Update Help Link and Fix Similar GeneSet Bug

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-legacy"
-version = "1.5.8"
+version = "1.5.9"
 description = ""
 authors = ["Alexander Berger <[email protected]>"]
 readme = "README.md"

src/templates/batchupload.html

@@ -508,7 +508,7 @@ <h3 class="panel-title"><strong>Batch GeneSet Upload</strong>
     $('#clickableGenes').popover({
         title: 'Gene Information', content: 'Provide a list of genes to associate with this record. ' +
         'A full description of the gene set format can be found ' +
-        '<a href="http://www.geneweaver.org/help/#uploading-gene-sets" target="_blank">' +
+        '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/web-application/uploading-genesets/" target="_blank">' +
         '       <strong>here</strong></a>.',
         html: 'true'
     });

src/templates/editgenesets.html

@@ -108,7 +108,7 @@ <h2 class="panel-title">
             <p>
                 Please complete the descriptive information about this GeneSet.
                 Follow the guidelines outlined in our
-                <a href="http://geneweaver.org/help/#curation">
+                <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/reference/curation/">
                     Curation Standards
                 </a>
                 to facilitate acceptance of your public data submission by
@@ -820,7 +820,7 @@ <h2 class="panel-title">
     $('#clickableGenes').popover({
         title: 'Gene Information', content: 'Provide a list of genes to associate with this record. ' +
                 'A full description of the gene set format can be found ' +
-                '<a href="http://www.geneweaver.org/help/#uploading-gene-sets">here</a>.',
+                '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/web-application/uploading-genesets/">here</a>.',
         html: 'true'
     });
 

src/templates/editgenesetsgenes.html

@@ -331,7 +331,7 @@ <h3 class="panel-title">
     $('#clickableGenes').popover({
         title: 'Gene Information', content: 'Provide a list of genes to associate with this record. ' +
         'A full description of the gene set format can be found ' +
-        '<a href="http://www.geneweaver.org/help/#uploading-gene-sets">here</a>.',
+        '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/web-application/uploading-genesets/">here</a>.',
         html: 'true'
     });
 

src/templates/footer.html

@@ -55,7 +55,7 @@ <h4>GeneWeaver Links</h4>
                         <hr>
                         <ul class="geneWeaverLinks">
                             <li><a href="/">Home Page</a></li>
-                            <li><a href="/help">Help</a></li>
+                            <li><a href="https://thejacksonlaboratory.github.io/geneweaver-docs/">Help</a></li>
                             <li><a href="/data">Data</a></li>
                             <li><a href="/about">About</a></li>
                             <li><a href="/funding">Funding</a></li>

src/templates/index.html

@@ -122,7 +122,7 @@ <h1><img src="{{ url_for('static', filename='images/GW2-logo.png') }}" alt="Gene
             </div>
         </a>
 
-        <a class="link-panel" href="/help">
+        <a class="link-panel" href="https://thejacksonlaboratory.github.io/geneweaver-docs/">
             <div class="col-md-3 link-panel" style="text-align: center;width:25%;height:25%">
                 <img src="{{ url_for('static', filename='images/GW2-help.png')|safe }}" style="width:50%" />
                 <br />
@@ -155,7 +155,7 @@ <h3 class="normal text-center">
                         commands and functions.
                     </h3>
                     <p class="text-center">
-                        <a href="https://geneweaver.org/help/GeneWeaverquickstart2018.pdf"><i class="fa fa-columns fa-2x"></i>
+                        <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/assets/GeneWeaverquickstart2018.pdf"><i class="fa fa-columns fa-2x"></i>
                             Download a Cheatsheet of commands.</a>
                     </p>
                 </div>

src/templates/similargenesets.html

@@ -392,7 +392,7 @@ <h3 class="panel-title">Top 1000 Similar GeneSets
                                     {{ i.description }}
                                 </td>
                                 <td width="10px" style="vertical-align: middle">
-                                    <div class="ui-checkbox" style="padding: 0; border: 0;">
+                                    <div class="ui-checkbox gsoptionsCheckBox" style="padding: 0; border: 0;">
                                         <label for="addGeneset{{ i.geneset_id }}">
                                             <input type="checkbox" name="gsoptions[]" id="addGeneset{{ i.geneset_id }}"
                                                    value="{{ i.geneset_id }}"/>
@@ -752,15 +752,13 @@ <h3 class="panel-title">Top 1000 Similar GeneSets
                 var gschecked = {};
 
                 // Called every time a checkbox is clicked
-                $("input[name='gsoptions[]']").on('click', function(event) {
-
-                    // The element object this event is referring to
-                    var box = event.target;
-                    var gsid = ($(this).val());
-                    if (box.checked)
+                $(document).on('change', '.gsoptionsCheckBox input[type="checkbox"]', function () {
+                    const gsid = $(this).val();
+                    if ($(this).is(':checked')) {
                         gschecked[gsid] = gsid;
-                    else
+                    } else {
                         delete gschecked[gsid];
+                    }
                 });
 
                 // The 'Add GeneSet(s) to Project' button

src/templates/tool/ABBA_options.html

@@ -445,6 +445,6 @@
 </div>
 <script>
     $('#abba-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#abba');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/abba/');
     });
 </script>

src/templates/tool/BooleanAlgebra_options.html

@@ -84,6 +84,6 @@
 
 
     $("#bool-wiki").click(function() {
-        window.open('http://geneweaver.org/help/#boolean-algebra');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/boolean-algebra/');
     });
 </script>

src/templates/tool/Combine_options.html

@@ -35,6 +35,6 @@
 </div>
 <script>
     $('#combine-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#combine');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/reference/geneset-utilities/#combine');
     });
 </script>

src/templates/tool/DBSCAN_options.html

@@ -45,6 +45,6 @@
 </div>
 <script>
     $('#dbscan-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#dbscan-gene-clustering');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/dbscan/');
     });
 </script>

src/templates/tool/FindVariants_options.html

@@ -40,7 +40,7 @@
 
 <script>
      $("#fv-wiki").click(function() {
-        window.open('http://geneweaver.org/help/#find-variants');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/find-variants/');
     });
     $('#clickableTranscript').popover({
        title: 'Transcript Warning', content: 'The "using Transcript" option may find millions of variants and take several hours.'

src/templates/tool/FindVariants_result.html

@@ -151,7 +151,7 @@ <h1>{{ title }}
                 </div>
                 <span style="color:#006400">
                     Visit our
-                    <a href="http://geneweaver.org/help/#clustering"
+                    <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/clustering/"
                        style="color:#006400; font-weight:600;"
                        target="_blank">wiki</a>
                     for more information.
@@ -205,7 +205,7 @@ <h1>{{ title }}
 var imgAltKey = '<img src="{{url_for('static', filename='images/altkey.png')}}">';
 var imgShiftKey = '<img src="{{url_for('static', filename='images/shiftkey.png')}}">';
 var wikiIcon = '<img src="{{url_for('static', filename='images/wikiIcon.png')}}">';
-var wikiImg = '<a href="http://geneweaver.org/help/#jaccard-similarity">' + wikiIcon +'</i></a>';
+var wikiImg = '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/jaccard-similarity/">' + wikiIcon +'</i></a>';
 
 // Cooresponds to the information or what button (gives users instructions how to work tool)
 $('#what').popover({

src/templates/tool/GeneSetViewer_options.html

@@ -38,6 +38,6 @@
 </div>
 <script>
     $('#gsgraph-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#geneset-graph');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/geneset-graph/');
     });
 </script>

src/templates/tool/GeneSetViewer_result.html

@@ -79,7 +79,7 @@ <h1>{{ title }}</h1>
             </div>
             <span style="color:#006400">
                 Visit our 
-                <a href="http://geneweaver.org/help/#geneset-graph"
+                <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/geneset-graph/"
                    style="color:#006400; font-weight:600;" 
                    target="_blank">wiki</a>
                 for more information.

src/templates/tool/JaccardClustering_options.html

@@ -36,6 +36,6 @@
 
 <script>
     $('#clustering-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#clustering');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/clustering/');
     });
 </script>

src/templates/tool/JaccardClustering_result.html

@@ -198,7 +198,7 @@ <h1>{{ title }}</h1>
                 </div>
                 <span style="color:#006400">
                     Visit our 
-                    <a href="http://geneweaver.org/help/#clustering"
+                    <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/clustering/"
                        style="color:#006400; font-weight:600;" 
                        target="_blank">wiki</a>
                     for more information.

src/templates/tool/JaccardSimilarity_options.html

@@ -37,6 +37,6 @@
 </div>
 <script>
     $('#jaccard-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#jaccard-similarity');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/jaccard-similarity/');
     });
 </script>

src/templates/tool/JaccardSimilarity_result.html

@@ -271,7 +271,7 @@ <h1>{{ title }}
             </div>
             <span style="color:#006400">
                 Visit our 
-                <a href="http://geneweaver.org/help/#jaccard-similarity"
+                <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/jaccard-similarity/"
                    style="color:#006400; font-weight:600;" 
                    target="_blank">wiki</a>
                 for more information.
@@ -464,7 +464,7 @@ <h2 id="pthresh">P-Value Threshold (0.01 increments):
 var imgAltKey = '<img src="{{url_for('static', filename='images/altkey.png')}}">';
 var imgShiftKey = '<img src="{{url_for('static', filename='images/shiftkey.png')}}">';
 var wikiIcon = '<img src="{{url_for('static', filename='images/wikiIcon.png')}}">';
-var wikiImg = '<a href="http://geneweaver.org/help/#jaccard-similarity">' + wikiIcon +'</i></a>';
+var wikiImg = '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/jaccard-similarity/">' + wikiIcon +'</i></a>';
 
 // Cooresponds to the information or what button (gives users instructions how to work tool)
 $('#what').popover({

src/templates/tool/MSET_options.html

@@ -35,7 +35,7 @@
 </div>
 <script>
     $('#mset-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#mset');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/mset/');
     });
 
     function updateMultiSelects() {

src/templates/tool/PhenomeMap_options.html

@@ -76,6 +76,6 @@
 </div>
 <script>
     $('#hisim-wiki').click(function() {
-        window.open('http://geneweaver.org/help/#hisim-graph');
+        window.open('https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/hisim-graph/');
     });
 </script>

src/templates/tool/PhenomeMap_result.html

@@ -322,7 +322,7 @@ <h1>{{ title }}
             </div>
             <span style="color:#006400">
                 Visit our 
-                <a href="http://geneweaver.org/help/#hisim-graph"
+                <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/analysis-tools/hisim-graph/"
                    style="color:#006400; font-weight:600;" 
                    target="_blank">wiki</a>
                 for more information.

src/templates/uploadgeneset.html

@@ -108,7 +108,7 @@ <h2 class="panel-title">
 
             <p>
                 Please enter some descriptive info about this GeneSet. please confirm that your GeneSet MetaContent meets the
-                guidlines outlined in our <a href="http://geneweaver.org/help/#curation" target="_blank">
+                guidlines outlined in our <a href="https://thejacksonlaboratory.github.io/geneweaver-docs/reference/curation/" target="_blank">
                 <strong>Curation Standards <i class="fa fa-mail-forward"></i></strong></a> to ensure rapid acceptance by
                 our curation team, or, in the case of private data, maximum integration into available GeneWeaver datasets.
 
@@ -822,7 +822,7 @@ <h2 class="panel-title">
     $('#clickableGenes').popover({
         title: 'Gene Information', content: 'Provide a list of genes to associate with this record. ' +
         'A full description of the gene set format can be found ' +
-        '<a href="http://www.geneweaver.org/help/#uploading-gene-sets" target="_blank">' +
+        '<a href="https://thejacksonlaboratory.github.io/geneweaver-docs/web-application/uploading-genesets/" target="_blank">' +
         '       <strong>here</strong></a>.',
         html: 'true'
     });