Merge branch 'pjotr-gn2' into zsloan

12 files changed, 383 insertions, 139 deletions

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..843c7ed9 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 +394,145 @@
                 "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,
+                   hideSubpixelGlyphs: 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 +551,9 @@
             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 +569,3 @@
     </script>
 
 {% endblock %}
-
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ec5035ce..a6184ef5 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
@@ -51,11 +52,12 @@ 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
@@ -145,10 +147,16 @@ 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")
@@ -233,6 +241,10 @@ 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")
@@ -507,10 +519,27 @@ 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']:
@@ -530,6 +559,9 @@ 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))
@@ -539,22 +571,6 @@ 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