Fix some cursed regex buried in JSON string to find assembly name

Author: kevinlul

jbrowse/plugins/ExportSequence/js/ExportSequence.js

@@ -9,30 +9,30 @@ define( ["dojo/_base/declare", 'dojo/_base/array','dojo/_base/lang','dojo/aspect
 	  endCoord = endCoord.replace(/\.\d+$/,'');
 	  //var coordStr = visibleRegion.ref+":"+visibleRegion.start+"-"+visibleRegion.end;
 	  var current_url = window.location.href;
-	  var genome_regex = /data\=data\.(.+?)\&/;
+	  var genome_regex = /data\=data%2F(.+?)\&/;
 	  var genome_regex_matches = current_url.match(genome_regex);
 	  var coordStr = "searchInput=" + visibleRegion.ref+":"+startCoord+"-"+endCoord;
-	  //console.log(genome_regex_matches[1]); 
+	  //console.log(genome_regex_matches[1]);
 	  if (genome_regex_matches!== null && genome_regex_matches[1].length >0){
 
 	  	coordStr +="&genome="+genome_regex_matches[1];
 
 	  }
           var opts=this.inherited(arguments); //call the parent classes function
            opts.push( // add an extra menu item to the array returned from parent class function
-               {        
+               {
                    label: "Search for Guides",
                    type: 'dijit/LinkPane',
                    onClick: function() {
-		
+
 			window.open("http://"+location.hostname+"/src/guide-finder/GuideInitialize.py?action=initialize&"+coordStr);
-	
-                   },  
+
+                   },
                    iconClass: "dijitIconPackage"
-               }   
-           );  
+               }
+           );
            return opts;
-       }   
-   }); 
-   }   
+       }
+   });
+   }
 );

src/setup/trackList.json

@@ -33,7 +33,7 @@
             "modify" : "function( track, feature, div ) { setColor='green'; if(feature.get('type') == 'ncRNA_gene'){ setColor='#8F6F8B';} else if(feature.get('type') == 'pseudogene'){setColor='#575256';} div.style.backgroundColor = setColor; }"
          },
          "onClick" : {
-            "url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={Name}&ensid={gene_id}&org='+genome_match[1] }", 
+            "url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={Name}&ensid={gene_id}&org='+genome_match[1] }",
             "action" : "iframeDialog",
             "label" : "{Name} Info, Guides, and Primers"
          },
@@ -76,7 +76,7 @@
          "onClick" : {
             "action" : "iframeDialog",
             "iconClass" : "dijitIconDatabase",
-            "url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }", 
+            "url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }",
             "title" : "{batchName} Info, Guides and Primers",
             "label": "<b>{label}</b><ul><li>Specificity Score: <b>{guideScore}</b></li><li>Off-targets for 0-1-2-3-4 mismatches:<b> {otDesc}</b>&nbsp&nbsp</li><p><b>{Notes}</b></p></ul>"
          }
@@ -97,10 +97,10 @@
 	"onClick" : {
 		"action" : "iframeDialog",
 		"iconClass" : "dijitIconDatabase",
-		"url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }", 
+		"url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }",
 		"title" : "{batchName} Info, Guides, and Primers",
 		"label" : "<ul><li>Gene: <b>{batchName}&nbsp&nbsp&nbsp</b></li><li>TM: <b>{tm}&nbsp&nbsp&nbsp</b></li><li>GC%: <b>{gc}&nbsp&nbsp&nbsp&nbsp</b></li><p>Notes: {pair_notes}</li></p></ul>"
-	}	
+	}
       },
       {
          "compress" : 0,

src/setup/trackList_no_regulatory.json

@@ -33,7 +33,7 @@
             "modify" : "function( track, feature, div ) { setColor='green'; if(feature.get('type') == 'ncRNA_gene'){ setColor='#8F6F8B';} else if(feature.get('type') == 'pseudogene'){setColor='#575256';} div.style.backgroundColor = setColor; }"
          },
          "onClick" : {
-            "url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={Name}&ensid={gene_id}&org='+genome_match[1] }", 
+            "url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={Name}&ensid={gene_id}&org='+genome_match[1] }",
             "action" : "iframeDialog",
             "label" : "{Name} Info, Guides, and Primers"
          },
@@ -64,7 +64,7 @@
          "onClick" : {
             "action" : "iframeDialog",
             "iconClass" : "dijitIconDatabase",
-            "url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }", 
+            "url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }",
             "title" : "{batchName} Info, Guides and Primers",
             "label" : "<b>{label}</b><ul><li>Specificity Score: <b>{guideScore}</b></li><li>Off-targets for 0-1-2-3-4 mismatches:<b> {otDesc}</b>&nbsp&nbsp</li><p><b>{Notes}</b></p></ul>"         }
       },
@@ -84,10 +84,10 @@
 	"onClick" : {
 		"action" : "iframeDialog",
 		"iconClass" : "dijitIconDatabase",
-		"url" : "function(){ var genome_match = location.href.match(/data=data\.(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }", 
+		"url" : "function(){ var genome_match = location.href.match(/data=data%2F(.+?)\&/); return location.protocol+'//'+location.hostname+'/src/primer-design/web/geneFeatures.html?gene={batchName}&ensid={ensid}&org='+genome_match[1] }",
 		"title" : "{batchName} Info, Guides, and Primers",
 		"label" : "<ul><li>Gene: <b>{batchName}&nbsp&nbsp&nbsp</b></li><li>TM: <b>{tm}&nbsp&nbsp&nbsp</b></li><li>GC%: <b>{gc}&nbsp&nbsp&nbsp&nbsp</b></li><p>Notes: {pair_notes}</li></p></ul>"
-	}	
+	}
       },
       {
          "compress" : 0,