Rewrite BD sources; use computed QTL data in BD

2 files changed, 32 insertions, 12 deletions

diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js
index 3af223f3..b6808d8a 100644
--- a/wqflask/wqflask/static/new/javascript/biodalliance.js
+++ b/wqflask/wqflask/static/new/javascript/biodalliance.js
@@ -4,6 +4,7 @@
 var BD = {};
 BD.browser = null;
 BD.data = {};
+BD.sources = [];
 
 var getChrLen = function(chr) {
     return js_data[chr * 1];
@@ -50,21 +51,18 @@ BD.putData = function(data) {
     }
 };
 
+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,
-                                     [{name: 'Genome',
-                                       twoBitURI:  'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
-                                       desc: 'Mouse reference genome build GRCm38',
-                                       tier_type: 'sequence',
-                                       provides_entrypoints: true},
-                                      {name: 'QTL',
-                                       tier_type: 'qtl',
-                                       uri: 'http://localhost:8880/static/qtl/lod2.csv',
-                                       stylesheet_uri: "http://localhost:8880/stylesheets/qtl-stylesheet.xml"
-                                      }]
-                                    );
+        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);
     }
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index e83a8cec..47e282cf 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -362,6 +362,28 @@
                          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: 'QTL',
+                   tier_type: 'qtl',
+                   uri: 'http://localhost:5003/generated_text/{{csv_filename}}',
+                   style: [{
+                       type: 'default',
+                       style: {
+                           glyph: "LINEPLOT",
+                           MIN: 0,
+                           MAX: 2.5,
+                           HEIGHT: 120,
+                           STEPS: 500,
+                           COLOR1: "blue",
+                       }
+                   }]
+     });
     </script>