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-rw-r--r--etc/default_settings.py19
-rw-r--r--wqflask/runserver.py11
-rw-r--r--wqflask/utility/logger.py2
-rw-r--r--wqflask/utility/tools.py13
-rw-r--r--wqflask/wqflask/static/new/javascript/biodalliance.js72
-rw-r--r--wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee37
-rw-r--r--wqflask/wqflask/static/new/javascript/chr_lod_chart.js31
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.coffee16
-rw-r--r--wqflask/wqflask/static/new/javascript/create_lodchart.js11
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.coffee2
-rw-r--r--wqflask/wqflask/static/new/javascript/lod_chart.js63
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html209
-rw-r--r--wqflask/wqflask/views.py54
13 files changed, 395 insertions, 145 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py
index 6acea637..08eae024 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -2,18 +2,22 @@
# webserver running in developer mode with limited console
# output. Copy this file and run it from ./bin/genenetwork2 configfile
#
-# Note that these settings are fetched in ./wqflask/utilities/tools.py
+# Note: these settings are fetched in ./wqflask/utilities/tools.py
# which has support for overriding them through environment variables,
# e.g.
#
# env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2
# env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py
#
-# Note also that in the near future we will additionally fetch
+# Note: in the near future we will additionally fetch
# settings from a JSON file
#
-# Note that values for False and 0 have to be strings here - otherwise
+# Note: values for False and 0 have to be strings here - otherwise
# Flask won't pick them up
+#
+# For GNU Guix deployment also check the paths in
+#
+# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py
import os
import sys
@@ -22,7 +26,7 @@ GN_VERSION = open("../VERSION","r").read()
SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s"
SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s'
SQLALCHEMY_POOL_RECYCLE = 3600
-GN_SERVER_URL = "http://localhost:8880/"
+GN_SERVER_URL = "http://test-gn2.genenetwork.org/"
# ---- Flask configuration (see website)
TRAP_BAD_REQUEST_ERRORS = True
@@ -33,7 +37,7 @@ SECURITY_RECOVERABLE = True
SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org"
SECURITY_POST_LOGIN_VIEW = "/thank_you"
-SERVER_PORT = 5003
+SERVER_PORT = 5003 # running on localhost
SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc'
# ---- Behavioural settings (defaults) note that logger and log levels can
@@ -41,6 +45,7 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a
WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD)
WEBSERVER_BRANDING = None # Set the branding (nyi)
WEBSERVER_DEPLOY = None # Deployment specifics (nyi)
+WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all)
@@ -53,7 +58,8 @@ USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls
# Paths to JS libraries
-TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher"
+JS_BIODALLIANCE = os.environ['HOME']+"/genenetwork/biodalliance"
+JS_TWITTER_POST_FETCHER = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher"
# ---- Path overrides for Genenetwork
# TMPDIR is normally picked up from the environment
@@ -63,6 +69,7 @@ GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files
LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files
# ---- GN2 Executables
+# Paths to invoked binaries
PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read())
PLINK_COMMAND = str.strip(os.popen("which plink2").read())
GEMMA_COMMAND = str.strip(os.popen("which gemma").read())
diff --git a/wqflask/runserver.py b/wqflask/runserver.py
index 0342b7ad..adacc712 100644
--- a/wqflask/runserver.py
+++ b/wqflask/runserver.py
@@ -19,11 +19,18 @@ ENDC = '\033[0m'
import os
app.config['SECRET_KEY'] = os.urandom(24)
-from utility.tools import WEBSERVER_MODE,get_setting_int
+from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting
port = get_setting_int("SERVER_PORT")
-logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC))
+print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]")
+
+import requests
+page = requests.get(get_setting("GN_SERVER_URL"))
+if page.status_code != 200:
+ raise Exception("API server not found!")
+
+print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
werkzeug_logger = logging.getLogger('werkzeug')
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index bacb0aa4..128706df 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI).
def warning(self,*args):
"""Call logging.warning for multiple args"""
self.collect(self.logger.warning,*args)
- self.logger.warning(self.collect(*args))
+ # self.logger.warning(self.collect(*args))
def error(self,*args):
"""Call logging.error for multiple args"""
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index df032e48..9860f63e 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -121,9 +121,14 @@ def assert_writable_dir(dir):
fh.close()
os.remove(fn)
except IOError:
- raise Exception('Unable to write test.txt to directory ' + dir )
+ raise Exception('Unable to write test.txt to directory ' + dir)
return dir
+def assert_file(fn):
+ if not valid_file(fn):
+ raise Exception('Unable to find file '+fn)
+ return fn
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
@@ -233,4 +238,8 @@ if os.environ.get('WQFLASK_OVERRIDES'):
OVERRIDES[k] = cmd
logger.debug(OVERRIDES)
-assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH"))
+assert_dir(get_setting("JS_BIODALLIANCE"))
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js")
+assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js")
+assert_dir(get_setting("JS_TWITTER_POST_FETCHER"))
+assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js")
diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
new file mode 100644
index 00000000..3b9e3b7f
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -0,0 +1,72 @@
+"use strict";
+
+
+var BD = {};
+BD.browser = null;
+BD.data = {};
+BD.sources = [];
+
+var getChrLen = function(chr) {
+ return js_data[chr * 1];
+};
+
+BD.createBrowser = function(chr, start, end, speciesName, sources) {
+ console.log("creating BD browser");
+ var b = new Browser({
+ chr: chr,
+ viewStart: start,
+ viewEnd: end,
+
+ coordSystem: {
+ speciesName: speciesName
+ },
+
+ sources: sources,
+
+ maxHeight: 1400,
+ setDocumentTitle: false,
+ prefix: '/dalliance/',
+ workerPrefix: 'build/',
+ noPersist: true,
+ pageName: 'bd_container'
+ });
+
+ console.log("created BD browser");
+ return b;
+};
+
+BD.showButton = function() {
+ $('#open_bd').show();
+ $('#close_bd').hide();
+};
+
+BD.hideButton = function() {
+ $('#close_bd').show();
+ $('#open_bd').hide();
+};
+
+
+BD.putData = function(data) {
+ for (var key in data) {
+ BD.data[key] = data[key];
+ }
+};
+
+BD.putSource = function(source) {
+ BD.sources.push(source);
+};
+
+BD.openBrowser = function() {
+ console.log("opening browser");
+ if (!BD.browser) {
+ BD.browser = BD.createBrowser(BD.data.chr,
+ 0,
+ BD.data.length * 1000000,
+ BD.data.species,
+ BD.sources);
+ } else {
+ BD.browser.setLocation(BD.data.chr, 0, BD.data.length * 1000000);
+ }
+
+ BD.browser.maxViewWidth = BD.data.length * 1000000;
+};
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
index e00694be..8a5a3569 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
@@ -5,7 +5,7 @@ class Chr_Lod_Chart
@qtl_results = js_data.qtl_results
console.log("qtl_results are:", @qtl_results)
console.log("chr is:", @chr)
-
+
@get_max_chr()
@filter_qtl_results()
@@ -21,16 +21,16 @@ class Chr_Lod_Chart
console.log("@x_coords: ", @x_coords)
console.log("@y_coords: ", @y_coords)
console.timeEnd('Create coordinates')
-
+
# Buffer to allow for the ticks/labels to be drawn
@x_buffer = @plot_width/30
@y_buffer = @plot_height/20
-
+
@x_max = d3.max(@x_coords)
@y_max = d3.max(@y_coords) * 1.2
-
+
@y_threshold = @get_lod_threshold()
-
+
@svg = @create_svg()
@plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)
@@ -43,14 +43,14 @@ class Chr_Lod_Chart
console.time('Create graph')
@create_graph()
console.timeEnd('Create graph')
-
+
get_max_chr: () ->
@max_chr = 0
for key of js_data.chromosomes
console.log("key is:", key)
if parseInt(key) > @max_chr
@max_chr = parseInt(key)
-
+
filter_qtl_results: () ->
@these_results = []
this_chr = 100
@@ -59,8 +59,8 @@ class Chr_Lod_Chart
this_chr = @max_chr
else
this_chr = result.chr
- console.log("this_chr is:", this_chr)
- console.log("@chr[0] is:", parseInt(@chr[0]))
+ # console.log("this_chr is:", this_chr)
+ # console.log("@chr[0] is:", parseInt(@chr[0]))
if this_chr > parseInt(@chr[0])
break
if parseInt(this_chr) == parseInt(@chr[0])
@@ -72,7 +72,7 @@ class Chr_Lod_Chart
if result.lod_score > 1
high_qtl_count += 1
console.log("high_qtl_count:", high_qtl_count)
-
+
#if high_qtl_count > 10000
@y_axis_filter = 2
#else if high_qtl_count > 1000
@@ -85,7 +85,7 @@ class Chr_Lod_Chart
@x_coords.push(parseFloat(result.Mb))
@y_coords.push(result.lod_score)
@marker_names.push(result.name)
-
+
create_svg: () ->
svg = d3.select("#topchart")
.append("svg")
@@ -102,7 +102,7 @@ class Chr_Lod_Chart
@y_scale = d3.scale.linear()
.domain([0, @y_max])
.range([@plot_height, @y_buffer])
-
+
get_lod_threshold: () ->
if @y_max/2 > 2
return @y_max/2
@@ -125,7 +125,7 @@ class Chr_Lod_Chart
[@y_buffer, @plot_height, @plot_width, @plot_width],
[@y_buffer, @y_buffer, @x_buffer, @plot_width],
[@plot_height, @plot_height, @x_buffer, @plot_width]]
-
+
@svg.selectAll("line")
.data(border_coords)
.enter()
@@ -141,7 +141,7 @@ class Chr_Lod_Chart
)
.attr("x2", (d) =>
return d[3]
- )
+ )
.style("stroke", "#000")
add_x_axis: () ->
@@ -166,13 +166,13 @@ class Chr_Lod_Chart
.attr("transform", (d) =>
return "translate(-12,0) rotate(-90)"
)
-
+
add_y_axis: () ->
@yAxis = d3.svg.axis()
.scale(@y_scale)
.orient("left")
.ticks(5)
-
+
@svg.append("g")
.attr("class", "y_axis")
.attr("transform", "translate(" + @x_buffer + ",0)")
@@ -200,7 +200,7 @@ class Chr_Lod_Chart
.x( (d) => return @x_scale(d[0]))
.y( (d) => return @y_scale(d[1]))
.interpolate("linear")
-
+
line_graph = @svg.append("path")
.attr("d", line_function(@plot_coordinates))
.attr("stroke", "blue")
@@ -273,6 +273,9 @@ class Chr_Lod_Chart
$("#return_to_full_view").hide()
$('#topchart').remove()
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')
+ BD.hideButton()
+ $('#close_bd').hide();
+ $('#bd_container').hide()
create_lod_chart()
show_marker_in_table: (marker_info) ->
diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
index c6cbd01b..bae4565d 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
@@ -1,13 +1,12 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
var Chr_Lod_Chart;
Chr_Lod_Chart = (function() {
- function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) {
+ function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) {
this.plot_height = plot_height;
this.plot_width = plot_width;
this.chr = chr;
this.manhattanPlot = manhattanPlot;
- this.mappingScale = mappingScale;
this.qtl_results = js_data.qtl_results;
console.log("qtl_results are:", this.qtl_results);
console.log("chr is:", this.chr);
@@ -95,18 +94,11 @@ Chr_Lod_Chart = (function() {
Chr_Lod_Chart.prototype.create_coordinates = function() {
var i, len, ref, result, results;
ref = this.these_results;
- console.log("THESE_RESULTS:", ref)
results = [];
for (i = 0, len = ref.length; i < len; i++) {
result = ref[i];
this.x_coords.push(parseFloat(result.Mb));
- if (js_data.result_score_type == "LOD") {
- this.y_coords.push(result.lod_score);
- }
- else {
- console.log("LRS VALUE:", result['lrs_value'])
- this.y_coords.push(result['lrs_value']);
- }
+ this.y_coords.push(result.lod_score);
results.push(this.marker_names.push(result.name));
}
return results;
@@ -119,19 +111,7 @@ Chr_Lod_Chart = (function() {
};
Chr_Lod_Chart.prototype.create_scales = function() {
- if (this.mappingScale == "morgan") {
- max_pos = 0
- for (i = 0, len = this.these_results.length; i < len; i++) {
- marker = this.these_results[i]
- if (parseFloat(marker['Mb']) > max_pos){
- max_pos = parseFloat(marker.Mb)
- }
- }
- this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]);
- }
- else {
- this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
- }
+ this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
};
@@ -278,6 +258,9 @@ Chr_Lod_Chart = (function() {
$("#return_to_full_view").hide();
$('#topchart').remove();
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+ BD.hideButton();
+ $('#close_bd').hide();
+ $('#bd_container').hide();
return create_lod_chart();
};
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
index 88003f4e..f6dfd7a3 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
@@ -9,9 +9,9 @@ create_lod_chart = ->
additive = js_data.additive
else
additive = false
-
+
console.log("js_data:", js_data)
-
+
# simplest use
#d3.json "data.json", (data) ->
mychart = lodchart().lodvarname("lod.hk")
@@ -21,13 +21,13 @@ create_lod_chart = ->
.ylab(js_data.result_score_type + " score")
.manhattanPlot(js_data.manhattan_plot)
#.additive(additive)
-
+
data = js_data.json_data
-
+
d3.select("div#topchart")
.datum(data)
.call(mychart)
-
+
# grab chromosome rectangles; color pink on hover
chrrect = mychart.chrSelect()
chrrect.on "mouseover", ->
@@ -36,7 +36,7 @@ create_lod_chart = ->
d3.select(this).attr("fill", ->
return "#F1F1F9" if i % 2
"#FBFBFF")
-
+
# animate points at markers on click
mychart.markerSelect()
.on "click", (d) ->
@@ -44,7 +44,3 @@ create_lod_chart = ->
d3.select(this)
.transition().duration(500).attr("r", r*3)
.transition().duration(500).attr("r", r)
-
-$ ->
- root.create_lod_chart = create_lod_chart
-
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js
index 778eed3a..d2c531f9 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -1,4 +1,5 @@
-//var create_lod_chart;
+// Generated by CoffeeScript 1.10.0
+var create_lod_chart;
create_lod_chart = function() {
var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
@@ -40,11 +41,3 @@ create_lod_chart = function() {
return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
});
};
-
-create_lod_chart()
-
-/*
-$(function() {
- return root.create_lod_chart = create_lod_chart;
-});
-*/ \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 55ffdce0..a65df84f 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -123,6 +123,8 @@ lodchart = () ->
.on("click", (d) ->
console.log("d is:", d)
redraw_plot(d)
+ BD.putData({chr: d[0], length: d[1]});
+ BD.showButton()
)
# x-axis labels
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 014bf59b..f1df6bd8 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
var lodchart;
lodchart = function() {
- var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+ var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
width = 800;
height = 500;
margin = {
@@ -20,6 +20,7 @@ lodchart = function() {
};
titlepos = 20;
manhattanPlot = false;
+ additive = false;
ylim = null;
additive_ylim = null;
nyticks = 5;
@@ -29,8 +30,7 @@ lodchart = function() {
darkrect = "#F1F1F9";
lightrect = "#FBFBFF";
lodlinecolor = "darkslateblue";
- additivelinecolor_plus = "red";
- additivelinecolor_negative = "green";
+ additivelinecolor = "red";
linewidth = 2;
suggestivecolor = "gainsboro";
significantcolor = "#EBC7C7";
@@ -70,15 +70,14 @@ lodchart = function() {
return results;
})();
ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
-
- if ('additive' in data) {
+ if (additive) {
data['additive'] = (function() {
var j, len, ref, results;
ref = data['additive'];
results = [];
for (j = 0, len = ref.length; j < len; j++) {
x = ref[j];
- results.push(x);
+ results.push(Math.abs(x));
}
return results;
})();
@@ -92,12 +91,12 @@ lodchart = function() {
g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
yticks = yticks != null ? yticks : yscale.ticks(nyticks);
- if ('additive' in data) {
+ if (additive) {
additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
}
reorgLodData(data, lodvarname);
- data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale);
+ data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
xscale = data.xscale;
chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
return "chrrect" + d[0];
@@ -118,7 +117,12 @@ lodchart = function() {
return lightrect;
}).attr("stroke", "none").on("click", function(d) {
console.log("d is:", d);
- return redraw_plot(d);
+ redraw_plot(d);
+ BD.putData({
+ chr: d[0],
+ length: d[1]
+ });
+ return BD.showButton();
});
xaxis = g.append("g").attr("class", "x axis");
xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
@@ -133,7 +137,7 @@ lodchart = function() {
var chr_plot;
$('#topchart').remove();
$('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
- return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale);
+ return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot);
};
rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
yaxis = g.append("g").attr("class", "y axis");
@@ -148,7 +152,7 @@ lodchart = function() {
return formatAxis(yticks)(d);
});
yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
- if ('additive' in data) {
+ if (additive) {
rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
additive_yaxis = g.append("g").attr("class", "y axis");
additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
@@ -187,19 +191,13 @@ lodchart = function() {
return yscale(data.lodByChr[chr][i][lodcolumn]);
});
};
- if ('additive' in data) {
+ if (additive) {
additivecurve = function(chr, lodcolumn) {
- if (data.additiveByChr[chr][0] < 0) {
- pos_neg = "negative"
- }
- else {
- pos_neg = "positive"
- }
- return [pos_neg, d3.svg.line().x(function(d) {
+ return d3.svg.line().x(function(d) {
return xscale[chr](d);
}).y(function(d, i) {
- return additive_yscale(Math.abs(data.additiveByChr[chr][i]));
- })];
+ return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
+ });
};
}
curves = g.append("g").attr("id", "curves");
@@ -210,17 +208,12 @@ lodchart = function() {
curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
}
}
- if ('additive' in data) {
+ if (additive) {
ref1 = data.chrnames;
for (k = 0, len1 = ref1.length; k < len1; k++) {
chr = ref1[k];
if (chr.indexOf(data['chr'])) {
- if (additivecurve(chr[0], lodvarnum)[0] == "negative") {
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
- }
- else {
- curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
- }
+ curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
}
}
}
@@ -305,13 +298,6 @@ lodchart = function() {
manhattanPlot = value;
return chart;
};
- chart.mappingScale = function(value) {
- if (!arguments.length) {
- return mappingScale;
- }
- mappingScale = value;
- return chart;
- };
chart.ylim = function(value) {
if (!arguments.length) {
return ylim;
@@ -449,6 +435,9 @@ lodchart = function() {
chart.yscale = function() {
return yscale;
};
+ chart.additive = function() {
+ return additive;
+ };
chart.additive_yscale = function() {
return additive_yscale;
};
@@ -470,4 +459,4 @@ lodchart = function() {
return chrSelect;
};
return chart;
-}; \ No newline at end of file
+};
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 7454b650..268e3e1c 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -29,7 +29,7 @@
<input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
<input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
<input type="hidden" name="pair_scan" value="{{ pair_scan }}">
-
+
<div class="container">
<div class="col-xs-5">
<h2>Map Viewer: Whole Genome</h2><br>
@@ -78,7 +78,7 @@
<tr>
<td></td>
<td style="padding: 5px;">
- <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span>
+ <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span>
</td>
</tr>
<tr>
@@ -91,14 +91,14 @@
</div>
<div class="col-xs-4" style="padding: 0px;">
{% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
- <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test
+ <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test
<a href="http://genenetwork.org/glossary.html#Permutation" target="_blank">
<sup style="color:#f00"> ?</sup>
</a>
<br>
{% endif %}
{% if mapping_method == "reaper" and nboot > 0 %}
- <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test
+ <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test
<a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank">
<sup style="color:#f00"> ?</sup>
</a>
@@ -128,7 +128,7 @@
</div>
</div>
</div>
-
+
<div class="tabbable" style="margin: 10px;">
<ul class="nav nav-tabs">
<li id="gn1_map_tab">
@@ -160,8 +160,23 @@
</div>
{% if mapping_method != "gemma" %}
<div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
- <div id="chart_container">
- <div class="qtlcharts" id="topchart"></div>
+ <div id="chart_container">
+ <ul class="nav nav-tabs">
+ <li id="return_to_full_view" class="btn btn-default buttons-html5" style="display:none">
+ Return to full view
+ </li>
+ <li id="open_bd" class="btn btn-default buttons-html5" style="display:none">
+ Open BioDalliance view
+ </li>
+ <li id="close_bd" class="btn btn-default buttons-html5" style="display:none">
+ Return to vector map
+ </li>
+ </ul>
+
+ <div class="qtlcharts" id="topchart"></div>
+
+ <div id="bd_container" class="qtlcharts">
+ </div>
</div>
</div>
{% endif %}
@@ -262,7 +277,37 @@
{% endblock %}
-{% block js %}
+{% block js %}
+
+ <script>
+ /* This section checks for paths to JS libraries by
+ checking the headers */
+ list = [
+ /* check for static path */
+ "/static/new/javascript/biodalliance.js",
+ "/static/new/js_external/underscore-min.js",
+ /* check for dalliance JS (see ./etc/default_settings.py) */
+ "/dalliance/build/dalliance-all.js",
+ /* D3 path (FIXME) */
+ "http://d3js.org/d3.v3.min.js",
+ /* datatables path (FIXME) */
+ "https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"
+ ];
+ for (var i = 0; i < list.length; i++) {
+ url = list[i];
+ $.ajax({
+ type: 'HEAD',
+ url: url,
+ success: function() {
+ // page exists
+ },
+ error: function() {
+ // page does not exist
+ console.log("Failed to load "+this.url);
+ alert("Failed to load Javascript for "+this.url);
+ }
+ })};
+ </script>
<script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
@@ -278,19 +323,19 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
- <script>
- js_data = {{ js_data | safe }}
- </script>
{% if mapping_method != "gemma" %}
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.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/create_lodchart.js"></script>
+
+ <script language="javascript" type="text/javascript" src="/dalliance/build/dalliance-all.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/biodalliance.js"></script>
{% endif %}
- <script type="text/javascript" charset="utf-8">
- $(document).ready( function () {
+ <script>
+ createTable = function() {
console.time("Creating table");
$('#qtl_results').DataTable( {
"columns": [
@@ -349,15 +394,144 @@
"scrollCollapse": false,
"paging": false
} );
+ };
+
+ filename = "{{json_filename}}";
+ js_data = null;
+ $.ajax("/generated_text/{{json_filename}}",
+ {success:
+ function(data) {
+ js_data = data;
+ create_lod_chart();
+ createTable();
+ }
+ });
+
+ BD.putSource({name: 'Genome',
+ twoBitURI: 'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
+ desc: 'Mouse reference genome build GRCm38',
+ tier_type: 'sequence',
+ provides_entrypoints: true
+ });
+ BD.putSource({name: 'Genotype',
+ controlURI: "{{gn_server_url}}/api_pre1/genotype/mouse/BXD.json",
+ URIBase: "{{gn_server_url}}/api_pre1/genotype/mouse/",
+ tier_type: 'rqtl-genotype',
+ vOffset: 8,
+ pinned: true,
+ transposed: true,
+ style: [
+ { type: "default",
+ method: "U",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "black",
+ BGCOLOR: "white",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "B",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "blue",
+ BGCOLOR: "blue",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "H",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "green",
+ BGCOLOR: "green",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ { type: "default",
+ method: "D",
+ style: { glyph: "BOX",
+ LINE: "0.5",
+ FGCOLOR: "red",
+ BGCOLOR: "red",
+ BGITEM: "true",
+ HEIGHT: "2",
+ BUMP: "true",
+ }},
+ ]
+ });
+ BD.putSource({name: 'QTL',
+ tier_type: 'qtl',
+ uri: '/generated_text/{{csv_filename}}',
+ style: [{
+ type: 'default',
+ style: {
+ glyph: "LINEPLOT",
+ AUTOMAX: "true",
+ MIN: 0,
+ MAX: 3,
+ HEIGHT: 200,
+ STEPS: 500,
+ COLOR1: "blue",
+ }
+ }],
+ });
+ BD.putSource({name: 'SNP density',
+ jbURI: "{{gn_server_url}}/api_pre1/snp",
+ jbQuery: "",
+ refetchOnZoom: true,
+ style: [{
+ type: 'default',
+ style: {
+ glyph: "HISTOGRAM",
+ MIN: 0,
+ MAX: 5000,
+ AUTOMAX: "true",
+ HEIGHT: 60,
+ STEPS: 100,
+ COLOR1: "red",
+ COLOR2: "red",
+ COLOR3: "red",
+ AXISCENTER: "true",
+ }
+ }]
+ });
+ </script>
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ BD.putData({species: "{{ dataset.group.species }}" });
+
$('#vector_map_tab').click(function(){
$('div#gn1_map_options').hide();
});
$('#gn1_map_tab').click(function(){
- $('div#gn1_map_options').show();
+ $('#gn1_map_options').show();
+ $('div#bd_container').hide();
});
+ $('#close_bd').click(function() {
+ $('#open_bd').show();
+ $('#close_bd').hide();
+
+ $('#bd_container').hide();
+ $('#topchart').show();
+ });
+
+ $('#open_bd').click(function() {
+ $('#close_bd').show();
+ $('#open_bd').hide()
+
+ $('#topchart').hide();
+ $('#bd_container').show();
+
+ BD.openBrowser();
+ })
});
chrView = function(this_chr, chr_mb_list) {
@@ -376,9 +550,9 @@
return $('#marker_regression_form').submit();
};
- remap = function() {
+ remap = function() {
$('input[name=selected_chr]').val($('select[name=chromosomes]').val());
- return $('#marker_regression_form').submit();
+ return $('#marker_regression_form').submit();
};
export_perm_data = function() {
@@ -394,4 +568,3 @@
</script>
{% endblock %}
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fb52165a..9fdaabf3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -21,6 +21,7 @@ import uuid
import simplejson as json
import yaml
+import csv
#Switching from Redis to StrictRedis; might cause some issues
import redis
@@ -50,11 +51,12 @@ from wqflask.correlation import corr_scatter_plot
from wqflask.wgcna import wgcna_analysis
from wqflask.ctl import ctl_analysis
+from utility import webqtlUtil
from utility import temp_data
from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION
from base import webqtlFormData
-from base.webqtlConfig import GENERATED_IMAGE_DIR
+from base.webqtlConfig import GENERATED_IMAGE_DIR, GENERATED_TEXT_DIR
from utility.benchmark import Bench
from pprint import pformat as pf
@@ -144,10 +146,16 @@ def tmp_page(img_path):
img_base64 = bytesarray )
@app.route("/twitter/<path:filename>")
-def bd_files(filename):
- bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH']
+def twitter_js(filename):
+ bd_path = app.config['JS_TWITTER_POST_FETCHER']
+ return send_from_directory(bd_path, filename)
+
+@app.route("/dalliance/<path:filename>")
+def biodalliance_js(filename):
+ bd_path = app.config['JS_BIODALLIANCE']
return send_from_directory(bd_path, filename)
+
#@app.route("/data_sharing")
#def data_sharing_page():
# logger.info("In data_sharing")
@@ -232,6 +240,10 @@ def docedit():
def generated_file(filename):
return send_from_directory(GENERATED_IMAGE_DIR,filename)
+@app.route('/generated_text/<filename>')
+def generated_text(filename):
+ return send_from_directory(GENERATED_TEXT_DIR, filename)
+
@app.route("/help")
def help():
doc = docs.Docs("help")
@@ -495,10 +507,27 @@ def marker_regression_page():
with Bench("Total time in MarkerRegression"):
template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
+
+ qtl_results = template_vars.js_data['qtl_results']
+
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")
+
+ json_filename = webqtlUtil.genRandStr("") + ".json"
+ with open(GENERATED_TEXT_DIR + "/" + json_filename, "wb") as json_file:
+ json_file.write(template_vars.js_data)
+
+ csv_filename = webqtlUtil.genRandStr("") + ".csv"
+ with open(GENERATED_TEXT_DIR + "/" + csv_filename, "wb") as csv_file:
+ writer = csv.writer(csv_file)
+ writer.writerow(("Locus", "Chr", "Mb", "LOD"))
+ for (row) in qtl_results:
+ score = row["lod_score"] if "lod_score" in row else row["lrs_value"]
+ writer.writerow((row["name"], row["chr"], row["Mb"], score))
+
+
result = template_vars.__dict__
if result['pair_scan']:
@@ -518,6 +547,9 @@ def marker_regression_page():
# logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+ gn1_template_vars['json_filename'] = json_filename;
+ gn1_template_vars['csv_filename'] = csv_filename;
+ gn1_template_vars['gn_server_url'] = GN_SERVER_URL;
pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
logger.info("pickled result length:", len(pickled_result))
@@ -527,22 +559,6 @@ def marker_regression_page():
with Bench("Rendering template"):
rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
- # with Bench("Rendering template"):
- # if result['pair_scan'] == True:
- # img_path = result['pair_scan_filename']
- # logger.info("img_path:", img_path)
- # initial_start_vars = request.form
- # logger.info("initial_start_vars:", initial_start_vars)
- # imgfile = open(TEMPDIR + '/' + img_path, 'rb')
- # imgdata = imgfile.read()
- # imgB64 = imgdata.encode("base64")
- # bytesarray = array.array('B', imgB64)
- # result['pair_scan_array'] = bytesarray
- # rendered_template = render_template("pair_scan_results.html", **result)
- # else:
- # rendered_template = render_template("marker_regression.html", **result)
- # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
-
return rendered_template
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 05:44:51 +0000