Merge branch 'master' of github.com:genenetwork/genenetwork2 into development

Conflicts:
	wqflask/base/trait.py

8 files changed, 105 insertions, 30 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 0bc10b97..af22b5a1 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -308,6 +308,7 @@ class GeneralTrait(object):
                 if isinstance(trait_info[i], basestring):
                     holder = unicode(trait_info[i], "utf8", "ignore")
                 setattr(self, field, holder)
+<<<<<<< HEAD
 
             description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
             target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
@@ -345,6 +346,8 @@ class GeneralTrait(object):
                 self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
                 self.location_value = trait_location_value
                 
+=======
+>>>>>>> e0c5c1aae3aaaa1d81bcec36835a97e169dcc2e2
                 
             if self.dataset.type == 'Publish':
                 self.confidential = 0
@@ -379,8 +382,8 @@ class GeneralTrait(object):
                 if self.pubmed_id:
                     self.pubmed_link = webqtlConfig.PUBMEDLINK_URL % self.pubmed_id
                     
+                    
             self.homologeneid = None
-
             if self.dataset.type == 'ProbeSet' and self.dataset.group and self.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.
@@ -408,6 +411,43 @@ class GeneralTrait(object):
 
                 if result:
                     self.homologeneid = result[0]
+                    
+                description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
+                target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+
+                if len(description_string) > 1 and description_string != 'None':
+                    description_display = description_string
+                else:
+                    description_display = self.symbol
+
+                if (len(description_display) > 1 and description_display != 'N/A' and
+                        len(target_string) > 1 and target_string != 'None'):
+                    description_display = description_display + '; ' + target_string.strip()
+
+                # Save it for the jinja2 template
+                self.description_display = description_display
+
+                #XZ: trait_location_value is used for sorting
+                trait_location_repr = 'N/A'
+                trait_location_value = 1000000
+
+                if self.chr and self.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(self.chr, self.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"
+                    self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
+                    self.location_value = trait_location_value
+                    
 
             if get_qtl_info:
                 #LRS and its location
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 63f62411..01303b0f 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -2007,6 +2007,7 @@ class MarkerRegression(object):
 
         previous_chr = 1
         previous_chr_as_int = 0
+        lineWidth = 1
         oldStartPosX = 0
         startPosX = xLeftOffset
         for i, qtlresult in enumerate(self.qtlresults):
@@ -2015,6 +2016,41 @@ class MarkerRegression(object):
             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))
+                    
+                if not self.multipleInterval and self.additiveChecked:
+                    plusColor = self.ADDITIVE_COLOR_POSITIVE
+                    minusColor = self.ADDITIVE_COLOR_NEGATIVE
+                    for k, aPoint in enumerate(AdditiveCoordXY):
+                        if k > 0:
+                            Xc0, Yc0 = AdditiveCoordXY[k-1]
+                            Xc, Yc = aPoint
+                            if (Yc0-yZero)*(Yc-yZero) < 0:
+                                if Xc == Xc0: #genotype , locus distance is 0
+                                    Xcm = Xc
+                                else:
+                                    Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+                                if Yc0 < yZero:
+                                    canvas.drawLine(Xc0, Yc0, Xcm, yZero, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                                    canvas.drawLine(Xcm, yZero, Xc, yZero-(Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                                else:
+                                    canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xcm, yZero, color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                                    canvas.drawLine(Xcm, yZero, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                            elif (Yc0-yZero)*(Yc-yZero) > 0:
+                                if Yc < yZero:
+                                    canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                                else:
+                                    canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                            else:
+                                minYc = min(Yc-yZero, Yc0-yZero)
+                                if minYc < 0:
+                                    canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                                else:
+                                    canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                    
+                LRSCoordXY = []
+                AdditiveCoordXY = []
                 previous_chr = qtlresult['chr']
                 previous_chr_as_int += 1
 
@@ -2032,7 +2068,6 @@ class MarkerRegression(object):
             else:
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
-                #LRSCoordXY = []
                 #AdditiveCoordXY = []
                 #DominanceCoordXY = []
                 #for k, _locus in enumerate(_chr):
@@ -2087,10 +2122,11 @@ class MarkerRegression(object):
                        # 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))
 
-        lineWidth = 1
+        if self.manhattan_plot != True:
+            canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+            
         if not self.multipleInterval and self.additiveChecked:
             plusColor = self.ADDITIVE_COLOR_POSITIVE
             minusColor = self.ADDITIVE_COLOR_NEGATIVE
@@ -2120,6 +2156,7 @@ class MarkerRegression(object):
                             canvas.drawLine(Xc0, Yc0, Xc, Yc, color=plusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                         else:
                             canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+                    
         if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
             plusColor = self.DOMINANCE_COLOR_POSITIVE
             minusColor = self.DOMINANCE_COLOR_NEGATIVE
@@ -2151,9 +2188,6 @@ class MarkerRegression(object):
                             canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
                 
 
-        if self.manhattan_plot != True:
-		    canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
             additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fb03f027..a57bfffe 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -119,9 +119,9 @@ class SearchResultPage(object):
             
             #### Excel file needs to be generated ####
 
-            print("foo locals are:", locals())
+            #print("foo locals are:", locals())
             trait_id = result[0]
-            this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True)
+            this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
             self.trait_list.append(this_trait)
 
         self.dataset.get_trait_info(self.trait_list, species)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3cc6121f..2d4c952a 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -152,10 +152,11 @@ class ShowTrait(object):
 
         self.trait_table_width = get_trait_table_width(self.sample_groups)
 
-        js_data = dict(sample_group_types = self.sample_group_types,
-                        sample_lists = sample_lists,
-                        attribute_names = self.sample_groups[0].attributes,
-                        temp_uuid = self.temp_uuid)
+        js_data = dict(dataset_type = self.dataset.type,
+                       sample_group_types = self.sample_group_types,
+                       sample_lists = sample_lists,
+                       attribute_names = self.sample_groups[0].attributes,
+                       temp_uuid = self.temp_uuid)
         self.js_data = js_data
 
     def get_mapping_methods(self):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8d5982b7..9e249c28 100755..100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -174,7 +174,6 @@
     make_table = function() {
       var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
       header = "<thead><tr><th>&nbsp;</th>";
-      console.log("js_data.sample_group_types:", js_data.sample_group_types);
       _ref = js_data.sample_group_types;
       for (key in _ref) {
         if (!__hasProp.call(_ref, key)) continue;
@@ -186,14 +185,15 @@
       the_rows = "<tbody>";
       for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
         row = Stat_Table_Rows[_i];
-        console.log("rowing");
+        if ((row.vn == "range_fold" || row.vn == "range") && js_data.dataset_type == "Publish"){
+            continue;
+        }
         row_line = "<tr>";
         if (row.url != null) {
           row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
         } else {
           row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
         }
-        console.log("box - js_data.sample_group_types:", js_data.sample_group_types);
         _ref1 = js_data.sample_group_types;
         for (key in _ref1) {
           if (!__hasProp.call(_ref1, key)) continue;
@@ -202,12 +202,10 @@
           row_line += "<td id=\"" + the_id + "\">foo</td>";
         }
         row_line += "</tr>";
-        console.log("row line:", row_line);
         the_rows += row_line;
       }
       the_rows += "</tbody>";
       table = header + the_rows;
-      console.log("table is:", table);
       return $("#stats_table").append(table);
     };
     process_id = function() {
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index d7950754..f3f33fad 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -87,8 +87,8 @@
                   </td>
                 </tr>
               </table>
-              </div>
-              <div class="col-xs-4" style="padding: 0px;">
+            </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 
                     <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank">
@@ -121,7 +121,10 @@
                   {% if plotScale != "morgan" %}
                   <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span>
                   {% endif %}
-              </div>
+            </div>
+            <div class="col-xs-12" align="center" style="padding: 5px;">
+              <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span>
+            </div>
           </div>
         </div>
  
@@ -162,6 +165,7 @@
         </div>
 
         </form>
+        {% if selectedChr == -1 %}
         <div style="width:48%;">
             <h2>
                 Results
@@ -219,6 +223,7 @@
                 </tbody>
             </table>
         </div>
+        {% endif %}
     </div>
 
     <!-- End of body -->
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 62a08d85..7429cd5f 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -257,12 +257,10 @@
                 console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types)
                 if (Object.keys(js_data.sample_group_types).length > 1) {
                     $('#stats_table').DataTable( {
-                        "columns": [
-                            { "bSortable": false },
-                            { "bSortable": false },
-                            { "bSortable": false },
-                            { "bSortable": false }
+                        "columnDefs": [
+                            { "orderable": false, "targets": [0, 1, 2, 3] }
                         ],
+                        "order": [],
                         "sDom": "tr",
                         "iDisplayLength": -1,
                         "autoWidth": false,
@@ -274,10 +272,10 @@
                 }
                 else {
                     $('#stats_table').DataTable( {
-                        "columns": [
-                            { "bSortable": false },
-                            { "bSortable": false }
+                        "columnDefs": [
+                            { "orderable": false, "targets": [0, 1] }
                         ],
+                        "order": [],
                         "sDom": "tr",
                         "iDisplayLength": -1,
                         "autoWidth": false,
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 2183dd30..9c5c94b2 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -27,7 +27,6 @@
                 <div class="tab-pane active" id="stats_tab">
                     <div style="padding: 20px" class="form-horizontal">
                             <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
-
                     </div>
                 </div>   
                 <div class="tab-pane" id="histogram_tab">