_row.append("Y")
+        for sample in sample_list:
+            this_row.append(sample_dict[sample][i])
+        geno_rows.append(this_row)
+
+    print(exclude_count)
+
+    return geno_rows
+
+    #for i, marker in enumerate(marker_list):
+    #    this_row = []
+    #    this_row.append(marker)
+    #    this_row.append("X")
+    #    this_row.append("Y")
+    #    with open(filename, 'r') as the_file:
+    #        for j, line in enumerate(the_file):
+    #            if j > 0:
+    #                this_row.append(line.split(" ")[i+2])
+    #        print("row: " + str(i))
+    #        geno_rows.append(this_row)
+    #            
+    #return geno_rows
+
+def write_bimbam_files(geno_rows):
+    with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
+        for row in geno_rows:
+            geno_fh.write(", ".join(row) + "\n")
+
+def convert_dryad_to_bimbam(filename):
+    geno_file_rows = read_dryad_file(filename)
+    write_bimbam_files(geno_file_rows)
+
+if __name__=="__main__":
+    input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
+    convert_dryad_to_bimbam(input_filename)
\ No newline at end of file
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 2825c6ea..18b2dac9 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -63,7 +63,7 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
-def parse_db_uri(db_uri):
+def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
     parsed_uri = urlparse.urlparse(SQL_URI)
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index c11073fb..41a3aad8 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -59,7 +59,7 @@ def set_data(dataset_name):
     orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
 
     sample_list = []
-    with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh:
+    with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh:
         for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)):
             trait_dict = {}
             sample_list = []
@@ -118,7 +118,7 @@ if __name__ == '__main__':
 
     #out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
 
-    #success, _ = bulk(es, set_data(sys.argv[1]))
+    success, _ = bulk(es, set_data(sys.argv[1]))
 
     response = es.search(
         index = "traits", doc_type = "trait", body = {
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index d00b52b8..c605329b 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1966,6 +1966,21 @@
                   "470",
                   "EPFLADEL1013",
                   "EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Exon Level (Oct13) RMA"
+               ],
+               [
+                  "777",
+                  "EL_BXDCDHFDScWAT_0216",
+                  "EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+               ],
+               [
+                  "778",
+                  "EL_BXDHFDScWAT_0216",
+                  "EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+               ],
+               [
+                  "779",
+                  "EL_BXDCDScWAT_0216",
+                  "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA **"
                ]
             ],
             "Adrenal Gland mRNA": [
@@ -3355,6 +3370,15 @@
                ]
             ]
          },
+         "D2GM": {
+            "Retina mRNA": [
+               [
+                  "847",
+                  "JAX_D2GM_RSeq_log2Z_0418",
+                  "JAX Retina (Apr18) RNA-Seq log2-Z"
+               ]
+            ]
+         },
          "EMSR": {},
          "HS": {
             "Hippocampus mRNA": [
@@ -3954,6 +3978,10 @@
             "CXB",
             "CXB"
          ],
+         [
+            "D2GM",
+            "D2 Glaucoma Model"
+         ],
          [
             "EMSR",
             "Ethanol-Medicated Stress Reduction"
@@ -5236,6 +5264,12 @@
                "Spleen mRNA"
             ]
          ],
+         "D2GM": [
+            [
+               "Retina mRNA",
+               "Retina mRNA"
+            ]
+         ],
          "EMSR": [],
          "HS": [
             [
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index d652f2e9..132bae90 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -62,9 +62,17 @@ class AnonUser(object):
             self.anon_id, self.cookie = create_signed_cookie()
         self.key = "anon_collection:v1:{}".format(self.anon_id)
 
-        @after.after_this_request
+        #ZS: This was originally the commented out function below
+        #    For some reason I don't yet understand the commented out code works on production, 
+        #    but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
+        @app.after_request
         def set_cookie(response):
             response.set_cookie(self.cookie_name, self.cookie)
+            return response
+
+        #@after.after_this_request
+        #def set_cookie(response):
+        #    response.set_cookie(self.cookie_name, self.cookie)
 
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,
-- 
cgit v1.2.3


From 59273293d3815066301a5fba0a096016a4d8ba44 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Jun 2018 18:32:30 +0000
Subject: User collections (now stored in ElasticSearch) are reimplemented now
 and should have their full functionality back (adding/removing collections,
 adding/removing traits, etc)

---
 wqflask/wqflask/collect.py                         | 109 ++-----
 wqflask/wqflask/templates/base.html                |   6 +-
 wqflask/wqflask/templates/collections/list.html    |  15 +-
 .../templates/show_trait_mapping_tools.html        |   2 +-
 .../wqflask/templates/show_trait_statistics.html   |   6 +-
 wqflask/wqflask/user_manager.py                    | 319 ++++++++++++++++-----
 6 files changed, 284 insertions(+), 173 deletions(-)

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 2bd4b721..e1aceac8 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -88,7 +88,6 @@ class AnonCollection(object):
     def add_traits(self, params):
         #assert collection_name == "Default", "Unexpected collection name for anonymous user"
         self.traits = list(process_traits(params['traits']))
-        #len_before = len(Redis.smembers(self.key))
         existing_collections = Redis.get(self.key)
         logger.debug("existing_collections:", existing_collections)
         if existing_collections != None and existing_collections != "None":
@@ -138,54 +137,12 @@ class AnonCollection(object):
         collections_list[collection_position]['num_members'] = len(collections_list[collection_position]['members'])
         collections_list[collection_position]['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
         len_now = collections_list[collection_position]['num_members']
-        #print("before in redis:", json.loads(Redis.get(self.key)))
         Redis.set(self.key, json.dumps(collections_list))
-        #print("currently in redis:", json.loads(Redis.get(self.key)))
 
         # We need to return something so we'll return this...maybe in the future
         # we can use it to check the results
         return str(len_now)
 
-
-class UserCollection(object):
-    """User is logged in"""
-
-    def add_traits(self, params, collection_name):
-        logger.debug("---> params are:", params.keys())
-        logger.debug("     type(params):", type(params))
-        if collection_name=="Default":
-            uc = g.user_session.user_ob.get_collection_by_name("Default")
-            # Doesn't exist so we'll create it
-            if not uc:
-                return create_new("Default")
-        else:
-            uc = model.UserCollection.query.get(params['existing_collection'].split(":")[0])
-        members =  list(uc.members_as_set()) #set(json.loads(uc.members))
-        len_before = len(members)
-
-        traits = process_traits(params['traits'])
-
-        members_now = members
-        for trait in traits:
-            if trait in members:
-                continue
-            else:
-                members_now.append(trait)
-
-        #members_now = list(members | traits)
-        len_now = len(members_now)
-        uc.members = json.dumps(members_now)
-
-        uc.changed_timestamp = datetime.datetime.utcnow()
-
-        db_session.commit()
-
-        logger.debug("added to existing, now set is:" + str(uc.members))
-        report_change(len_before, len_now)
-
-        # Probably have to change that
-        return redirect(url_for('view_collection', uc_id=uc.id))
-
 def process_traits(unprocessed_traits):
     #print("unprocessed_traits are:", unprocessed_traits)
     if isinstance(unprocessed_traits, basestring):
@@ -216,9 +173,8 @@ def collections_add():
     traits=request.args['traits']
 
     if g.user_session.logged_in:
-        logger.debug("user_session",g.user_session)
-        user_collections = g.user_session.user_ob.user_collections
-        logger.debug("user_collections are:", user_collections)
+        user_collections = g.user_session.user_collections
+        #logger.debug("user_collections are:", user_collections)
         return render_template("collections/add.html",
                                traits = traits,
                                collections = user_collections,
@@ -262,14 +218,9 @@ def create_new(collection_name):
     traits = process_traits(unprocessed_traits)
 
     if g.user_session.logged_in:
-        uc = model.UserCollection()
-        uc.name = collection_name
-        logger.debug("user_session:", g.user_session.__dict__)
-        uc.user = g.user_session.user_id
-        uc.members = json.dumps(list(traits))
-        db_session.add(uc)
-        db_session.commit()
-        return redirect(url_for('view_collection', uc_id=uc.id))
+        uc_id = g.user_session.add_collection(collection_name, traits)
+
+        return redirect(url_for('view_collection', uc_id=uc_id))
     else:
         ac = AnonCollection(collection_name)
         ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
@@ -279,17 +230,17 @@ def create_new(collection_name):
 @app.route("/collections/list")
 def list_collections():
     params = request.args
-    logger.debug("PARAMS:", params)
+    #logger.debug("PARAMS:", params)
     if g.user_session.logged_in:
-        user_collections = list(g.user_session.user_ob.user_collections)
-        logger.debug("user_collections are:", user_collections)
+        user_collections = list(g.user_session.user_collections)
+        #logger.debug("user_collections are:", user_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = user_collections,
                                )
     else:
         anon_collections = user_manager.AnonUser().get_collections()
-        logger.debug("anon_collections are:", anon_collections)
+        #logger.debug("anon_collections are:", anon_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = anon_collections)
@@ -298,20 +249,14 @@ def list_collections():
 @app.route("/collections/remove", methods=('POST',))
 def remove_traits():
     params = request.form
-    logger.debug("params are:", params)
 
     if "uc_id" in params:
         uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
         traits_to_remove = params.getlist('traits[]')
         traits_to_remove = process_traits(traits_to_remove)
         logger.debug("\n\n  after processing, traits_to_remove:", traits_to_remove)
-        all_traits = uc.members_as_set()
-        members_now = all_traits - traits_to_remove
-        logger.debug("  members_now:", members_now)
-        uc.members = json.dumps(list(members_now))
-        uc.changed_timestamp = datetime.datetime.utcnow()
-        db_session.commit()
+
+        members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove)
     else:
         collection_name = params['collection_name']
         members_now = AnonCollection(collection_name).remove_traits(params)
@@ -325,22 +270,13 @@ def remove_traits():
 @app.route("/collections/delete", methods=('POST',))
 def delete_collection():
     params = request.form
-    logger.debug("params:", params)
     if g.user_session.logged_in:
         uc_id = params['uc_id']
         if len(uc_id.split(":")) > 1:
             for this_uc_id in uc_id.split(":"):
-                uc = model.UserCollection.query.get(this_uc_id)
-                collection_name = uc.name
-                db_session.delete(uc)
-                db_session.commit()
+                collection_name = g.user_session.delete_collection(this_uc_id)
         else:
-            uc = model.UserCollection.query.get(uc_id)
-            # Todo: For now having the id is good enough since it's so unique
-            # But might want to check ownership in the future
-            collection_name = uc.name
-            db_session.delete(uc)
-            db_session.commit()
+            collection_name = g.user_session.delete_collection(uc_id)
     else:
         if "collection_name" in params:
             collection_name = params['collection_name']
@@ -348,7 +284,10 @@ def delete_collection():
             for this_collection in params['uc_id'].split(":"):
                 user_manager.AnonUser().delete_collection(this_collection)
 
-    flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
+    if len(uc_id.split(":")) > 1:
+        flash("We've deleted the selected collections.", "alert-info")
+    else:
+        flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
 
     return redirect(url_for('list_collections'))
 
@@ -356,12 +295,11 @@ def delete_collection():
 @app.route("/collections/view")
 def view_collection():
     params = request.args
-    logger.debug("PARAMS in view collection:", params)
 
-    if "uc_id" in params:
+    if g.user_session.logged_in and "uc_id" in params:
         uc_id = params['uc_id']
-        uc = model.UserCollection.query.get(uc_id)
-        traits = json.loads(uc.members)
+        uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next()
+        traits = uc["members"]
     else:
         user_collections = json.loads(Redis.get(user_manager.AnonUser().key))
         this_collection = {}
@@ -369,10 +307,8 @@ def view_collection():
             if collection['id'] == params['collection_id']:
                 this_collection = collection
                 break
-        #this_collection = user_collections[params['collection_id']]
-        traits = this_collection['members']
 
-    logger.debug("in view_collection traits are:", traits)
+        traits = this_collection['members']
 
     trait_obs = []
     json_version = []
@@ -398,9 +334,8 @@ def view_collection():
         collection_info = dict(trait_obs=trait_obs,
                                collection_name=this_collection['name'])
     if "json" in params:
-        logger.debug("json_version:", json_version)
         return json.dumps(json_version)
     else:
         return render_template("collections/view.html",
                            **collection_info
-                           )
+                           )
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index e8b51523..3df4c81a 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -44,8 +44,8 @@
                         </li>
                         <li class="">
                             <a href="/collections/list">Collections
-                                {% if g.user_session.user_ob %}
-                                <span class="badge badge-info">{{ g.user_session.user_ob.display_num_collections() }}</span>
+                                {% if g.user_session.logged_in %}
+                                <span class="badge badge-info">{{ g.user_session.num_collections }}</span>
                                 {% else %}
                                 <span class="badge badge-info">{{ g.cookie_session.display_num_collections() }}</span>
                                 {% endif %}
@@ -71,7 +71,7 @@
                         </li>
                         <li class="">
                             {% if g.user_session.logged_in %}
-                            <a id="login_out" title="Signed in as {{ g.user_session.user_ob.name_and_org }}." href="/n/logout">Sign out</a>
+                            <a id="login_out" title="Signed in as {{ g.user_session.user_name }}" href="/n/logout">Sign out</a>
                             {% else %}
                             <a id="login_in" href="/n/login">Sign in</a>
                             {% endif %}
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index e7f3229b..11c33673 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -8,7 +8,7 @@
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
-    {% if g.user_session.user_ob %}
+    {% if g.user_session.logged_in %}
     {{ header("Your Collections",
         'You have {}.'.format(numify(collections|count, "collection", "collections"))) }}
     {% else %}
@@ -19,8 +19,8 @@
 
     <div class="container">
         <div class="page-header">
-            {% if g.user_session.user_ob %}
-            <h1>Collections owned by {{ g.user_session.user_ob.full_name }}</h1>
+            {% if g.user_session.logged_in %}
+            <h1>Collections owned by {{ g.user_session.user_name }}</h1>
             {% else %}
             <h1>Your Collections</h1>
             {% endif %}
@@ -51,19 +51,24 @@
             <tbody>
             {% for uc in collections %}
                 <tr class="collection_line">
-                    {% if g.user_session.user_ob %}
+                    {% if g.user_session.logged_in %}
                     <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
                     {% else %}
                     <td style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.name }}"></td>
                     {% endif %}
                     <td align="right">{{ loop.index }}
-                    {% if g.user_session.user_ob %}
+                    {% if g.user_session.logged_in %}
                     <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
                     {% else %}
                     <td><a class="collection_name" href="{{ url_for('view_collection', collection_id=uc.id) }}">{{ uc.name }}</a></td>
                     {% endif %}
+                    {% if g.user_session.logged_in %}
+                    <td>{{ uc.created_timestamp }}</td>
+                    <td>{{ uc.changed_timestamp }}</td>
+                    {% else %}
                     <td>{{ timeago(uc.created_timestamp.isoformat() + "Z") }}</td>
                     <td>{{ timeago(uc.changed_timestamp.isoformat() + "Z") }}</td>
+                    {% endif %}
                     <td align="right">{{ uc.num_members }}</td>
                 </tr>
             {% endfor %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3d31797a..9c19028c 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -71,7 +71,7 @@
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
+                              {% if g.user_session.logged_in and (g.user_session.num_collections > 0) %}
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% elif g.cookie_session.display_num_collections() == "" %}
                               No collections available. Please add traits to a collection to use them as covariates.
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 09df3245..988c8047 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -13,7 +13,7 @@
                 <li>
                     <a href="#probability_plot" data-toggle="tab">Probability Plot</a>
                 </li>
-                {% if g.user_session.user_ob %}
+                {% if g.user_session.logged_in %}
                 <li>
                     <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
                 </li>
@@ -72,7 +72,7 @@
                             <i class="icon-signal"></i> Sort By Value
                             </button>
                         </div>
-                        {% if g.user_session.user_ob %}
+                        {% if g.user_session.logged_in %}
                         <div class="btn-group">
                             <button type="button" class="btn btn-default" id="color_by_trait">
                                 <i class="icon-tint"></i> Color by Trait
@@ -126,7 +126,7 @@
                         <div id="box_plot"></div>
                     </div>
                 </div>
-                {% if g.user_session.user_ob %}
+                {% if g.user_session.logged_in %}
                 <div class="tab-pane" id="scatterplot_matrix">
                     
                     <div style="margin-bottom:40px;" class="btn-group">
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 132bae90..3772414c 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -54,11 +54,11 @@ class AnonUser(object):
     def __init__(self):
         self.cookie = request.cookies.get(self.cookie_name)
         if self.cookie:
-            logger.debug("already is cookie")
+            logger.debug("ANON COOKIE ALREADY EXISTS")
             self.anon_id = verify_cookie(self.cookie)
 
         else:
-            logger.debug("creating new cookie")
+            logger.debug("CREATING NEW ANON COOKIE")
             self.anon_id, self.cookie = create_signed_cookie()
         self.key = "anon_collection:v1:{}".format(self.anon_id)
 
@@ -117,16 +117,11 @@ class AnonUser(object):
         result = Redis.get(self.key)
         collections_list = json.loads(result if result else "[]")
         for collection in collections_list:
-            uc = model.UserCollection()
-            uc.name = collection['name']
-            collection_exists = g.user_session.user_ob.get_collection_by_name(uc.name)
+            collection_exists = g.user_session.get_collection_by_name(collection['name'])
             if collection_exists:
                 continue
             else:
-                uc.user = g.user_session.user_id
-                uc.members = json.dumps(collection['members'])
-                db_session.add(uc)
-                db_session.commit()
+                g.user_session.add_collection(collection['name'], collection['members'])
 
     def display_num_collections(self):
         """
@@ -164,11 +159,12 @@ def create_signed_cookie():
 class UserSession(object):
     """Logged in user handling"""
 
-    cookie_name = 'session_id_v2'
+    cookie_name = 'session_id_v1'
 
     def __init__(self):
         cookie = request.cookies.get(self.cookie_name)
         if not cookie:
+            logger.debug("NO USER COOKIE")
             self.logged_in = False
             return
         else:
@@ -179,7 +175,6 @@ class UserSession(object):
             self.session_id = session_id
             self.record = Redis.hgetall(self.redis_key)
 
-
             if not self.record:
                 # This will occur, for example, when the browser has been left open over a long
                 # weekend and the site hasn't been visited by the user
@@ -211,21 +206,190 @@ class UserSession(object):
             return ''
 
     @property
-    def user_ob(self):
-        """Actual sqlalchemy record"""
-        # Only look it up once if needed, then store it
-        # raise "OBSOLETE: use ElasticSearch instead"
-        try:
-            if LOG_SQL_ALCHEMY:
-                logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
+    def es_user_id(self):
+        """User id from ElasticSearch (need to check if this is the same as the id stored in self.records)"""
+
+        es = get_elasticsearch_connection()
+        user_email = self.record['user_email_address']
+
+        #ZS: Get user's collections if they exist
+        response = es.search(
+                       index = "users", doc_type = "local", body = {
+                       "query": { "match": { "email_address": user_email } }
+                   })
 
-            # Already did this before
-            return self.db_object
-        except AttributeError:
-            # Doesn't exist so we'll create it
-            self.db_object = model.User.query.get(self.user_id)
-            return self.db_object
+        user_id = response['hits']['hits'][0]['_id']
+        return user_id
+
+    @property
+    def user_name(self):
+        """Shortcut to the user_name"""
+        if 'user_name' in self.record:
+            return self.record['user_name']
+        else:
+            return ''
+
+    @property
+    def user_collections(self):
+        """List of user's collections"""
+
+        es = get_elasticsearch_connection()
+
+        user_email = self.record['user_email_address']
+
+        #ZS: Get user's collections if they exist
+        response = es.search(
+                       index = "users", doc_type = "local", body = {
+                       "query": { "match": { "email_address": user_email } }
+                   })
+        user_info = response['hits']['hits'][0]['_source']
+        if 'collections' in user_info.keys():
+            if len(user_info['collections']) > 0:
+                return json.loads(user_info['collections'])
+            else:
+                return []
+        else:
+            return []
+
+    @property
+    def num_collections(self):
+        """Number of user's collections"""
+
+        es = get_elasticsearch_connection()
+
+        user_email = self.record['user_email_address']
+
+        #ZS: Get user's collections if they exist
+        response = es.search(
+                       index = "users", doc_type = "local", body = {
+                       "query": { "match": { "email_address": user_email } }
+                   })
+
+        user_info = response['hits']['hits'][0]['_source']
+        logger.debug("USER NUM COLL:", user_info)
+        if 'collections' in user_info.keys():
+            if user_info['collections'] != "[]" and len(user_info['collections']) > 0:
+                collections_json = json.loads(user_info['collections'])
+                return len(collections_json)
+            else:
+                return 0
+        else:
+            return 0
+
+###
+# ZS: This is currently not used, but I'm leaving it here commented out because the old "set superuser" code (at the bottom of this file) used it
+###
+#    @property
+#    def user_ob(self):
+#        """Actual sqlalchemy record"""
+#        # Only look it up once if needed, then store it
+#        # raise "OBSOLETE: use ElasticSearch instead"
+#        try:
+#            if LOG_SQL_ALCHEMY:
+#                logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
+#
+#            # Already did this before
+#            return self.db_object
+#        except AttributeError:
+#            # Doesn't exist so we'll create it
+#            self.db_object = model.User.query.get(self.user_id)
+#            return self.db_object
+
+    def add_collection(self, collection_name, traits):
+        """Add collection into ElasticSearch"""
+
+        collection_dict = {'id': unicode(uuid.uuid4()),
+                           'name': collection_name,
+                           'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+                           'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+                           'num_members': len(traits),
+                           'members': list(traits) }
+
+        es = get_elasticsearch_connection()
+
+        user_email = self.record['user_email_address']
+        response = es.search(
+                       index = "users", doc_type = "local", body = {
+                       "query": { "match": { "email_address": user_email } }
+                   })
+
+        user_id = response['hits']['hits'][0]['_id']
+        user_info = response['hits']['hits'][0]['_source']
+
+        if 'collections' in user_info.keys():
+            if user_info['collections'] != [] and user_info['collections'] != "[]":
+                current_collections = json.loads(user_info['collections'])
+                current_collections.append(collection_dict)
+                collections_json = json.dumps(current_collections)
+            else:
+                collections_json = json.dumps([collection_dict])
+        else:
+            collections_json = json.dumps([collection_dict])
 
+        collection_body = {'doc': {'collections': collections_json}}
+        es.update(index='users', doc_type='local', id=user_id, refresh='wait_for', body=collection_body)
+
+        return collection_dict['id']
+
+    def delete_collection(self, collection_id):
+        """Remove collection with given ID"""
+
+        updated_collections = []
+        for collection in self.user_collections:
+            if collection['id'] == collection_id:
+                continue
+            else:
+                updated_collections.append(collection)
+
+        es = get_elasticsearch_connection()
+
+        collection_body = {'doc': {'collections': json.dumps(updated_collections)}}
+        es.update(index='users', doc_type='local', id=self.es_user_id, refresh='wait_for', body=collection_body)
+
+        return collection['name']
+
+    def remove_traits_from_collection(self, collection_id, traits_to_remove):
+        """Remove specified traits from a collection"""
+
+        this_collection = self.get_collection_by_id(collection_id)
+
+        updated_collection = this_collection
+        updated_traits = []
+        for trait in this_collection['members']:
+            if trait in traits_to_remove:
+                continue
+            else:
+                updated_traits.append(trait)
+
+        updated_collection['members'] = updated_traits
+        updated_collection['num_members'] = len(updated_traits)
+        updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+
+        updated_collections = []
+        for collection in self.user_collections:
+            if collection['id'] == collection_id:
+                updated_collections.append(updated_collection)
+            else:
+                updated_collections.append(collection)
+
+        es = get_elasticsearch_connection()
+
+        collection_body = {'doc': {'collections': json.dumps(updated_collections)}}
+        es.update(index='users', doc_type='local', id=self.es_user_id, refresh='wait_for', body=collection_body)
+
+        return updated_traits
+
+    def get_collection_by_id(self, collection_id):
+        for collection in self.user_collections:
+            if collection['id'] == collection_id:
+                return collection
+
+    def get_collection_by_name(self, collection_name):
+        for collection in self.user_collections:
+            if collection['name'] == collection_name:
+                return collection
+
+        return None
 
     def delete_session(self):
         # And more importantly delete the redis record
@@ -602,6 +766,7 @@ class LoginUser(object):
 
     def __init__(self):
         self.remember_me = False
+        self.logged_in = False
 
     def oauth2_login(self, login_type, user_id):
         """Login via an OAuth2 provider"""
@@ -672,6 +837,8 @@ class LoginUser(object):
 
             #g.cookie_session.import_traits_to_user()
 
+            self.logged_in = True
+
             return self.actual_login(user, import_collections=import_col)
 
         else:
@@ -691,6 +858,7 @@ class LoginUser(object):
             max_age = self.remember_time
         else:
             max_age = None
+
         response.set_cookie(UserSession.cookie_name, session_id_signed, max_age=max_age)
         return response
 
@@ -706,6 +874,7 @@ class LoginUser(object):
 
         session = dict(login_time = time.time(),
                        user_id = user.id,
+                       user_name = user.full_name,
                        user_email_address = user.email_address)
 
         key = UserSession.cookie_name + ":" + login_rec.session_id
@@ -716,6 +885,7 @@ class LoginUser(object):
         else:
             expire_time = THREE_DAYS
         Redis.expire(key, expire_time)
+
         return session_id_signed
 
     def unsuccessful_login(self, user):
@@ -767,56 +937,57 @@ def forgot_password_submit():
 def unauthorized(error):
     return redirect(url_for('login'))
 
-def super_only():
-    try:
-        superuser = g.user_session.user_ob.superuser
-    except AttributeError:
-        superuser = False
-    if not superuser:
-        flash("You must be a superuser to access that page.", "alert-error")
-        abort(401)
-
-
-
-@app.route("/manage/users")
-def manage_users():
-    super_only()
-    template_vars = UsersManager()
-    return render_template("admin/user_manager.html", **template_vars.__dict__)
-
-@app.route("/manage/user")
-def manage_user():
-    super_only()
-    template_vars = UserManager(request.args)
-    return render_template("admin/ind_user_manager.html", **template_vars.__dict__)
-
-@app.route("/manage/groups")
-def manage_groups():
-    super_only()
-    template_vars = GroupsManager(request.args)
-    return render_template("admin/group_manager.html", **template_vars.__dict__)
-
-@app.route("/manage/make_superuser")
-def make_superuser():
-    super_only()
-    params = request.args
-    user_id = params['user_id']
-    user = model.User.query.get(user_id)
-    superuser_info = basic_info()
-    superuser_info['crowned_by'] = g.user_session.user_id
-    user.superuser = json.dumps(superuser_info, sort_keys=True)
-    db_session.commit()
-    flash("We've made {} a superuser!".format(user.name_and_org))
-    return redirect(url_for("manage_users"))
-
-@app.route("/manage/assume_identity")
-def assume_identity():
-    super_only()
-    params = request.args
-    user_id = params['user_id']
-    user = model.User.query.get(user_id)
-    assumed_by = g.user_session.user_id
-    return LoginUser().actual_login(user, assumed_by=assumed_by)
+###
+# ZS: The following 6 functions require the old MySQL User accounts; I'm leaving them commented out just in case we decide to reimplement them using ElasticSearch
+###
+#def super_only():
+#    try:
+#        superuser = g.user_session.user_ob.superuser
+#    except AttributeError:
+#        superuser = False
+#    if not superuser:
+#        flash("You must be a superuser to access that page.", "alert-error")
+#        abort(401)
+
+#@app.route("/manage/users")
+#def manage_users():
+#    super_only()
+#    template_vars = UsersManager()
+#    return render_template("admin/user_manager.html", **template_vars.__dict__)
+
+#@app.route("/manage/user")
+#def manage_user():
+#    super_only()
+#    template_vars = UserManager(request.args)
+#    return render_template("admin/ind_user_manager.html", **template_vars.__dict__)
+
+#@app.route("/manage/groups")
+#def manage_groups():
+#    super_only()
+#    template_vars = GroupsManager(request.args)
+#    return render_template("admin/group_manager.html", **template_vars.__dict__)
+
+#@app.route("/manage/make_superuser")
+#def make_superuser():
+#    super_only()
+#    params = request.args
+#    user_id = params['user_id']
+#    user = model.User.query.get(user_id)
+#    superuser_info = basic_info()
+#    superuser_info['crowned_by'] = g.user_session.user_id
+#    user.superuser = json.dumps(superuser_info, sort_keys=True)
+#    db_session.commit()
+#    flash("We've made {} a superuser!".format(user.name_and_org))
+#    return redirect(url_for("manage_users"))
+
+#@app.route("/manage/assume_identity")
+#def assume_identity():
+#    super_only()
+#    params = request.args
+#    user_id = params['user_id']
+#    user = model.User.query.get(user_id)
+#    assumed_by = g.user_session.user_id
+#    return LoginUser().actual_login(user, assumed_by=assumed_by)
 
 
 @app.route("/n/register", methods=('GET', 'POST'))
-- 
cgit v1.2.3


From a057a6549500eec595c068e9b7da1d4cbfcd50cf Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 8 Jun 2018 18:57:13 +0000
Subject: Added option to add traits to existing collection, which I had
 forgotten previously

---
 wqflask/wqflask/collect.py      |  5 ++++-
 wqflask/wqflask/user_manager.py | 49 +++++++++++++++++++++++++++++------------
 2 files changed, 39 insertions(+), 15 deletions(-)

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index e1aceac8..ecc02c06 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -201,9 +201,12 @@ def collections_new():
         return create_new(collection_name)
     elif "add_to_existing" in params:
         logger.debug("in add to existing")
+        collection_id = params['existing_collection'].split(":")[0]
         collection_name = params['existing_collection'].split(":")[1]
         if g.user_session.logged_in:
-            return UserCollection().add_traits(params, collection_name)
+            traits = list(process_traits(params['traits']))
+            g.user_session.add_traits_to_collection(collection_id, traits)
+            return redirect(url_for('view_collection', uc_id=collection_id))
         else:
             ac = AnonCollection(collection_name)
             ac.add_traits(params)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 3772414c..5d388d66 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -320,14 +320,14 @@ class UserSession(object):
             if user_info['collections'] != [] and user_info['collections'] != "[]":
                 current_collections = json.loads(user_info['collections'])
                 current_collections.append(collection_dict)
-                collections_json = json.dumps(current_collections)
+                self.update_collections(current_collections)
+                #collections_json = json.dumps(current_collections)
             else:
-                collections_json = json.dumps([collection_dict])
+                self.update_collections([collection_dict])
+                #collections_json = json.dumps([collection_dict])
         else:
-            collections_json = json.dumps([collection_dict])
-
-        collection_body = {'doc': {'collections': collections_json}}
-        es.update(index='users', doc_type='local', id=user_id, refresh='wait_for', body=collection_body)
+            self.update_collections([collection_dict])
+            #collections_json = json.dumps([collection_dict])
 
         return collection_dict['id']
 
@@ -341,13 +341,31 @@ class UserSession(object):
             else:
                 updated_collections.append(collection)
 
-        es = get_elasticsearch_connection()
-
-        collection_body = {'doc': {'collections': json.dumps(updated_collections)}}
-        es.update(index='users', doc_type='local', id=self.es_user_id, refresh='wait_for', body=collection_body)
+        self.update_collections(updated_collections)
 
         return collection['name']
 
+    def add_traits_to_collection(self, collection_id, traits_to_add):
+        """Add specified traits to a collection"""
+
+        this_collection = self.get_collection_by_id(collection_id)
+
+        updated_collection = this_collection
+        updated_traits = this_collection['members'] + traits_to_add
+
+        updated_collection['members'] = updated_traits
+        updated_collection['num_members'] = len(updated_traits)
+        updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+
+        updated_collections = []
+        for collection in self.user_collections:
+            if collection['id'] == collection_id:
+                updated_collections.append(updated_collection)
+            else:
+                updated_collections.append(collection)
+
+        self.update_collections(updated_collections)
+
     def remove_traits_from_collection(self, collection_id, traits_to_remove):
         """Remove specified traits from a collection"""
 
@@ -372,10 +390,7 @@ class UserSession(object):
             else:
                 updated_collections.append(collection)
 
-        es = get_elasticsearch_connection()
-
-        collection_body = {'doc': {'collections': json.dumps(updated_collections)}}
-        es.update(index='users', doc_type='local', id=self.es_user_id, refresh='wait_for', body=collection_body)
+        self.update_collections(updated_collections)
 
         return updated_traits
 
@@ -391,6 +406,12 @@ class UserSession(object):
 
         return None
 
+    def update_collections(self, updated_collections):
+        es = get_elasticsearch_connection()
+
+        collection_body = {'doc': {'collections': json.dumps(updated_collections)}}
+        es.update(index='users', doc_type='local', id=self.es_user_id, refresh='wait_for', body=collection_body)
+
     def delete_session(self):
         # And more importantly delete the redis record
         Redis.delete(self.cookie_name)
-- 
cgit v1.2.3


From 6f7732f06ab01bbb67443cc6270671fc1cd76860 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 2 Jul 2018 16:09:41 +0000
Subject: Added option to transform/normalize trait sample values (log2 and
 qnorm) on trait page

Got figures mostly working with transformed values, except for changing the y-axis range of one

Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general)

Added timeout to Elasticsearch connection to fix related error
---
 wqflask/utility/elasticsearch_tools.py             |  2 +-
 wqflask/wqflask/marker_regression/gemma_mapping.py | 14 ++++--
 wqflask/wqflask/show_trait/SampleList.py           |  2 +-
 wqflask/wqflask/show_trait/show_trait.py           | 42 +++++++++++++++++
 .../wqflask/static/new/javascript/show_trait.js    | 52 +++++++++++++++++++++-
 wqflask/wqflask/templates/index_page_orig.html     | 44 +++++++++---------
 wqflask/wqflask/templates/show_trait.html          |  1 +
 .../wqflask/templates/show_trait_edit_data.html    | 20 ++++++---
 .../templates/show_trait_mapping_tools.html        |  4 +-
 wqflask/wqflask/user_manager.py                    |  5 ++-
 10 files changed, 147 insertions(+), 39 deletions(-)

diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 293a9ae6..15cdd0bc 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -63,7 +63,7 @@ def get_elasticsearch_connection(for_user=True):
 
         es = Elasticsearch([{
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
-        }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+        }], timeout=30, retry_on_timeout=True) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
         if for_user:
             setup_users_index(es)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index dc13afc3..5ebab611 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -144,13 +144,16 @@ def parse_gemma_output(genofile_name):
 
     with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
         for line in output_file:
-            if line.startswith("chr"):
+            if line.startswith("chr\t"):
                 continue
             else:
                 marker = {}
                 marker['name'] = line.split("\t")[1]
                 if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
-                    marker['chr'] = int(line.split("\t")[0])
+                    if "chr" in line.split("\t")[0]:
+                        marker['chr'] = int(line.split("\t")[0][3:])
+                    else:
+                        marker['chr'] = int(line.split("\t")[0])
                 else:
                     marker['chr'] = line.split("\t")[0]
                 marker['Mb'] = float(line.split("\t")[2]) / 1000000
@@ -186,13 +189,16 @@ def parse_loco_output(this_dataset, gwa_output_filename):
     for this_file in output_filelist:
         with open(this_file) as output_file:
             for line in output_file:
-                if line.startswith("chr"):
+                if line.startswith("chr\t"):
                     continue
                 else:
                     marker = {}
                     marker['name'] = line.split("\t")[1]
                     if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
-                        marker['chr'] = int(line.split("\t")[0])
+                        if "chr" in line.split("\t")[0]:
+                            marker['chr'] = int(line.split("\t")[0][3:])
+                        else:
+                            marker['chr'] = int(line.split("\t")[0])
                         if marker['chr'] > previous_chr:
                             previous_chr = marker['chr']
                         elif marker['chr'] < previous_chr:
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 78bb3b42..8dbba530 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -37,7 +37,7 @@ class SampleList(object):
 
         self.get_attributes()
 
-        self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
+        #self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
 
         if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
             self.get_extra_attribute_values()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d6d83c02..7b952af4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -12,6 +12,8 @@ from collections import OrderedDict
 import redis
 Redis = redis.StrictRedis()
 
+import scipy.stats as ss
+
 from flask import Flask, g
 
 from htmlgen import HTMLgen2 as HT
@@ -137,6 +139,8 @@ class ShowTrait(object):
 
         self.make_sample_lists()
 
+        self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
+
         # Todo: Add back in the ones we actually need from below, as we discover we need them
         hddn = OrderedDict()
 
@@ -281,6 +285,44 @@ class ShowTrait(object):
             self.sample_groups = (primary_samples,)
         self.dataset.group.allsamples = all_samples_ordered
 
+def quantile_normalize_vals(sample_groups):
+    def normf(trait_vals):
+        ranked_vals = ss.rankdata(trait_vals)
+        p_list = []
+        for i, val in enumerate(trait_vals):
+            p_list.append(((i+1) - 0.5)/len(trait_vals))
+
+        z = ss.norm.ppf(p_list)
+        normed_vals = []
+        for rank in ranked_vals:
+            normed_vals.append("%0.3f" % z[int(rank)-1])
+
+        return normed_vals
+
+    qnorm_by_group = []
+    for sample_type in sample_groups:
+        trait_vals = []
+        for sample in sample_type.sample_list:
+            try:
+                trait_vals.append(float(sample.value))
+            except:
+                continue
+
+        qnorm_vals = normf(trait_vals)
+
+        qnorm_vals_with_x = []
+        counter = 0
+        for sample in sample_type.sample_list:
+            if sample.display_value == "x":
+                qnorm_vals_with_x.append("x")
+            else:
+                qnorm_vals_with_x.append(qnorm_vals[counter])
+                counter += 1
+
+        qnorm_by_group.append(qnorm_vals_with_x)
+
+    return qnorm_by_group
+
 def get_nearest_marker(this_trait, this_db):
     this_chr = this_trait.locus_chr
     logger.debug("this_chr:", this_chr)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 17afc814..5e2ecc33 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -549,6 +549,7 @@
     };
     $('#block_outliers').click(block_outliers);
     reset_samples_table = function() {
+      $('input[name="transform"]').val("");
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
           console.log("value is:", $(element).val());
@@ -559,6 +560,52 @@
       })(this));
     };
     $('#reset').click(reset_samples_table);
+
+    log_normalize_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = $(element).data("value");
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val(Math.log2(current_value).toFixed(3));
+            return Math.log2(current_value).toFixed(3)
+          }
+        };
+      })(this));
+    };
+
+    qnorm_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = $(element).data("value");
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val($(element).data("qnorm"));
+            return $(element).data("qnorm");
+          }
+        };
+      })(this));
+    };
+
+    normalize_data = function() {
+      if ($('#norm_method option:selected').val() == 'log2'){
+        if ($('input[name="transform"]').val() != "log2") {
+          log_normalize_data()
+          $('input[name="transform"]').val("log2")
+        }
+      }
+      else if ($('#norm_method option:selected').val() == 'qnorm'){
+        if ($('input[name="transform"]').val() != "qnorm") {
+          qnorm_data()
+          $('input[name="transform"]').val("qnorm")
+        }
+      }
+    }
+
+    $('#normalize').click(normalize_data);
+
     switch_qnorm_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
@@ -734,7 +781,7 @@
         box_data = [trace1, trace2, trace3]
     } else {
         var box_layout = {
-            width: 500,
+            width: 300,
             height: 500,
             margin: {
                 l: 50,
@@ -834,7 +881,7 @@
 
     var layout = {
         yaxis: {
-            range: [range_bottom, range_top]
+            range: [range_bottom, range_top],
         },
         width: 1200,
         height: 500,
@@ -884,6 +931,7 @@
     $('#block_outliers').click(edit_data_change);
     $('#reset').click(edit_data_change);
     $('#qnorm').click(edit_data_change);
+    $('#normalize').click(edit_data_change);
     return console.log("end");
   });
 
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 2a5556ea..dba3e266 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -34,11 +34,11 @@
 
                                 <div class="form-group">
                                     <label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
-                                    <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
-                                        <div class="col-xs-8">
-                                          <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="species" id="species" class="form-control" style="width: 280px !important;"></select>
                                         </div>
-                                        <div class="col-xs-4">
+                                        <div class="col-4" style="margin-left: 10px;">
                                           <button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
                                         </div>
                                     </div>
@@ -46,9 +46,9 @@
 
                                 <div class="form-group">
                                     <label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-8">
-                                          <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="group" id="group" class="form-control" style="width: 280px !important;"></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
                                     </div>
@@ -56,21 +56,21 @@
 
                                 <div class="form-group">
                                     <label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
-                                          <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
+                                          <select name="type" id="type" class="form-control" style="width: 280px !important;"></select>
                                         </div>
                                     </div>
                                 </div>
 
                                 <div class="form-group">
                                     <label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
-                                    <div class="col-xs-10 controls input-append">
-                                        <div class="col-xs-10">
-                                          <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
+                                    <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+                                        <div class="col-9">
+                                          <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select>
                                           <i class="icon-question-sign"></i>
                                         </div>
-                                        <div class="col-xs-2">
+                                        <div class="col-3" style="margin-left: 10px;">
                                           <button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
                                         </div>
                                     </div>
@@ -85,8 +85,8 @@
 
                                 <div class="form-group">
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
                                           <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
@@ -95,8 +95,8 @@
                                 <!--  GET ANY HELP   -->
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-12 controls">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-12 controls">
                                             Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
                                             Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
                                             Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
@@ -106,8 +106,8 @@
 
                                 <div class="form-group">
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-8">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-8">
                                           <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
@@ -115,8 +115,8 @@
 
                                 <div class="form-group">
                                     <label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
-                                    <div class="col-xs-10 controls">
-                                        <div class="col-xs-2 controls" style="width: 100px !important;">
+                                    <div class="col-xs-10 controls" style="padding-left: 20px;">
+                                        <div class="col-2 controls" style="width: 100px !important;">
                                             <input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
                                         </div>
                                     </div>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 4aad4242..f67fff90 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
         <input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="genofile" value="">
         <input type="hidden" name="covariates" value="">
+        <input type="hidden" name="transform" value="">
 
         <div class="container">
             <div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 1402db47..482d1d88 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -9,7 +9,7 @@
                 needed.
             </p>
 
-            <div id="blockMenuSpan" class="input-append">
+            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
                 <label for="remove_samples_field">Block samples by index:</label>
                 <input type="text" id="remove_samples_field">
                 <select id="block_group" size="1">
@@ -25,11 +25,8 @@
             <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
                   Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
             </div>
-
-            <br>
-
             {% if sample_groups[0].attributes %}
-            <div class="input-append">
+            <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
                 <label for="exclude_menu">Block samples by group:</label>
                 <select id="exclude_menu" size=1>
                   {% for attribute in sample_groups[0].attributes %}
@@ -42,7 +39,6 @@
                 <input type="button" id="exclude_group" class="btn" value="Block">
             </div>
             {% endif %}
-            <br>
             <div>
               <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
               <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
@@ -55,9 +51,18 @@
                 </select>
               </span>
               <br>
+              <div style="margin-top:10px;">
+              <input type="button" id="normalize" class="btn btn-default" value="Normalize">
+              <select id="norm_method" class="select optional span2">
+                <option value="log2">Log2</option>
+                <option value="qnorm">Quantile</option>
+              </select>
+              </div>
+              <!--
               {% if sample_groups[0].sample_qnorm is not none %}
               <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
               {% endif %}
+              -->
             </div>
         </fieldset>
         <br>
@@ -79,6 +84,7 @@
 
     <!--<div id="edit_sample_lists">-->
     {% for sample_type in sample_groups %}
+        {% set outer_loop = loop %}
         <div class="sample_group" style="width:{{ trait_table_width }}%;">
             <h3>{{ sample_type.header }}</h3>
             <hr>
@@ -115,7 +121,7 @@
         
                         {# Todo: Add IDs #}
                         <td class="column_name-Value" align="right">
-                          <input type="text" data-value="{{ sample.display_value }}" data-transform="{{ sample_type.sample_qnorm[sample.name] }}" name="{{ 'value:' + sample.name }}"
+                          <input type="text" data-value="{{ sample.display_value }}" data-qnorm="{{ qnorm_vals[outer_loop.index - 1][loop.index - 1] }}" name="{{ 'value:' + sample.name }}"
                                  style="text-align:right;"
                                  class="trait_value_input edit_sample_value"
                                  value="{{ sample.display_value }}"
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 9c19028c..a54b595b 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -71,8 +71,10 @@
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.logged_in and (g.user_session.num_collections > 0) %}
+                              {% if g.user_session.logged_in %}
+                              {% if g.user_session.num_collections < 1 %}
                               No collections available. Please add traits to a collection to use them as covariates.
+                              {% endif %}
                               {% elif g.cookie_session.display_num_collections() == "" %}
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% else %}
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5d388d66..830c7864 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -67,7 +67,10 @@ class AnonUser(object):
         #    but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
         @app.after_request
         def set_cookie(response):
-            response.set_cookie(self.cookie_name, self.cookie)
+            if self.cookie:
+                pass
+            else:
+                response.set_cookie(self.cookie_name, self.cookie)
             return response
 
         #@after.after_this_request
-- 
cgit v1.2.3


From b964a8b732c1066978ce88073c009803f36a9173 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 6 Jul 2018 16:27:46 +0000
Subject: Added square root transform options

Figures now correctly rescale when transforms are applied

Fixed height of probability plot

Removed some text related to pylmm since it's currently not being used
---
 .../static/new/javascript/draw_probability_plot.js |  2 +-
 .../new/javascript/plotly_probability_plot.js      |  2 +-
 .../wqflask/static/new/javascript/show_trait.js    | 25 +++++++++++++++++++++-
 .../wqflask/templates/show_trait_edit_data.html    |  1 +
 .../templates/show_trait_mapping_tools.html        |  4 ++++
 5 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index f23dad0c..3d756303 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -26,7 +26,7 @@
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
     h = 600;
-    w = 600;
+    w = 500;
     margin = {
       left: 60,
       top: 40,
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index 49fd53b1..185de8a9 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -25,7 +25,7 @@
 
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
-    h = 600;
+    h = 370;
     w = 600;
     margin = {
       left: 60,
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5e2ecc33..d641dc67 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -247,6 +247,9 @@
       }
       root.bar_data[0]['x'] = trait_samples
       Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout);
+      Plotly.relayout('bar_chart', {
+          'yaxis.autorange': true
+      });
     };
 
     redraw_box_plot = function() {
@@ -564,7 +567,7 @@
     log_normalize_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
-          current_value = $(element).data("value");
+          current_value = parseFloat($(element).data("value")) + 1;
           if(isNaN(current_value)) {
             return current_value
           } else {
@@ -575,6 +578,20 @@
       })(this));
     };
 
+    sqrt_normalize_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = parseFloat($(element).data("value")) + 1;
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val(Math.sqrt(current_value).toFixed(3));
+            return Math.sqrt(current_value).toFixed(3)
+          }
+        };
+      })(this));
+    };
+
     qnorm_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
@@ -596,6 +613,12 @@
           $('input[name="transform"]').val("log2")
         }
       }
+      else if ($('#norm_method option:selected').val() == 'sqrt'){
+        if ($('input[name="transform"]').val() != "sqrt") {
+          sqrt_normalize_data()
+          $('input[name="transform"]').val("sqrt")
+        }
+      }
       else if ($('#norm_method option:selected').val() == 'qnorm'){
         if ($('input[name="transform"]').val() != "qnorm") {
           qnorm_data()
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 482d1d88..ac2f1078 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -56,6 +56,7 @@
               <select id="norm_method" class="select optional span2">
                 <option value="log2">Log2</option>
                 <option value="qnorm">Quantile</option>
+                <option value="sqrt">Square Root</option>
               </select>
               </div>
               <!--
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a54b595b..53b6646c 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -14,9 +14,11 @@
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
+<!--
                 <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
+-->
                 {% endif %}
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
@@ -330,8 +332,10 @@
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+<!--
              <dt>pyLMM</dt>
              <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+-->
              {% endif %}
         </dl>
     </div>
-- 
cgit v1.2.3


From 6b49398fab75304146d76d5fe58ff558ed2b75f6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 10 Aug 2018 15:52:55 -0500
Subject: Added the command needed to start up elasticsearch

I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now.---
 doc/README.org | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/README.org b/doc/README.org
index 937a9549..f290480d 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -257,6 +257,12 @@ if that works run genenetwork after setting SQL_URI to something like
 
 : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s
 
+* Running ElasticSearch
+
+In order to start up elasticsearch, use the following command:
+
+: env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch
+
 * Read more
 
 If you want to understand the architecture of GN2 read
-- 
cgit v1.2.3


From 18ef3e74e7e898cbec200b7ed18b83db26741b62 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 14 Aug 2018 17:19:46 +0000
Subject: Added cofactors to correlation scatterplot and changed it to use
 Plotly

Added Phenogen track to mapping results

Added comparison bar chart figure

Simplified global search to not build trait/dataset objects, which speeds thing up considerably

Fixed correlation matrix to correctly deal with 0 values

Fixed issue where anonymous collections couldn't be created if none already existed
---
 etc/default_settings.py                            |   2 +-
 wqflask/base/trait.py                              |  26 +-
 wqflask/utility/corr_result_helpers.py             |   2 +-
 wqflask/wqflask/comparison_bar_chart/__init__.py   |   0
 .../comparison_bar_chart/comparison_bar_chart.py   | 118 +++++
 wqflask/wqflask/gsearch.py                         |  58 ++-
 .../marker_regression/marker_regression_gn1.py     |  76 +++-
 .../static/new/javascript/comparison_bar_chart.js  |  25 ++
 .../new/javascript/dataset_menu_structure.json     |  52 ++-
 .../static/new/javascript/draw_corr_scatterplot.js | 491 +++++++++++++--------
 .../new/javascript/get_traits_from_collection.js   |  92 +++-
 .../new/javascript/plotly_probability_plot.js      |  11 +-
 .../wqflask/static/new/javascript/show_trait.js    |   1 +
 wqflask/wqflask/templates/collections/add.html     |  32 +-
 wqflask/wqflask/templates/collections/list.html    |   1 -
 wqflask/wqflask/templates/collections/view.html    |  25 +-
 .../wqflask/templates/comparison_bar_chart.html    |  39 ++
 wqflask/wqflask/templates/corr_scatterplot.html    | 348 ++++++++-------
 wqflask/wqflask/templates/correlation_matrix.html  |   4 -
 wqflask/wqflask/templates/gsearch_gene.html        |  20 +-
 wqflask/wqflask/templates/gsearch_pheno.html       |  16 +-
 .../templates/show_trait_mapping_tools.html        |   6 +
 wqflask/wqflask/user_manager.py                    |  19 +-
 wqflask/wqflask/views.py                           |  22 +
 24 files changed, 1004 insertions(+), 482 deletions(-)
 create mode 100644 wqflask/wqflask/comparison_bar_chart/__init__.py
 create mode 100644 wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
 create mode 100644 wqflask/wqflask/static/new/javascript/comparison_bar_chart.js
 create mode 100644 wqflask/wqflask/templates/comparison_bar_chart.html

diff --git a/etc/default_settings.py b/etc/default_settings.py
index da8cbb7c..3e54ad1f 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -77,7 +77,7 @@ USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
 HOME            = os.environ['HOME']
 
 # ---- Default locations
-GENENETWORK_FILES   = HOME+"/gn2_data"  # base dir for all static data files
+GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data files
 
 # ---- Path overrides for Genenetwork - the defaults are normally
 #      picked up from Guix or in the HOME directory
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index b71dacf6..3daf9ea9 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -18,7 +18,7 @@ import simplejson as json
 from MySQLdb import escape_string as escape
 from pprint import pformat as pf
 
-from flask import Flask, g, request
+from flask import Flask, g, request, url_for
 
 from utility.logger import getLogger
 logger = getLogger(__name__ )
@@ -176,13 +176,23 @@ def get_sample_data():
 
     trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
 
-    return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
-
-    #jsonable_sample_data = {}
-    #for sample in trait_ob.data.iteritems():
-    #    jsonable_sample_data[sample] = trait_ob.data[sample].value
-    #
-    #return jsonable_sample_data
+    trait_dict = {}
+    trait_dict['name'] = trait
+    trait_dict['db'] = dataset
+    trait_dict['type'] = trait_ob.dataset.type
+    trait_dict['group'] = trait_ob.dataset.group.name
+    trait_dict['tissue'] = trait_ob.dataset.tissue
+    trait_dict['species'] = trait_ob.dataset.group.species
+    trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+    trait_dict['description'] = trait_ob.description_display
+    if trait_ob.dataset.type == "ProbeSet":
+        trait_dict['symbol'] = trait_ob.symbol
+        trait_dict['location'] = trait_ob.location_repr
+    elif trait_ob.dataset.type == "Publish":
+        trait_dict['pubmed_link'] = trait_ob.pubmed_link
+        trait_dict['pubmed_text'] = trait_ob.pubmed_text
+
+    return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
     
 def jsonable(trait):
     """Return a dict suitable for using as json
diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py
index ef644d85..b543c589 100644
--- a/wqflask/utility/corr_result_helpers.py
+++ b/wqflask/utility/corr_result_helpers.py
@@ -15,7 +15,7 @@ def normalize_values(a_values, b_values):
     a_new = []
     b_new = []
     for counter in range(min_length):
-        if a_values[counter] and b_values[counter]:
+        if (a_values[counter] or a_values[counter] == 0) and (b_values[counter] or b_values[counter] == 0):
             a_new.append(a_values[counter])
             b_new.append(b_values[counter])
 
diff --git a/wqflask/wqflask/comparison_bar_chart/__init__.py b/wqflask/wqflask/comparison_bar_chart/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
new file mode 100644
index 00000000..b9e6f450
--- /dev/null
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -0,0 +1,118 @@
+## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Dr. Robert W. Williams at rwilliams@uthsc.edu
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import absolute_import, print_function, division
+
+import sys
+# sys.path.append(".")   Never do this in a webserver!
+
+import string
+import cPickle
+import os
+import time
+import pp
+import math
+import collections
+import resource
+
+
+from pprint import pformat as pf
+
+from htmlgen import HTMLgen2 as HT
+import reaper
+
+from base.trait import GeneralTrait
+from base import data_set
+from utility import webqtlUtil, helper_functions, corr_result_helpers
+from db import webqtlDatabaseFunction
+import utility.webqtlUtil #this is for parallel computing only.
+from wqflask.correlation import correlation_functions
+from utility.benchmark import Bench
+
+from MySQLdb import escape_string as escape
+
+from pprint import pformat as pf
+
+from flask import Flask, g
+
+
+class ComparisonBarChart(object):
+
+    def __init__(self, start_vars):
+        trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+
+        helper_functions.get_trait_db_obs(self, trait_db_list)
+
+        self.all_sample_list = []
+        self.traits = []
+        self.insufficient_shared_samples = False
+        this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+        for trait_db in self.trait_list:
+            
+            if trait_db[1].group.name != this_group:
+                self.insufficient_shared_samples = True
+                break
+            else:
+                this_group = trait_db[1].group.name
+            this_trait = trait_db[0]
+            self.traits.append(this_trait)
+            
+            this_sample_data = this_trait.data
+
+            for sample in this_sample_data:
+                if sample not in self.all_sample_list:
+                    self.all_sample_list.append(sample)
+
+        if self.insufficient_shared_samples:
+            pass
+        else:
+            self.sample_data = []
+            for trait_db in self.trait_list:
+                this_trait = trait_db[0]
+                this_sample_data = this_trait.data
+
+                this_trait_vals = []
+                for sample in self.all_sample_list:
+                    if sample in this_sample_data:
+                        this_trait_vals.append(this_sample_data[sample].value)
+                    else:
+                        this_trait_vals.append('')
+                self.sample_data.append(this_trait_vals)
+
+            self.js_data = dict(traits = [trait.name for trait in self.traits],
+                                samples = self.all_sample_list,
+                                sample_data = self.sample_data,)
+        
+    def get_trait_db_obs(self, trait_db_list):
+
+        self.trait_list = []
+        for i, trait_db in enumerate(trait_db_list):
+            if i == (len(trait_db_list) - 1):
+                break
+            trait_name, dataset_name = trait_db.split(":")
+            #print("dataset_name:", dataset_name)
+            dataset_ob = data_set.create_dataset(dataset_name)
+            trait_ob = GeneralTrait(dataset=dataset_ob,
+                                   name=trait_name,
+                                   cellid=None)
+            self.trait_list.append((trait_ob, dataset_ob))
+
+        #print("trait_list:", self.trait_list)
+
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index fe1e17d2..37eb46cb 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -5,6 +5,8 @@ from base.data_set import create_dataset
 from base.trait import GeneralTrait
 from db import webqtlDatabaseFunction
 
+from base import webqtlConfig
+
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 from utility.benchmark import Bench
 
@@ -57,10 +59,29 @@ class GSearch(object):
             self.trait_list = []
             with Bench("Creating trait objects"):
                 for line in re:
-                    dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-                    trait_id = line[4]
+                    this_trait = {}
+                    this_trait['name'] = line[4]
+                    this_trait['dataset'] = line[3]
+                    this_trait['species'] = line[0]
+                    this_trait['group'] = line[1]
+                    this_trait['tissue'] = line[2]
+                    this_trait['symbol'] = line[5]
+                    this_trait['description'] = line[6]
+                    this_trait['location_repr'] = 'N/A'
+                    if (line[7] != "NULL" and line[7] != "") and (line[8] != 0):
+                        this_trait['location_repr'] = 'Chr%s: %.6f' % (line[7], float(line[8]))
+                    this_trait['mean'] = line[9]
+                    this_trait['LRS_score_repr'] = "N/A"
+                    if line[10] != "" and line[10] != None:
+                        this_trait['LRS_score_repr'] = '%3.1f' % line[10]
+                    this_trait['additive'] = "N/A"
+                    if line[13] != "":
+                        this_trait['additive'] = line[13]
+
+                    #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+                    #trait_id = line[4]
                     #with Bench("Building trait object"):
-                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=False, get_sample_info=False)
                     self.trait_list.append(this_trait)
 
         elif self.type == "phenotype":
@@ -73,8 +94,8 @@ class GSearch(object):
                 Phenotype.`Post_publication_description`,
                 Publication.`Authors`,
                 Publication.`Year`,
+                Publication.`PubMed_ID`,
                 PublishXRef.`LRS`,
-                PublishXRef.`Locus`,
                 PublishXRef.`additive`
                 FROM Species,InbredSet,PublishFreeze,PublishXRef,Phenotype,Publication
                 WHERE PublishXRef.`InbredSetId`=InbredSet.`Id`
@@ -100,7 +121,30 @@ class GSearch(object):
             self.trait_list = []
             with Bench("Creating trait objects"):
                 for line in re:
-                    dataset = create_dataset(line[2], "Publish")
-                    trait_id = line[3]
-                    this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+                    this_trait = {}
+                    this_trait['name'] = line[3]
+                    this_trait['dataset'] = line[2]
+                    this_trait['species'] = line[0]
+                    this_trait['group'] = line[1]
+                    this_trait['description'] = line[4]
+                    this_trait['authors'] = line[5]
+                    this_trait['year'] = line[6]
+                    if this_trait['year'].isdigit():
+                        this_trait['pubmed_text'] = this_trait['year']
+                    else:
+                        this_trait['pubmed_text'] = "N/A"
+                    if line[7] != "" and line[7] != None:
+                        this_trait['pubmed_link'] = webqtlConfig.PUBMEDLINK_URL % line[7]
+                    else:
+                        this_trait['pubmed_link'] = "N/A"
+                    this_trait['LRS_score_repr'] = "N/A"
+                    if line[8] != "" and line[8] != None:
+                        this_trait['LRS_score_repr'] = '%3.1f' % line[8]
+                    this_trait['additive'] = "N/A"
+                    if line[9] != "":
+                        this_trait['additive'] = line[9]
+
+                    #dataset = create_dataset(line[2], "Publish")
+                    #trait_id = line[3]
+                    #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
                     self.trait_list.append(this_trait)
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 40402597..94145bb3 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -68,12 +68,10 @@ class MarkerRegression(object):
     # ** GENES **********
     BAND_SPACING = 4
 
-    #ENSEMBL_BAND_Y      = UCSC_BAND_Y + UCSC_BAND_HEIGHT + BAND_SPACING
-    UCSC_BAND_HEIGHT = 10
-    ENSEMBL_BAND_HEIGHT = 10
-    WEBQTL_BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
+    BAND_HEIGHT = 10
 
-    #GENE_START_Y        = ENSEMBL_BAND_Y + ENSEMBL_BAND_HEIGHT + BAND_SPACING
     NUM_GENE_ROWS       = 10
     EACH_GENE_HEIGHT    = 6  # number of pixels tall, for each gene to display
     EACH_GENE_ARROW_WIDTH = 5
@@ -124,6 +122,10 @@ class MarkerRegression(object):
     CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = pid.HexColor(0xFCE9E9)
     CLICKABLE_WEBQTL_TEXT_COLOR       = pid.HexColor(0x912828)
 
+    CLICKABLE_PHENOGEN_REGION_COLOR   = pid.HexColor(0xA2FB94)
+    CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = pid.HexColor(0xCEFEC7)
+    CLICKABLE_PHENOGEN_TEXT_COLOR     = pid.HexColor(0x1FD504)
+
     CLICKABLE_UCSC_REGION_COLOR     = pid.HexColor(0xDDDDEE)
     CLICKABLE_UCSC_REGION_OUTLINE_COLOR = pid.HexColor(0xEDEDFF)
     CLICKABLE_UCSC_TEXT_COLOR       = pid.HexColor(0x333366)
@@ -498,7 +500,10 @@ class MarkerRegression(object):
         #Drawing Area Height
         drawAreaHeight = plotHeight
         if self.plotScale == 'physic' and self.selectedChr > -1:
-            drawAreaHeight -= self.ENSEMBL_BAND_HEIGHT + self.UCSC_BAND_HEIGHT+ self.WEBQTL_BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                drawAreaHeight -= 4*self.BAND_HEIGHT + 4*self.BAND_SPACING+ 10*zoom
+            else:
+                drawAreaHeight -= 3*self.BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
             if self.geneChecked:
                 drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
         else:
@@ -1023,7 +1028,10 @@ class MarkerRegression(object):
 
             #Draw Genes
             geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
-            geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+            else:
+                geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
 
             #draw the detail view
             if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
@@ -1217,7 +1225,10 @@ class MarkerRegression(object):
                 #Draw Genes
 
                 geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
-                geneYLocation += self.UCSC_BAND_HEIGHT + self.BAND_SPACING + self.ENSEMBL_BAND_HEIGHT + self.BAND_SPACING + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
+                if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                    geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+                else:
+                    geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
 
                 if self.genotype[0][i].name != " - " :
 
@@ -1335,49 +1346,70 @@ class MarkerRegression(object):
         i = 0
 
         paddingTop = yTopOffset
-        ucscPaddingTop = paddingTop + self.WEBQTL_BAND_HEIGHT + self.BAND_SPACING
-        ensemblPaddingTop = ucscPaddingTop + self.UCSC_BAND_HEIGHT + self.BAND_SPACING
+        if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+            phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
+            ucscPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
+            ensemblPaddingTop = paddingTop + 3*(self.BAND_HEIGHT + self.BAND_SPACING)
+        else:
+            ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
+            ensemblPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
 
         if zoom == 1:
             for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
 
                 calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
+                if pixel == (xLeftOffset + pixelStep*2):
+                  logger.debug("CALBASE:", calBase)
+                  logger.debug("FLANKING:", flankingWidthInBases)
 
                 xBrowse1 = pixel
                 xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
 
-                WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.WEBQTL_BAND_HEIGHT))
+                WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.BAND_HEIGHT))
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
                 gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
-                canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.WEBQTL_BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
-                canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.WEBQTL_BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT), edgeColor=self.CLICKABLE_WEBQTL_REGION_COLOR, fillColor=self.CLICKABLE_WEBQTL_REGION_COLOR)
+                canvas.drawLine(xBrowse1, paddingTop, xBrowse1, (paddingTop + self.BAND_HEIGHT), color=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
+
+                if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                    PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))
+                    if self.dataset.group.species == "mouse":
+                        PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    else:
+                        PHENOGEN_HREF = "https://phenogen.ucdenver.edu/PhenoGen/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+                    PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
+                    gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+                    canvas.drawRect(xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_PHENOGEN_REGION_COLOR, fillColor=self.CLICKABLE_PHENOGEN_REGION_COLOR)
+                    canvas.drawLine(xBrowse1, phenogenPaddingTop, xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
 
-                UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT))
+                UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
-                canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
-                canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.UCSC_BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_UCSC_REGION_COLOR, fillColor=self.CLICKABLE_UCSC_REGION_COLOR)
+                canvas.drawLine(xBrowse1, ucscPaddingTop, xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
 
-                ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT))
+                ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))
                 if self.dataset.group.species == "mouse":
                     ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
                 gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
-                canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
-                canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.ENSEMBL_BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
+                canvas.drawRect(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT), edgeColor=self.CLICKABLE_ENSEMBL_REGION_COLOR, fillColor=self.CLICKABLE_ENSEMBL_REGION_COLOR)
+                canvas.drawLine(xBrowse1, ensemblPaddingTop, xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT), color=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
             # end for
 
-            canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.WEBQTL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
-            canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.UCSC_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
-            canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.ENSEMBL_BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in an 8x expanded WebQTL map", (xLeftOffset + 10), paddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_WEBQTL_TEXT_COLOR)
+            if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
+                canvas.drawString("Click to view the corresponding section of the genome in PhenoGen", (xLeftOffset + 10), phenogenPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in the UCSC Genome Browser", (xLeftOffset + 10), ucscPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_UCSC_TEXT_COLOR)
+            canvas.drawString("Click to view the corresponding section of the genome in the Ensembl Genome Browser", (xLeftOffset+10), ensemblPaddingTop + self.BAND_HEIGHT/2, font=clickableRegionLabelFont, color=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
 
             #draw the gray text
             chrFont = pid.Font(ttf="verdana", size=26*zoom, bold=1)
diff --git a/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js b/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js
new file mode 100644
index 00000000..5e73807c
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/comparison_bar_chart.js
@@ -0,0 +1,25 @@
+generate_traces = function() {
+  traces = [];
+  for (i = 0, _len = js_data.traits.length; i < _len; i++) {
+    this_trace = {
+      x: js_data.samples,
+      y: js_data.sample_data[i],
+      name: js_data.traits[i],
+      type: 'bar',
+      bargap: 20
+    }
+
+    traces.push(this_trace)   
+  }
+
+  return traces
+}
+
+create_bar_chart = function() {
+  var data = generate_traces()
+  var layout = {barmode: 'group', bargap: 5};
+
+  Plotly.newPlot('comp_bar_chart', data, layout);
+}
+
+create_bar_chart();
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index c605329b..81185136 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1751,7 +1751,7 @@
             ],
             "Phenotypes": [
                [
-                  "None",
+                  "651",
                   "B6D2RIPublish",
                   "B6D2RI Published Phenotypes"
                ]
@@ -2615,6 +2615,16 @@
                   "EPFLMouseLiverBothExRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
                ],
+               [
+                  "849",
+                  "EPFLMouseLiverCDEx0413",
+                  "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
+                  "848",
+                  "EPFLMouseLiverHFCEx0413",
+                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
                [
                   "700",
                   "UTHSC-VGX_MmBXDHepatocytesRMA1014",
@@ -2783,7 +2793,7 @@
             ],
             "Phenotypes": [
                [
-                  "None",
+                  "602",
                   "BXDPublish",
                   "BXD Published Phenotypes"
                ]
@@ -3030,6 +3040,18 @@
                   "842",
                   "UTHSC-BXD-Liv-0917",
                   "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
+               ],
+               [
+                  "850",
+                  "UTHSC-BXD-Liv-0818",
+                  "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA **"
+               ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "BXD-HarvestedPublish",
+                  "BXD-Harvested Published Phenotypes"
                ]
             ]
          },
@@ -3638,7 +3660,7 @@
          "HSNIH-Palmer": {
             "Phenotypes": [
                [
-                  "None",
+                  "652",
                   "HSNIH-PalmerPublish",
                   "HSNIH-Palmer Published Phenotypes"
                ]
@@ -3892,11 +3914,11 @@
          ],
          [
             "AKXD",
-            "AKXD"
+            "AKXD RI Family"
          ],
          [
             "AXBXA",
-            "AXB/BXA"
+            "AXB/BXA RI Family"
          ],
          [
             "B6BTBRF2",
@@ -3930,10 +3952,6 @@
             "BHF2",
             "BHF2 (Apoe Null) UCLA"
          ],
-         [
-            "BXD",
-            "BXD"
-         ],
          [
             "B6D2RI",
             "BXD Aged"
@@ -3946,13 +3964,17 @@
             "BXD-Harvested",
             "BXD NIA Longevity Study"
          ],
+         [
+            "BXD",
+            "BXD RI Family"
+         ],
          [
             "BXD300",
             "BXD300"
          ],
          [
             "BXH",
-            "BXH"
+            "BXH RI Family"
          ],
          [
             "CTB6F2",
@@ -3976,7 +3998,7 @@
          ],
          [
             "CXB",
-            "CXB"
+            "CXB RI Family (strain means)"
          ],
          [
             "D2GM",
@@ -4000,11 +4022,11 @@
          ],
          [
             "LXS",
-            "LXS"
+            "ILSXISS (LXS) RI Family (strain means)"
          ],
          [
             "MDP",
-            "Mouse Diversity Panel"
+            "Mouse Diversity Panel (strain means)"
          ],
          [
             "NZBXFVB-N2",
@@ -5113,6 +5135,10 @@
             ]
          ],
          "BXD-Harvested": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ],
             [
                "Liver mRNA",
                "Liver mRNA"
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index c290cdfe..57dae378 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -1,75 +1,80 @@
-// http://gn2-lei.genenetwork.org/corr_scatter_plot2?dataset_1=HC_M2_0606_P&dataset_2=HC_M2_0606_P&dataset_3=HC_M2_0606_P&trait_1=1427571_at&trait_2=1457022_at&trait_3=1427571_at
-
 var chart;
 var srchart;
 
+var layout = {
+    height: 700,
+    width: 800,
+    margin: {
+        l: 60,
+        r: 30,
+        t: 80,
+        b: 50
+    },
+    xaxis: {
+        title: js_data.trait_1,
+        zeroline: false,
+        visible: true,
+        linecolor: 'black',
+        linewidth: 1,
+    },
+    yaxis: {
+        title: js_data.trait_2,
+        zeroline: false,
+        visible: true,
+        linecolor: 'black',
+        linewidth: 1,
+    }
+}
+
+cofactor1_dict = {}
+ranked_cofactor1_dict = {}
+cofactor1_values = []
+ranked_cofactor1_values = []
+cofactor2_dict = {}
+ranked_cofactor2_dict = {}
+
 function drawg() {
-    //
-    chart = nv.models.scatterChart();
-    //
-    chart.showLegend(false);
-    chart.duration(300);
-    //chart.color(d3.scale.category10().range());
-    chart.pointRange([0, 400]);
-    chart.pointDomain([0, 10]);
-    //
-    chart.xAxis.axisLabel(js_data.trait_1);
-    chart.xAxis.axisLabelDistance(11);
-    chart.yAxis.axisLabel(js_data.trait_2);
-    chart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.data[0]);
-    xmax = d3.max(js_data.data[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.data[1]);
-    ymax = d3.max(js_data.data[1]);
-    yrange = ymax - ymin;
-    chart.xDomain([xmin - xrange/10, xmax + xrange/10]);
-    chart.yDomain([ymin - yrange/10, ymax + yrange/10]);
-    chart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    chart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    chart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
+    x_values = []
+    y_values = []
+    sample_names = []
+    for (j = 0; j < js_data.data[0].length; j++) {
+      x_values.push(js_data.data[0][j])
+      y_values.push(js_data.data[1][j])
+      sample_names.push(js_data.indIDs[j])
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: sample_names
+    }
+
+    Plotly.newPlot('scatterplot2', [trace], layout)
+
 }
 
 function srdrawg() {
-    //
-    srchart = nv.models.scatterChart();
-    //
-    srchart.showLegend(false);
-    srchart.duration(300);
-    srchart.color(d3.scale.category10().range());
-    srchart.pointRange([0, 400]);
-    srchart.pointDomain([0, 10]);
-    //
-    srchart.xAxis.axisLabel(js_data.trait_1);
-    srchart.xAxis.axisLabelDistance(11);
-    srchart.yAxis.axisLabel(js_data.trait_2);
-    srchart.yAxis.axisLabelDistance(11);
-    //
-    xmin = d3.min(js_data.rdata[0]);
-    xmax = d3.max(js_data.rdata[0]);
-    xrange = xmax - xmin;
-    ymin = d3.min(js_data.rdata[1]);
-    ymax = d3.max(js_data.rdata[1]);
-    yrange = ymax - ymin;
-    srchart.xDomain([0, xmax + xrange/10]);
-    srchart.yDomain([0, ymax + yrange/10]);
-    srchart.xAxis.tickFormat(d3.format(checkformat(xrange)));
-    srchart.yAxis.tickFormat(d3.format(checkformat(yrange)));
-    //
-    srchart.tooltip.contentGenerator(function (obj) {
-        return tiptext(obj);
-    });
-}
+    x_values = []
+    y_values = []
+    sample_names = []
+    for (j = 0; j < js_data.rdata[0].length; j++) {
+      x_values.push(js_data.rdata[0][j])
+      y_values.push(js_data.rdata[1][j])
+      sample_names.push(js_data.indIDs[j])
+    }
 
-function tiptext(obj) {
-    return '<b style="font-size: 18px">' + obj.point.name + " (" + obj.point.x + ', ' + obj.point.y + ')</b>';
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: sample_names
+    }
+
+    Plotly.newPlot('srscatterplot2', [trace], layout)
 }
 
-function getdata(size, shape) {
+function getdata() {
     var data = [];
     data.push({
             values: [],
@@ -79,37 +84,91 @@ function getdata(size, shape) {
 
     sizemin = 1;
     sizemax = 50;
-    if ('vals_3' in js_data) {
-        datamin = d3.min(js_data.vals_3);
-        datamax = d3.max(js_data.vals_3);
-        colormin = $("#cocolorfrom").val();
-        colormax = $("#cocolorto").val();
-        compute = d3.interpolate(colormin, colormax);
-        linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+
+    if ($('input[name=cofactor1_vals]').val()){
+        just_vals = []
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=cofactor1_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          just_vals.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1])
+        }
+
+        cofactor1_dict = val_sample_dict
+        cofactor1_values = just_vals
+    }
+
+    if ($('input[name=cofactor2_vals]').val()){
+        vals_3 = [];
+        samples_3 = [];
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=cofactor2_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          samples_3.push(val_sample_pairs[i].split(":")[0])
+          vals_3.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1]
+        }
+        datamin = d3.min(vals_3);
+        datamax = d3.max(vals_3);
+
+        cofactor2_dict = val_sample_dict
     }
 
+    x_values = []
+    y_values = []
+    sample_names = []
+    sizes = []
+
     for (j = 0; j < js_data.data[0].length; j++) {
-        if ('trait3' in js_data) {
-          if (js_data.indIDs[j] in js_data.trait3) {
-            datav = js_data.trait3[js_data.indIDs[j]].value;
-            // size = (sizemax - sizemin) * (datav - datamin) / (datamax - datamin) + sizemin;
+        if ($('input[name=cofactor2_vals]').val()){
+          if (samples_3.indexOf(js_data.indIDs[j])) {
+            datav = vals_3[j]
             sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
           }
         } else {
             datav = 0;
-            sizev = sizemin;
+            sizev = 10;
         }
+
+        x_values.push(js_data.data[0][j])
+        y_values.push(js_data.data[1][j])
+        sample_names.push(js_data.indIDs[j])
+        sizes.push(sizev)
+
         data[0].values.push({
+            type: "normal",
             x: js_data.data[0][j],
             y: js_data.data[1][j],
             name: js_data.indIDs[j],
             size: sizev,
-            shape: shape,
             v3: datav
         });
     }
-    console.log(data);
-    return data;
+
+    point_text = []
+    for (j = 0; j < sample_names.length; j++) {
+      this_text = ""
+      this_text += sample_names[j]
+      if (sample_names[j] in cofactor1_dict){
+        this_text += "<br>Cofactor 1: " + cofactor1_dict[sample_names[j]]
+      }
+      if (sample_names[j] in cofactor2_dict){
+        this_text += "<br>Cofactor 2: " + cofactor2_dict[sample_names[j]]
+      }
+      point_text.push(this_text)
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: point_text,
+        marker: {
+          size: sizes
+        }
+    }
+
+    return [trace];
 }
 
 function map1to2 (min1, max1, min2, max2, v1) {
@@ -117,167 +176,223 @@ function map1to2 (min1, max1, min2, max2, v1) {
     return v2;
 }
 
-function srgetdata(size, shape) {
+function srgetdata() {
     var data = [];
     data.push({
             values: [],
             slope: js_data.srslope,
             intercept: js_data.srintercept
         });
+
+    sizemin = 1;
+    sizemax = 50;
+
+    x_values = []
+    y_values = []
+    sample_names = []
+    sizes = []
+
+    if ($('input[name=ranked_cofactor1_vals]').val()){
+        just_vals = []
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=ranked_cofactor1_vals]').val().split(",")
+        for (i=0; i < val_sample_pairs.length; i++) {
+          just_vals.push(parseFloat(val_sample_pairs[i].split(":")[1]))
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1])
+        }
+
+        ranked_cofactor1_dict = val_sample_dict
+        ranked_cofactor1_values = just_vals
+    }
+
+    if ($('input[name=ranked_cofactor2_vals]').val()){
+        vals_3 = []
+        samples_3 = [];
+        val_sample_dict = {}
+        val_sample_pairs = $('input[name=ranked_cofactor2_vals]').val().split(",")
+        for (i=0; i<val_sample_pairs.length; i++){
+          samples_3.push(val_sample_pairs[i].split(":")[0])
+          vals_3.push(val_sample_pairs[i].split(":")[1])
+          val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1]
+        }
+        datamin = d3.min(vals_3);
+        datamax = d3.max(vals_3);
+
+        ranked_cofactor2_dict = val_sample_dict
+    }
+
     for (j = 0; j < js_data.rdata[0].length; j++) {
-        if (js_data.indIDs[j] in js_data.trait3) {
-            size = js_data.trait3[js_data.indIDs[j]].value;
-            //console.log("yes "+js_data.indIDs[j]+", "+size);
+        if ($('input[name=ranked_cofactor2_vals]').val()){
+          if (samples_3.indexOf(js_data.indIDs[j])) {
+            datav = vals_3[j]
+            sizev = map1to2(datamin, datamax, sizemin, sizemax, datav);
+          }
         } else {
-            //console.log("no "+js_data.indIDs[j]);
+            sizev = 10;
         }
+
+        x_values.push(js_data.rdata[0][j])
+        y_values.push(js_data.rdata[1][j])
+        sample_names.push(js_data.indIDs[j])
+        sizes.push(sizev)
+
         data[0].values.push({
+            type: "ranked",
             x: js_data.rdata[0][j],
             y: js_data.rdata[1][j],
             name: js_data.indIDs[j],
-            size: size,
-            shape: shape
+            size: sizev,
         });
     }
-    return data;
-}
-    
-function checkformat(range) {
-    cell = range / 10.0;
-    if (cell >= 1) {
-        return ",r";
-    } else {
-        cell = -Math.log(cell);
-        n = cell.toString().split(".")[0].length;
-        return ",.0" + n + "f";
+
+    point_text = []
+    for (j = 0; j < sample_names.length; j++) {
+      this_text = ""
+      this_text += sample_names[j]
+      if (sample_names[j] in ranked_cofactor1_dict){
+        this_text += "<br>Cofactor 1: " + ranked_cofactor1_dict[sample_names[j]]
+      }
+      if (sample_names[j] in ranked_cofactor2_dict){
+        this_text += "<br>Cofactor 2: " + ranked_cofactor2_dict[sample_names[j]]
+      }
+      point_text.push(this_text)
+    }
+
+    var trace = {
+        x: x_values,
+        y: y_values,
+        mode: 'markers',
+        text: point_text,
+        marker: {
+          size: sizes
+        }
     }
-}
 
-function chartupdate() {
-    //
-    var labelcolor = $("#labelcolor").val();
-    $(".nvd3 .nv-axis.nv-x text").css("fill", labelcolor);
-    $(".nvd3 .nv-axis.nv-y text").css("fill", labelcolor);
-    //
-    var labelfont = $("#labelfont").val();
-    $(".nvd3 .nv-axis.nv-x text").css("font-size", labelfont);
-    $(".nvd3 .nv-axis.nv-y text").css("font-size", labelfont);
-    //
-    var numbercolor = $("#numbercolor").val();
-    $("g.tick text").css("fill", numbercolor);
-    //
-    var numberfont = $("#numberfont").val();
-    $("g.tick text").css("font-size", numberfont);
-    //
-    var axiscolor = $("#axiscolor").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke", axiscolor);
-    $(".nv-y .nv-axis g path.domain").css("stroke", axiscolor);
-    //
-    var axiswidth = $("#axiswidth").val();
-    $(".nv-x .nv-axis g path.domain").css("stroke-width", axiswidth);
-    $(".nv-y .nv-axis g path.domain").css("stroke-width", axiswidth);
-    //
-    var linecolor = $("#linecolor").val();
-    $("line.nv-regLine").css("stroke", linecolor);
-    //
-    var linewidth = $("#linewidth").val();
-    $("line.nv-regLine").css("stroke-width", linewidth);
-    //
-    var markcolor = $("#markcolor").val();
-    $(".nvd3 g path").css("fill", markcolor);
+    return [trace];
 }
 
 function chartupdatewh() {
-    //
     var width = $("#width").val();
-    $("#scatterplot2 svg").css("width", width);
-    $("#srscatterplot2 svg").css("width", width);
-    //
     var height = $("#height").val();
-    $("#scatterplot2 svg").css("height", height);
-    $("#srscatterplot2 svg").css("height", height);
-    //
-    window.dispatchEvent(new Event('resize'));
+
+    width_height_update = {
+      height: height,
+      width: width
+    }
+
+    Plotly.newPlot('scatterplot2', getdata(), layout)
+    Plotly.relayout('scatterplot2', width_height_update)
+    Plotly.newPlot('srscatterplot2', srgetdata(), layout)
+    Plotly.relayout('srscatterplot2', width_height_update)
 }
 
- function colorer(d) {
-    datamin = d3.min(js_data.vals_3);
-    datamax = d3.max(js_data.vals_3);
-    //colormin = d3.rgb(255,0,0);
-    //colormax = d3.rgb(0,255,0);
+function colorer(d) {
+    datamin = d3.min(cofactor1_values);
+    datamax = d3.max(cofactor1_values);
     colormin = $("#cocolorfrom").val();
     colormax = $("#cocolorto").val();
 
-    console.log("colormin: "+colormin);
-    console.log("colormax: "+colormax);
+    compute = d3.interpolate(colormin, colormax);
+    linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
+
+    this_sample = d.tx.split("<br>")[0]
+
+    c = compute(linear(cofactor1_dict[this_sample]));
+
+    return c;
+}
+
+function ranked_colorer(d) {
+    datamin = d3.min(ranked_cofactor1_values);
+    datamax = d3.max(ranked_cofactor1_values);
+    colormin = $("#cocolorfrom").val();
+    colormax = $("#cocolorto").val();
 
     compute = d3.interpolate(colormin, colormax);
     linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]);
-    //console.log(d[0].x);
-          c= compute(linear(d[0].x));
-          //console.log(c);
-          return c;
-  }
+
+    this_sample = d.tx.split("<br>")[0]
+
+    c= compute(linear(ranked_cofactor1_dict[this_sample]));
+
+    return c;
+}
 
 function chartupdatedata() {
-    //
     var size = $("#marksize").val();
     var shape = $("#markshape").val();
-    //
-    d3.select('#scatterplot2 svg').datum(getdata(size, shape)).call(chart);
-    d3.select('#srscatterplot2 svg').datum(nv.log(srgetdata(size, shape))).call(srchart);
-    //
-    d3.selectAll('.nv-point')
-      .attr({
-          'stroke': colorer,
-          'fill':   colorer
-      });
-    //
-    nv.utils.windowResize(chart.update);
-    nv.utils.windowResize(srchart.update);
-}
 
-function savesvg(svgEl, name) {
-    svgEl.setAttribute("xmlns", "http://www.w3.org/2000/svg");
-    var svgData = svgEl.outerHTML;
-    var preface = '<?xml version="1.0" standalone="no"?>\r\n';
-    preface += '<?xml-stylesheet type="text/css" href="http://cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css"?>\r\n';
-    var svgBlob = new Blob([preface, svgData], {type:"image/svg+xml;charset=utf-8"});
-    var svgUrl = URL.createObjectURL(svgBlob);
-    var downloadLink = document.createElement("a");
-    downloadLink.href = svgUrl;
-    downloadLink.download = name;
-    document.body.appendChild(downloadLink);
-    downloadLink.click();
-    document.body.removeChild(downloadLink);
-}
+    var pearson_title_update = {
+      title: "Pearson Correlation Scatterplot"
+    }
+    var spearman_title_update = {
+      title: "Spearman Rank Correlation Scatterplot"
+    }
 
-function saveassvg_pcs() {
-    savesvg($("#svg_pcs")[0], "Pearson Correlation Scatterplot.svg");
-}
+    Plotly.newPlot('scatterplot2', getdata(), layout)
+    Plotly.relayout('scatterplot2', pearson_title_update)
+    Plotly.newPlot('srscatterplot2', srgetdata(), layout)
+    Plotly.relayout('srscatterplot2', spearman_title_update)
 
-function saveassvg_srcs() {
-    savesvg($("#svg_srcs")[0], "Spearman Rank Correlation Scatterplot.svg");
+    if ($('input[name=cofactor1_vals]').val()){
+      d3.select('#scatterplot2 svg').selectAll('.point')
+        .style({
+            'stroke': colorer,
+            'fill':   colorer
+      });
+      d3.select('#srscatterplot2 svg').selectAll('.point')
+        .style({
+            'stroke': ranked_colorer,
+            'fill':   ranked_colorer
+      });
+    }
 }
 
 drawg();
 srdrawg();
 
-$(".chartupdate").change(function () {
-    chartupdate();
-});
-
 $(".chartupdatewh").change(function () {
     chartupdatewh();
-    chartupdate();
 });
 
 $(".chartupdatedata").change(function () {
     chartupdatedata();
-    chartupdate();
 });
 
+$(".cofactor1_type").change(function () {
+    console.log("cofactor1 type:", $(".cofactor1_type").val())
+    if ($(".cofactor1_type").val() == "color"){
+      $(".cofactor2_type").val("size")
+    } else {
+      $(".cofactor2_type").val("color")
+    }
+});
+
+open_covariate_selection = function() {
+  return $('#collections_holder').load('/collections/list #collections_list', (function(_this) {
+    return function() {
+      $.colorbox({
+        inline: true,
+        href: "#collections_holder",
+        onComplete: function(){
+            $.getScript("/static/new/javascript/get_traits_from_collection.js");
+        }
+      });
+      return $('a.collection_name').attr('onClick', 'return false');
+    };
+  })(this));
+};
+
 $(document).ready(function(){
     chartupdatedata();
-    chartupdate();
+
+    $('#select_cofactor1').click(function () {
+        $('input[name=selecting_which_cofactor]').val("1");
+        open_covariate_selection();
+    });
+
+    $('#select_cofactor2').click(function () {
+        $('input[name=selecting_which_cofactor]').val("2");
+        open_covariate_selection();
+    });
 });
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index 4abb0735..8a79627a 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -4,7 +4,7 @@ var add_trait_data, assemble_into_json, back_to_collections, collection_click, c
 
 console.log("before get_traits_from_collection");
 
-collection_list = null;
+//collection_list = null;
 
 this_trait_data = null;
 
@@ -15,7 +15,6 @@ collection_click = function() {
   console.log("Clicking on:", $(this));
   this_collection_url = $(this).find('.collection_name').prop("href");
   this_collection_url += "&json";
-  console.log("this_collection_url", this_collection_url);
   collection_list = $("#collections_holder").html();
   return $.ajax({
     dataType: "json",
@@ -42,7 +41,6 @@ submit_click = function() {
       success: add_trait_data
     });
   });
-  console.log("SELECTED_TRAITS IS:", selected_traits);
   trait_names = [];
   samples = $('input[name=allsamples]').val().split(" ");
   all_vals = [];
@@ -117,7 +115,6 @@ trait_click = function() {
   trait = $(this).parent().find('.trait').text();
   dataset = $(this).parent().find('.dataset').text();
   this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset;
-  console.log("this_trait_url", this_trait_url);
   $.ajax({
     dataType: "json",
     url: this_trait_url,
@@ -134,28 +131,84 @@ add_trait_data = function(trait_data, textStatus, jqXHR) {
   return console.log("selected_traits:", selected_traits);
 };
 
+populate_cofactor_info = function(trait_info) {
+  if ($('input[name=selecting_which_cofactor]').val() == "1"){
+    $('#cofactor1_trait_link').attr("href", trait_info['url'])
+    if (trait_info['type'] == "ProbeSet"){
+      $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
+    } else {
+      $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
+    }
+    $('#select_cofactor1').text("Change Cofactor 1");
+    $('#cofactor1_info_container').css("display", "inline");
+    $('#cofactor2_button').css("display", "inline");
+  } else {
+    $('#cofactor2_trait_link').attr("href", trait_info['url'])
+    if (trait_info['type'] == "ProbeSet"){
+      $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
+    } else {
+      $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
+    }
+    $('#select_cofactor2').text("Change Cofactor 2");
+    $('#cofactor2_info_container').css("display", "inline");
+  }
+}
+
 get_trait_data = function(trait_data, textStatus, jqXHR) {
   var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len;
-  console.log("trait:", trait_data[0]);
   trait_sample_data = trait_data[1];
-  console.log("trait_sample_data:", trait_sample_data);
-  samples = $('input[name=allsamples]').val().split(" ");
+  if ( $('input[name=allsamples]').length ) {
+    samples = $('input[name=allsamples]').val().split(" ");
+  } else {
+    samples = js_data.indIDs
+  }
+  sample_vals = [];
   vals = [];
   for (_i = 0, _len = samples.length; _i < _len; _i++) {
     sample = samples[_i];
-    if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) {
-      vals.push(parseFloat(trait_sample_data[sample]));
+    if (sample in trait_sample_data) {
+      sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample]))
+      vals.push(parseFloat(trait_sample_data[sample]))
     } else {
-      vals.push(null);
+      sample_vals.push(null)
+      vals.push(null)
     }
   }
-  if ($('input[name=samples]').length < 1) {
-    $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
+  if ( $('input[name=allsamples]').length ) {
+    if ($('input[name=samples]').length < 1) {
+      $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />');
+    }
+    $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
+    this_trait_vals = get_this_trait_vals(samples);
+    return color_by_trait(trait_sample_data);
+  } else{
+    populate_cofactor_info(trait_data[0])
+    sorted = vals.slice().sort(function(a,b){return a-b})
+    ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 });
+    sample_ranks = []
+    for (_i = 0; _i < samples.length; _i++){
+      if (samples[_i] in trait_sample_data){
+        sample_ranks.push(samples[_i] + ":" + ranks[_i])
+      } else {
+        sample_ranks.push(null)
+      }
+    }
+
+    if ($('input[name=selecting_which_cofactor]').val() == "1"){
+      $('input[name=cofactor1_vals]').val(sample_vals)
+      $('input[name=ranked_cofactor1_vals]').val(sample_ranks)
+    } else {
+      $('input[name=cofactor2_vals]').val(sample_vals)
+      $('input[name=ranked_cofactor2_vals]').val(sample_ranks)
+    }
+    chartupdatedata();
+    chartupdate();
+    return false
   }
-  $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />');
-  this_trait_vals = get_this_trait_vals(samples);
-  console.log("THE LENGTH IS:", $('input[name=vals]').length);
-  return color_by_trait(trait_sample_data);
 };
 
 get_this_trait_vals = function(samples) {
@@ -215,14 +268,17 @@ process_traits = function(trait_data, textStatus, jqXHR) {
   }
   the_html += "</tbody>";
   the_html += "</table>";
+  the_html += "<div id=\"collection_list_html\" style=\"display: none;\">"
+  the_html += collection_list
+  the_html += "</div>"
   the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>"
   $("#collections_holder").html(the_html);
   return $('#collections_holder').colorbox.resize();
 };
 
 back_to_collections = function() {
-  console.log("collection_list:", collection_list);
-  $("#collections_holder").html(collection_list);
+  collection_list_html = $('#collection_list_html').html()
+  $("#collections_holder").html(collection_list_html);
   $(document).on("click", ".collection_line", collection_click);
   return $('#collections_holder').colorbox.resize();
 };
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index 185de8a9..97d768c8 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -71,11 +71,11 @@
     })();
     //ZS: 0.1 indicates buffer, increase to increase buffer
     y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1]
-    sw_result = ShapiroWilkW(sorted_values);
-    W = sw_result.w.toFixed(3);
-    pvalue = sw_result.p.toFixed(3);
-    pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
-    test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
+    //sw_result = ShapiroWilkW(sorted_values);
+    //W = sw_result.w.toFixed(3);
+    //pvalue = sw_result.p.toFixed(3);
+    //pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
+    //test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
     z_scores = get_z_scores(sorted_values.length);
     //ZS: 0.1 indicates buffer, increase to increase buffer
     x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1]
@@ -106,7 +106,6 @@
       };
     };
     data = [make_data('samples_primary'), make_data('samples_other'), make_data('samples_all')];
-    console.log("THE DATA IS:", data);
     x_values = {}
     y_values = {}
     point_names = {}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index d641dc67..e9dd3c9d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -889,6 +889,7 @@
     max_y_val = Math.max(...positive_error_vals)
 
     if (min_y_val == 0) {
+        range_top = max_y_val + Math.abs(max_y_val)*0.1
         range_bottom = 0;
     } else {
         range_top = max_y_val + Math.abs(max_y_val)*0.1
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index d45aa015..603947f4 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -1,36 +1,38 @@
 <div id="myModal">
     <div class="modal-header">
-        <h3>Add to collection</h3>
-        <p>You have two choices: Create and name a collection,
-        or add the traits to an existing collection.</p>
+        <h2>Define or Add to Collection</h2>
+        <p>You have two choices: Name a new collection
+        or add to an existing collection.</p>
     </div>
-    <div class="modal-body">
+    <div class="modal-body" style="margin-left: 20px;">
         <form action="/collections/new" data-validate="parsley" id="add_form">
             <input type="hidden" name="traits" value="{{ traits }}" />
             <fieldset>
-                <legend>Create a new named collection</legend>
-                <label>New collection name</label>
-                <input type="text" name="new_collection" placeholder="Name of new collection..."
-                    data-trigger="change" data-minlength="5" data-maxlength="50">
-                <span class="help-block">Type the name of the new collection.</span>
+              <legend>1. Create a new collection</legend>
+              <div style="margin-left: 20px;">
+                <!--<label>Collection name:</label>-->
+                <input type="text" name="new_collection" placeholder=" Name of new collection..."
+                    data-trigger="change" data-minlength="5" data-maxlength="50" style="width: 100%">
+                <button type="submit" name="create_new" class="btn btn-primary" style="margin-top: 20px;">Create collection</button>
                 {% if uc is not defined %}
                 <span class="help-block" style="color:red;">This collection will be saved to this computer for 5 days.</span>
                 {% endif %}
-                <button type="submit" name="create_new" class="btn">Create and add traits</button>
+              </div>
             </fieldset>
             <hr />
             <fieldset>
-                <legend>Or add to an existing collection</legend>
-                <label>Existing collection name</label>
-
+              <legend>2. Add to an existing collection</legend>
+              <div style="margin-left: 20px;">  
+                <!--<label>Existing collection name:</label>-->
                 <select name="existing_collection" class="form-control">
+                    <option selected disabled>Select Collection</option>
                 {% for col in collections %}
                     <option value="{{ col.id }}:{{ col.name }}">{{ col.name }}</option>
                 {% endfor %}
                 </select>
                 <br />
-
-                <button type="submit" name="add_to_existing" class="btn">Add to existing collection</button>
+                <button type="submit" name="add_to_existing" class="btn btn-primary">Add to existing collection</button>
+              </div>
             </fieldset>
         </form>
     </div>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 11c33673..64d5a676 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -3,7 +3,6 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index cae03b4a..864299a2 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -29,10 +29,6 @@
                 {{ this_trait.name }}:{{ this_trait.dataset.name }},
             {% endfor %}" >
 
-                <button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" >
-                Delete this collection
-                </button>
-
 
                 <button id="corr_matrix" class="btn btn-primary submit_special" data-url="/corr_matrix" title="Correlation Matrix" >
                     Correlation Matrix
@@ -58,6 +54,15 @@
                     Heatmap
                 </button>
 
+                <button id="comp_bar_chart" class="btn btn-primary submit_special" data-url="/comparison_bar_chart" title="Comparison Bar Chart" >
+                    Comparison Bar Chart
+                </button>
+
+
+                <button id="delete" class="btn btn-danger submit_special" style="margin-left: 15px;" data-url="/collections/delete" title="Delete this collection" >
+                    Delete Collection
+                </button>
+
           </form>
         </div>
 
@@ -66,8 +71,8 @@
             <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
-            <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
+            <button class="btn btn-danger" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Delete From Collection</button>
+            <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Copy Record to Other Collection</button>
             <br />
             <br />
             <form id="export_form" method="POST" action="/export_traits_csv">
@@ -246,6 +251,14 @@
                 url = $(this).data("url")
                 return submit_special(url)
             });
+            $("#comp_bar_chart").on("click", function() {
+                traits = $("#trait_table input:checked").map(function() {
+                    return $(this).val();
+                }).get();
+                $("#trait_list").val(traits)
+                url = $(this).data("url")
+                return submit_special(url)
+            });
         });
         
     </script>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
new file mode 100644
index 00000000..033ff0a4
--- /dev/null
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -0,0 +1,39 @@
+{% extends "base.html" %}
+{% block title %}Comparison Bar Chart{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+    {{ header("Comparison Bar Chart") }}
+
+    <div class="container">
+        <div>
+            <h3>
+                The following is a grouped bar chart with the sample values for each selected trait. 
+            </h3>
+        </div>
+        <div id="chart_container">
+            <div id="comp_bar_chart"></div>
+        </div>
+    
+    </div>
+
+    <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}  
+    <script>
+        js_data = {{ js_data | safe }}
+    </script>
+
+    <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
+
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index e0f017c2..6451fda5 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -12,124 +12,74 @@
 
 <div class="container-fluid">
 
-  <h2>Correlation Scatterplot</h2>
+  <input type="hidden" name="cofactor1_vals"></input>
+  <input type="hidden" name="ranked_cofactor1_vals"></input>
+  <input type="hidden" name="cofactor2_vals"></input>
+  <input type="hidden" name="ranked_cofactor2_vals"></input>
+  <input type="hidden" name="selecting_which_cofactor"></input>
 
-  <div style="margin-left: 0px;">
-    {% if trait_1.dataset.type == "ProbeSet" %}
-    <div>
-      X axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
-      </a>
-    </div>
-    <div>
-      [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
-      {{trait_1.description_display}}
-    </div>
-    {% elif trait_1.dataset.type == "Publish" %}
-    <div>
-      X axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
-        {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
-      </a>
-    </div>
-    <div>
-      <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
-        {{trait_1.description_display}}
-    </div>
-    {% endif %}
+  <h2>Correlation Scatterplot</h2>
 
-    <br/>
+  <table class="table">
+    <tr>
+      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
+      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="700" style="width: 44px; height: 22px;"> px</td>
+    </tr>
+  </table>
 
-    {% if trait_2.dataset.type == "ProbeSet" %}
-    <div>
-      Y axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
-      </a>
-    </div>
-    <div>
-      [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
-      {{trait_2.description_display}}
-    </div>
-    {% elif trait_2.dataset.type == "Publish" %}
-    <div>
-      Y axis:
-      <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
-        {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
-      </a>
-    </div>
-    <div>
-      <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
-        {{trait_2.description_display}}
+  <div>
+    <button type="button" class="btn btn-default" id="select_cofactor1">
+      Select Cofactor 1
+    </button>
+<!--
+    <select class="cofactor1_type">
+      <option value="color">Color</option>
+      <option value="size">Size</option>
+    </select>
+-->
+    <div id="cofactor2_button" style="margin-left: 10px; display: none;">
+      <button type="button" class="btn btn-default" id="select_cofactor2">
+        Add a Second Cofactor?
+      </button>
+<!--
+      <select class="cofactor2_type">
+        <option value="color">Color</option>
+        <option value="size" selected="selected">Size</option>
+      </select>
+-->
     </div>
-    {% endif %}
-
-    <br/>
+  </div>
+  <div id="collections_holder_wrapper" style="display:none;">
+      <div id="collections_holder"></div>
+  </div>
+  <br/>
 
-    {% if trait_3 %}
-    {% if trait_3.dataset.type == "ProbeSet" %}
+  <div id="cofactor1_info_container" style="margin-left: 0px; display: none;">
     <div>
-      Cofactor:
-      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
-        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.tissue + " "  + trait_3.dataset.name + ": " + trait_3.name|string}}
-      </a>
+      <b>Cofactor 1</b>: <a id="cofactor1_trait_link" href="#"></a>
     </div>
-    <div>
-      [{{trait_3.symbol}} on {{trait_3.location_repr}} Mb]
-      {{trait_3.description_display}}
+    <div id="cofactor1_description"></div>
+    <br>
+    <div style="margin-bottom: 10px;">
+    <b>Cofactor 1 Color Range:</b> 
+    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#D9D9D9">
+    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
     </div>
-    {% elif trait_3.dataset.type == "Publish" %}
+  </div>
+
+  <div id="cofactor2_info_container" style="margin-left: 0px; display: none;">
+    <hr>
     <div>
-      Cofactor:
-      <a href="{{url_for('show_trait_page', trait_id = trait_3.name, dataset = trait_3.dataset.name)}}">
-        {{trait_3.dataset.group.species + " " + trait_3.dataset.group.name + " " + trait_3.dataset.name + ": " + trait_3.name|string}}
-      </a>
+      <b>Cofactor 2</b>: <a id="cofactor2_trait_link" href="#"></a>
     </div>
-    <div>
-      <a href="{{trait_3.pubmed_link}}">PubMed: {{trait_3.pubmed_text}}</a>
-        {{trait_3.description_display}}
+    <div id="cofactor2_description"></div>
+    <br>
+    <div style="margin-bottom: 20px;">
+    <b>Cofactor 2 corresponds to point radius</b> 
     </div>
-    {% endif %}
-    {% endif %}
-
-    <input class="chartupdatedata" id="cocolorfrom" type="color" value="#000000">
-    <input class="chartupdatedata" id="cocolorto" type="color" value="#000000">
-
+    <br>
   </div>
 
-  <br>
-
-  <table class="table">
-    <tr>
-      <td style="vertical-align: middle;">Width <input class="chartupdatewh" id="width" type="text" value="1000" style="width: 44px; height: 22px;"> px</td>
-      <td style="vertical-align: middle;">Height <input class="chartupdatewh" id="height" type="text" value="800" style="width: 44px; height: 22px;"> px</td>
-    </tr>
-  </table>
-
-  <table class="table">
-    <tr>
-      <td style="vertical-align: middle;">Label
-        <input class="chartupdate" id="labelcolor" type="color" value="#000000">
-        <input class="chartupdate" id="labelfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Number
-        <input class="chartupdate" id="numbercolor" type="color" value="#000000">
-        <input class="chartupdate" id="numberfont" type="text" value="16" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Axis
-        <input class="chartupdate" id="axiscolor" type="color" value="#000000">
-        <input class="chartupdate" id="axiswidth" type="text" value="2" style="width: 44px; height: 22px;"> px
-      </td>
-      <td style="vertical-align: middle;">Line
-        <input class="chartupdate" id="linecolor" type="color" value="#8fbbda">
-        <input class="chartupdate" id="linewidth" type="text" value="1" style="width: 44px; height: 22px;"> px
-      </td>
-    </tr>
-  </table>
-
-  <br>
-
   <ul class="nav nav-tabs">
     <li class="active">
       <a href="#tp1" data-toggle="tab">Pearson</a>
@@ -143,17 +93,11 @@
 
     <div class="tab-pane active" id="tp1">
       <br>
-      <div>
-        <a id="a_svg_pcs" href="#" onclick="javascript:saveassvg_pcs();" class="btn btn-primary">Save as SVG</a>
-      </div>
-      <div style="width: 1000px; text-align: center;">
-        <h2>Pearson Correlation Scatterplot</h2>
-      </div>
-      <div id="scatterplot2">
-        <svg id="svg_pcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
-      </div>
+      <div id="scatterplot2"></div>
       <br>
-      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
+      <div class="row" style="width: 70%;">
+      <div class="col-xs-3">
+      <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
         <thead>
           <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
         </thead>
@@ -187,53 +131,147 @@
           </tr>
         </tbody>
       </table>
-    </div>
-
-    <div class="tab-pane" id="tp2">
+      </div>
+      <div class="col-xs-9">
+        {% if trait_1.dataset.type == "ProbeSet" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+          {{trait_1.description_display}}
+        </div>
+        {% elif trait_1.dataset.type == "Publish" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+            {{trait_1.description_display}}
+        </div>
+        {% endif %}
 
-      <br>
+        <br/>
 
-      <div>
-        <a id="a_svg_srcs" href="#" onclick="javascript:saveassvg_srcs();" class="btn btn-primary">Save as SVG</a>
-      </div>
-      <div style="width: 1000px; text-align: center;">
-        <h2>Spearman Rank Correlation Scatterplot</h2>
+        {% if trait_2.dataset.type == "ProbeSet" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+          {{trait_2.description_display}}
+        </div>
+        {% elif trait_2.dataset.type == "Publish" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+            {{trait_2.description_display}}
+        </div>
+        {% endif %}
       </div>
-      <div id="srscatterplot2">
-        <svg id="svg_srcs" style="width: 1000px; height: 800px; margin-left: 10px;"></svg>
       </div>
+    </div>
 
+    <div class="tab-pane" id="tp2">
+      <br>
+      <div id="srscatterplot2"></div>
       <br>
+      <div class="row" style="width: 70%;">
+      <div class="col-xs-3">
+        <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
+          <thead>
+            <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>Number</td>
+              <td>{{jsdata.num_overlap}}</td>
+            </tr>
+            <tr>
+              <td>Slope</td>
+              <td>{{'%0.3f' % jsdata.srslope}}</td>
+            </tr>
+            <tr>
+              <td>Intercept</td>
+              <td>{{'%0.3f' % jsdata.srintercept}}</td>
+            </tr>
+            <tr>
+              <td>r value</td>
+              <td>{{'%0.3f' % jsdata.srr_value}}</td>
+            </tr>
+	    <tr>
+              <td>P value</td>
+              <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+            </tr>
+          </tbody>
+        </table>
+      </div>
+      <div class="col-xs-9">
+        {% if trait_1.dataset.type == "ProbeSet" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.tissue + " "  + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_1.symbol}} on {{trait_1.location_repr}} Mb]
+          {{trait_1.description_display}}
+        </div>
+        {% elif trait_1.dataset.type == "Publish" %}
+        <div>
+          X axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_1.name, dataset = trait_1.dataset.name)}}">
+            {{trait_1.dataset.group.species + " " + trait_1.dataset.group.name + " " + trait_1.dataset.name + ": " + trait_1.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_1.pubmed_link}}">PubMed: {{trait_1.pubmed_text}}</a>
+            {{trait_1.description_display}}
+        </div>
+        {% endif %}
 
-      <table class="table table-hover table-striped table-bordered" style="width: 200px; margin-left: 80px; text-align: right;">
-        <thead>
-          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>Number</td>
-            <td>{{jsdata.num_overlap}}</td>
-          </tr>
-          <tr>
-            <td>Slope</td>
-            <td>{{'%0.3f' % jsdata.srslope}}</td>
-          </tr>
-          <tr>
-            <td>Intercept</td>
-            <td>{{'%0.3f' % jsdata.srintercept}}</td>
-          </tr>
-          <tr>
-            <td>r value</td>
-            <td>{{'%0.3f' % jsdata.srr_value}}</td>
-          </tr>
-	  <tr>
-            <td>P value</td>
-            <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
-          </tr>
-        </tbody>
-      </table>
-    </div>
+        <br/>
 
+        {% if trait_2.dataset.type == "ProbeSet" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.tissue + " "  + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          [{{trait_2.symbol}} on {{trait_2.location_repr}} Mb]
+          {{trait_2.description_display}}
+        </div>
+        {% elif trait_2.dataset.type == "Publish" %}
+        <div>
+          Y axis:
+          <a href="{{url_for('show_trait_page', trait_id = trait_2.name, dataset = trait_2.dataset.name)}}">
+            {{trait_2.dataset.group.species + " " + trait_2.dataset.group.name + " " + trait_2.dataset.name + ": " + trait_2.name|string}}
+          </a>
+        </div>
+        <div>
+          <a href="{{trait_2.pubmed_link}}">PubMed: {{trait_2.pubmed_text}}</a>
+            {{trait_2.description_display}}
+        </div>
+        {% endif %}
+      </div>
+      </div>
   </div>
 
 </div>
@@ -250,5 +288,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index c4668e05..e4fd3136 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,8 +1,6 @@
 {% extends "base.html" %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
@@ -107,8 +105,6 @@
     <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
     <script type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 6f2ad0b8..0612bfcc 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -43,26 +43,24 @@
                     <th data-export="Location">Location</th>
                     <th data-export="Mean">Mean</th>
                     <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                    <th data-export="Max LRS Location">Max LRS Location</th>
                     <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                   </tr>
                 </thead> 
                 <tbody>
                   {% for this_trait in trait_list %}
-                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                    <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}">
+                    <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td>
                     <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
-                    <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td>
-                    <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td>
-                    <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td>
-                    <td data-export="{{ this_trait.dataset.tissue }}">{{ this_trait.dataset.tissue }}</td>
-                    <td data-export="{{ this_trait.dataset.name }}">{{ this_trait.dataset.name }}</td>
+                    <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td>
+                    <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td>
+                    <td data-export="{{ this_trait.group }}">{{ this_trait.group }}</td>
+                    <td data-export="{{ this_trait.tissue }}">{{ this_trait.tissue }}</td>
+                    <td data-export="{{ this_trait.dataset }}">{{ this_trait.dataset }}</td>
                     <td data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</td>
-                    <td data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</td>
+                    <td data-export="{{ this_trait.description }}">{{ this_trait.description }}</td>
                     <td data-export="{{ this_trait.location_repr }}" align="right">{{ this_trait.location_repr }}</td>
                     <td data-export="{{ '%0.3f' % this_trait.mean|float }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</td>
                     <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                    <td data-export="{{ this_trait.LRS_location_repr }}" align="right">{{ this_trait.LRS_location_repr }}</td>
                     <td data-export="{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}</td>
                   </tr>
                   {% endfor %}
@@ -81,7 +79,6 @@
                     <th>Location</th>
                     <th>Mean</th>
                     <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                    <th data-export="LRS Location">Max LRS Location</th>
                     <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                   </tr>
                 </tfoot> 
@@ -142,7 +139,6 @@
                     { "type": "natural", "width": "7%" },
                     { "type": "natural", "width": "4%" },
                     { "type": "natural", "width": "5%" },
-                    { "type": "natural", "width": "7%" },
                     { "type": "natural", "width": "5%" }
                 ],
                 "columnDefs": [
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 7a8ca07b..c2cbdadd 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -40,23 +40,21 @@
                         <th data-export="Authors">Authors</th>
                         <th data-export="Year">Year</th>
                         <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                        <th data-export="LRS Location">Max LRS Location</th>
                         <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                     </tr>
                 </thead>
                 <tbody>
                  {% for this_trait in trait_list %}
-                    <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                        <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                    <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}">
+                        <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td>
                         <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
-                        <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td>
-                        <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td>
-                        <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td>
-                        <td data-export="{{ this_trait.description_display }}">{{ this_trait.description_display }}</td>
+                        <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td>
+                        <td data-export="{{ this_trait.group }}">{{ this_trait.group }}</td>
+                        <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td>
+                        <td data-export="{{ this_trait.description }}">{{ this_trait.description }}</td>
                         <td data-export="{{ this_trait.authors }}">{{ this_trait.authors }}</td>
                         <td data-export="{{ this_trait.pubmed_text }}" data-order="{{ this_trait.pubmed_text }}"><a href="{{ this_trait.pubmed_link }}">{{ this_trait.pubmed_text }}</a></td>
                         <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                        <td data-export="{{ this_trait.LRS_location_repr }}" align="right">{{ this_trait.LRS_location_repr }}</td>
                         <td data-export="{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}</td>
                     </tr>
                 {% endfor %}
@@ -72,7 +70,6 @@
                         <th>Authors</th>
                         <th>Year</th>
                         <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
-                        <th data-export="LRS Location">Max LRS Location</th>
                         <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
                     </tr>
                 </tfoot>
@@ -135,7 +132,6 @@
                     { "type": "natural", "width": "25%"},
                     { "type": "natural" },
                     { "type": "natural", "width": "8%"},
-                    { "type": "natural", "width": "12%"},
                     { "type": "natural" }
                 ],
                 "columnDefs": [
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 53b6646c..495a266e 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -76,6 +76,12 @@
                               {% if g.user_session.logged_in %}
                               {% if g.user_session.num_collections < 1 %}
                               No collections available. Please add traits to a collection to use them as covariates.
+                              {% else %}
+                              <div style="margin-bottom: 10px;" class="btn-group" role="group">
+                                <button type="button" id="select_covariates" class="btn btn-default">Select</button>
+                                <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
+                              </div>
+                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
                               {% endif %}
                               {% elif g.cookie_session.display_num_collections() == "" %}
                               No collections available. Please add traits to a collection to use them as covariates.
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 830c7864..d6f39e83 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -49,7 +49,7 @@ def timestamp():
 
 class AnonUser(object):
     """Anonymous user handling"""
-    cookie_name = 'anon_user_v8'
+    cookie_name = 'anon_user_v1'
 
     def __init__(self):
         self.cookie = request.cookies.get(self.cookie_name)
@@ -60,23 +60,10 @@ class AnonUser(object):
         else:
             logger.debug("CREATING NEW ANON COOKIE")
             self.anon_id, self.cookie = create_signed_cookie()
+            res = flask.make_response()
+            res.set_cookie(self.cookie_name, self.cookie)
         self.key = "anon_collection:v1:{}".format(self.anon_id)
 
-        #ZS: This was originally the commented out function below
-        #    For some reason I don't yet understand the commented out code works on production, 
-        #    but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
-        @app.after_request
-        def set_cookie(response):
-            if self.cookie:
-                pass
-            else:
-                response.set_cookie(self.cookie_name, self.cookie)
-            return response
-
-        #@after.after_this_request
-        #def set_cookie(response):
-        #    response.set_cookie(self.cookie_name, self.cookie)
-
     def add_collection(self, new_collection):
         collection_dict = dict(name = new_collection.name,
                                created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2089f9de..ae333e73 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -43,6 +43,7 @@ from base.data_set import DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.heatmap import heatmap
+from wqflask.comparison_bar_chart import comparison_bar_chart
 from wqflask.marker_regression import marker_regression
 from wqflask.marker_regression import marker_regression_gn1
 from wqflask.network_graph import network_graph
@@ -464,6 +465,27 @@ def heatmap_page():
 
     return rendered_template
 
+@app.route("/comparison_bar_chart", methods=('POST',))
+def comp_bar_chart_page():
+    logger.info("In comp bar chart, request.form is:", pf(request.form))
+    logger.info(request.url)
+
+    start_vars = request.form
+
+    traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+    if traits[0] != "":
+        template_vars = comparison_bar_chart.ComparisonBarChart(request.form)
+        template_vars.js_data = json.dumps(template_vars.js_data,
+                                               default=json_default_handler,
+                                               indent="   ")
+
+        result = template_vars.__dict__
+        rendered_template = render_template("comparison_bar_chart.html", **result)
+    else:
+        rendered_template = render_template("empty_collection.html", **{'tool':'Comparison Bar Chart'})
+
+    return rendered_template
+
 @app.route("/mapping_results_container")
 def mapping_results_container_page():
     return render_template("mapping_results_container.html")
-- 
cgit v1.2.3