Changed webservice.cgi name to rnaSeqMapCoverage

New feature:
• Changed webservice.cgi filename to rnaSeqMapCoverage.cgi

Bug fix:
• Fixed bug where sometimes bootstrap would not load
• Fixed bug where the dumpOutput was not showing the data in a readable-manner for ReadsMappedNucleotidePosition

In progress:
• MEDIAN control data
• Visual cue for directional arrows on RNA-Table
• Getting the eFP-Seq Browser to work for internet explorer

TODO:
• Make eFP Overview more responsive to screen's resolution
• TMM or TPM and median for additional normalization methods
• Expand the creation of the private database to include adding from public and private database to your creation

Known bugs:
• After generating new data, scrolling up doesn’t work unless the user scrolls down first
• Does not work on IE
• Google Drive repos do not work for IGB links

Author: AlexJSully

README.md

@@ -1,8 +1,5 @@
 # eFP-Seq-Browser
 
-[![TravisCI - Build Status](https://travis-ci.org/ASully/eFP-Seq-Browser.svg?branch=master)](https://travis-ci.org/ASully/eFP-Seq-Browser)
-[![Maintainability](https://api.codeclimate.com/v1/badges/c87696819acab6a6c803/maintainability)](https://codeclimate.com/github/ASully/eFP-Seq-Browser/maintainability)
-
 The eFP-Seq Browser is a RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a "electronic fluorescent pictopgrahic" (eFP) image. This web-tool also allows generation of new datasets if provided with SAM/BAM (with their index files) to allow visualization of any RNA-Seq mapping coverage. Gene expression levels and similarity is also shown by calculating the Reads per Kilobase per Million reads mapped (RPKM) expression levels and Pearson Correlation Coefficient (PCC) scores amongst its different splice variants.
 
 ## Getting Started

cgi-bin/Submission_page.html

@@ -15,9 +15,9 @@
 	<script defer src="Submission_page/mrDataConverter/DataGridRenderer.min.js"></script>
 	<link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
 	<!--Bootstrap -->
-	<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-	<link rel="stylesheet" href="core/bootstrap/bootstrap-theme-3-3-7.min.css" integrity="sha384-rHyoN1iRsVXV4nD0JutlnGaslCJuC7uwjduW9SVrLvRYooPp2bWYgmgJQIXwl/Sp" crossorigin="anonymous">
-	<script src="core/bootstrap/bootstrap3-3-7.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+	<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="" crossorigin="anonymous">
+	<link rel="stylesheet" href="core/bootstrap/bootstrap-theme-3-3-7.min.css" integrity="" crossorigin="anonymous">
+	<script src="core/bootstrap/bootstrap3-3-7.min.js" integrity="" crossorigin="anonymous"></script>
 	<!-- Google Analytics ID -->
 	<script>
 		(function (i, s, o, g, r, a, m) {

cgi-bin/core/custom.js

@@ -542,7 +542,7 @@ function parseIntArray(arr) {
   return arr;
 }
 
-var rnaseq_image_url = "cgi-bin/webservice.cgi";
+var rnaseq_image_url = "cgi-bin/rnaSeqMapCoverage.cgi";
 var match_drive = "";
 var progress_percent = 0;
 var sra_list_check = [];
@@ -652,7 +652,14 @@ function rnaseq_images(status) {
           if (callDumpOutputs == true) {
             dumpOutputs += '\t\telif (record == "' + response_rnaseq["record"] + '"):\n';
             if (dumpMethod == "complex") {
-              dumpOutputs += '\t\t\tdumpJSON(200, "' + response_rnaseq["locus"] + '", ' + response_rnaseq["variant"] + ', ' + response_rnaseq["chromosome"] + ', ' + response_rnaseq["start"] + ', ' + response_rnaseq["end"] + ', "' + response_rnaseq["record"] + '", "' + response_rnaseq["tissue"] + '", "' + response_rnaseq["rnaseqbase64"] + '", ' + response_rnaseq["reads_mapped_to_locus"] + ', ' + response_rnaseq["absolute-fpkm"] + ', [' + response_rnaseq["r"] + '], ' + response_rnaseq["totalReadsMapped"] + ', [' + response_rnaseq["exp_arr"] + '], [' + response_rnaseq["ReadsMappedNucleotidePosition"] + '], {';
+              dumpOutputs += '\t\t\tdumpJSON(200, "' + response_rnaseq["locus"] + '", ' + response_rnaseq["variant"] + ', ' + response_rnaseq["chromosome"] + ', ' + response_rnaseq["start"] + ', ' + response_rnaseq["end"] + ', "' + response_rnaseq["record"] + '", "' + response_rnaseq["tissue"] + '", "' + response_rnaseq["rnaseqbase64"] + '", ' + response_rnaseq["reads_mapped_to_locus"] + ', ' + response_rnaseq["absolute-fpkm"] + ', [' + response_rnaseq["r"] + '], ' + response_rnaseq["totalReadsMapped"] + ', [' + response_rnaseq["exp_arr"] + '], [';
+              for (r = 0; r < response_rnaseq["ReadsMappedNucleotidePosition"].length; r += 2) {
+                dumpOutputs += '[' + response_rnaseq["ReadsMappedNucleotidePosition"][r] + ']';
+                if (r != (response_rnaseq["ReadsMappedNucleotidePosition"].length - 2)) {
+                  dumpOutputs += ", "
+                };
+              }
+              dumpOutputs += '], {';
               for (e = 0; e < response_rnaseq["expected_expr_in_variant"].length; e++) {
                 dumpOutputs += '"' + GFF_List[e].replace(locus, '') + '": ';
                 dumpOutputs += '[' + response_rnaseq["expected_expr_in_variant"][e] + ']';

cgi-bin/core/custom.min.js

@@ -45,7 +45,7 @@
           }
 
           $.ajax({
-            url: 'cgi-bin/webservice.cgi?tissue=aerial&record=ERR274310&locus=' + locus + '&variant=1&start=' + response["locus_start"] + '&end=' + response["locus_end"],
+            url: 'cgi-bin/rnaSeqMapCoverage.cgi?tissue=aerial&record=ERR274310&locus=' + locus + '&variant=1&start=' + response["locus_start"] + '&end=' + response["locus_end"],
             dataType: 'json',
             success: function(res) { // When the file is retrieved:
               console.log("RNA-Seq request successful for tissue = aerial, record = ERR274310, locus = " + locus + ', variant = 1, start = ' + response["locus_start"] + ', end = ' + response["locus_end"]);

cgi-bin/get_gene_structures.html

@@ -48,7 +48,7 @@
       console.log("Y-scale requested: " + yscale);
 
       $.ajax({
-        url: 'cgi-bin/webservice.cgi?tissue=' + tissue + '&record=' + record + '&locus=' + locus + '&variant=1&start=' + locus_start + '&end=' + locus_end + '&yscale=' +
+        url: 'cgi-bin/rnaSeqMapCoverage.cgi?tissue=' + tissue + '&record=' + record + '&locus=' + locus + '&variant=1&start=' + locus_start + '&end=' + locus_end + '&yscale=' +
           yscale,
         dataType: 'json',
         success: function(response_rnaseq) {

cgi-bin/webservice.cgi cgi-bin/rnaSeqMapCoverage.cgi

@@ -15,11 +15,11 @@
   <link rel="stylesheet" href="cgi-bin/core/jquery-ui-1.12.1.custom/jquery-ui.css">
   <script async src="cgi-bin/core/jquery-ui-1.12.1.custom/jquery-ui-1.12.1.custom.min.js"></script>
   <!-- Bootstrap -->
-  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-  <link rel="stylesheet" href="cgi-bin/core/bootstrap/bootstrap4-0-0-beta-2.min.css" integrity="sha384-PsH8R72JQ3SOdhVi3uxftmaW6Vc51MKb0q5P2rRUpPvrszuE4W1povHYgTpBfshb" crossorigin="anonymous">
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="" crossorigin="anonymous">
+  <link rel="stylesheet" href="cgi-bin/core/bootstrap/bootstrap4-0-0-beta-2.min.css" integrity="" crossorigin="anonymous">
   <!-- jQuery's slim build -->
-  <script src="cgi-bin/core/bootstrap/popper.min.js" integrity="sha384-vFJXuSJphROIrBnz7yo7oB41mKfc8JzQZiCq4NCceLEaO4IHwicKwpJf9c9IpFgh" crossorigin="anonymous"></script>
-  <script async src="cgi-bin/core/bootstrap/bootstrap4-0-0.min.js" integrity="sha384-alpBpkh1PFOepccYVYDB4do5UnbKysX5WZXm3XxPqe5iKTfUKjNkCk9SaVuEZflJ" crossorigin="anonymous"></script>
+  <script src="cgi-bin/core/bootstrap/popper.min.js" integrity="" crossorigin="anonymous"></script>
+  <script async src="cgi-bin/core/bootstrap/bootstrap4-0-0.min.js" integrity="" crossorigin="anonymous"></script>
   <!-- tabletoCSV tool to create an option to download XML as CSV -->
   <script defer src="cgi-bin/core/tabletoCSV/jquery.tabletoCSV.js"></script>
   <!-- tablesort -->