add upload file

csw11004 · Oct 11, 2015 · c57eb45 · c57eb45
1 parent 9d92804
commit c57eb45
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Showing 7 changed files with 227,662 additions and 20 deletions.
diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
@@ -719,18 +719,28 @@ function VQI_GenomeBrowser(id, serviceURL) {
             {
                 if(key2 === 'custom' || key2 ==='genes')
                 {
-                    checkTableUpload(genomes[key][key2].table_name)
+                    checkTableUpload(genomes[key][key2].table_name, genomes[key][key2].file)
                 }
                 if(key2 === 'cpg')
                 {
                     var tempHandles = genomes[key][key2].table_name.split(",");
+                    var fileHandles = genomes[key][key2].file.split(",");
                     for(var i in tempHandles)
                     {
-                        checkTableUpload(tempHandles[i].trim())
+                        checkTableUpload(tempHandles[i].trim(), fileHandles[i].trim())
                     }
                 }
             }
         }
+        selectBox = $("#" + divId +" #genomes").get(0);
+        selectBox.options.length = 0;
+        var optionIndex = 0;
+        for (var key in genomes) {
+            var text = key;
+            var value = key;
+            selectBox.options[optionIndex++] = new Option(text, value);
+        }
+
     }
 
     this.setGenome = function(genome) {
@@ -741,19 +751,21 @@ function VQI_GenomeBrowser(id, serviceURL) {
             for(var key in genomes[genome])
             {
                 this.addTrack(genome+"_"+key, key, genomes[genome][key])
+                // console.log(genomes[genome][key]);
             }
         }
     }
 
-    var checkTableUpload = function(tableName) {
+    var checkTableUpload = function(tableName,filePath) {
 
         $.ajax({
             url: serviceURL,
             type: 'POST',
             dataType: "json",
             data: {
                 "checkTable": "",
-                "tableName": tableName
+                "tableName": tableName,
+                "filePath": filePath
             }
 
             }).success(function (returnData) {
@@ -1225,6 +1237,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
                 }
 
                 }).success(function (returnData) {
+                    // console.log(returnData);
                     drawTrack(returnData);
                     LoadingText.remove();
                 }
@@ -1490,6 +1503,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
                 }
 
                 }).success(function (returnData) {
+                    // console.log(returnData);
                     if(returnData.length == 2) {//exons exist
 
                         drawTrack(returnData[0], returnData[1]);

diff --git a/VQI_GenomeBrowserDemo.html b/VQI_GenomeBrowserDemo.html
@@ -45,21 +45,25 @@
                         /*fasta: {fasta: "../../genome/hg19.fa", index: "../../genome/hg19.fa.fai"},
                         genes: {file: "../../genome/hg19_genes.txt", table_name:'hg19_gene_annotation'},
                         cpg: {file: "../../genome/hg19_genes.txt", table_name:'hg19_cpg'},*/
-                        fasta: {fasta: "/Users/corywang/Downloads/hg19.fa.txt", index : "/Users/corywang/Downloads/hg19.fa.fai.txt"},
+                        //fasta: {fasta: "/Users/corywang/Downloads/hg19.fa.txt", index : "/Users/corywang/Downloads/hg19.fa.fai.txt"},
-                        genes: {file: "", table_name: "upload1436481988"},
+                        genes: {file: "hg19_refgene.txt", table_name: "hg19_refgene"},
-                        cpg: {file: "", table_name: "upload1437097194,upload1437098473,upload1437098556"},
+                        cpg: {file: "cpg_site_hg19.txt,shelve_hg19.txt,shoer_hg19.txt", table_name: "cpg_site_hg19,shelve_hg19,shoer_hg19"},
-                        custom: {file: "", table_name:'upload1436411775'}
+                        //custom: {file: "", table_name:'upload1436411775'}
                     },
-                    "MM9":{
+            //         "MM9":{
-                        fasta: {fasta: "/Users/corywang/Downloads/mm9.fa.txt", index: "/Users/corywang/Downloads/mm9.fa.fai.txt"},
+            //             fasta: {fasta: "/Users/corywang/Downloads/mm9.fa.txt", index: "/Users/corywang/Downloads/mm9.fa.fai.txt"},
-                        //genes: {file: "../../genome/mm9/mm9_genes.txt", table_name:'mm9_gene_annotation'},
+            //             //genes: {file: "../../genome/mm9/mm9_genes.txt", table_name:'mm9_gene_annotation'},
 
-            //            gene_annotation: {label: 'mm9', table_name:'mm9_gene_annotation'},
+            // //            gene_annotation: {label: 'mm9', table_name:'mm9_gene_annotation'},
-                    },
+            //         },
                 };
 
                 obj.loadGenomes(genomes);  //loads the genomes based on the datastructure described above
-                obj.setGenome("HG19");
+                setTimeout(function(){ hs()}, 3000);
+                function hs (){
+                    obj.setGenome("HG19");
+                }
+                //obj.setGenome("HG19");
              //   obj.setGenome("MM9"); //should set hg19 genome in dropdown and display fasta, cpg and genes tracks.
 
             //    addTrack(); should add track using the data array supplied.