Redid gene global search to take JSON data input instead of converting an HTML table, and adding loading text

Made some changes to make trait page SNPs link point to GN2 SNP Browser, as well as make other links open in new tabs/windows

5 files changed, 163 insertions, 107 deletions

diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 94965507..99dd087d 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -7,6 +7,8 @@ from db import webqtlDatabaseFunction
 
 from base import webqtlConfig
 
+from wqflask import user_manager
+
 from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 from utility.benchmark import Bench
 
@@ -30,6 +32,7 @@ class GSearch(object):
                 InbredSet.`Name` AS inbredset_name,
                 Tissue.`Name` AS tissue_name,
                 ProbeSetFreeze.Name AS probesetfreeze_name,
+                ProbeSetFreeze.FullName AS probesetfreeze_fullname,
                 ProbeSet.Name AS probeset_name,
                 ProbeSet.Symbol AS probeset_symbol,
                 ProbeSet.`description` AS probeset_description,
@@ -58,30 +61,38 @@ class GSearch(object):
                 re = g.db.execute(sql).fetchall()
             self.trait_list = []
             with Bench("Creating trait objects"):
-                for line in re:
+                for i, line in enumerate(re):
                     this_trait = {}
-                    this_trait['name'] = line[4]
+                    this_trait['index'] = i + 1
+                    this_trait['name'] = line[5]
                     this_trait['dataset'] = line[3]
+                    this_trait['dataset_fullname'] = line[4]
+                    this_trait['hmac'] = user_manager.data_hmac('{}:{}'.format(line[4], line[3]))
                     this_trait['species'] = line[0]
                     this_trait['group'] = line[1]
                     this_trait['tissue'] = line[2]
-                    this_trait['symbol'] = line[5]
-                    this_trait['description'] = line[6]
+                    this_trait['symbol'] = line[6]
+                    this_trait['description'] = line[7]
                     this_trait['location_repr'] = 'N/A'
-                    if (line[7] != "NULL" and line[7] != "") and (line[8] != 0):
-                        this_trait['location_repr'] = 'Chr%s: %.6f' % (line[7], float(line[8]))
-                    this_trait['mean'] = line[9]
+                    if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
+                        this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9]))
+                    this_trait['mean'] = round(line[10], 3)
                     this_trait['LRS_score_repr'] = "N/A"
-                    if line[10] != "" and line[10] != None:
-                        this_trait['LRS_score_repr'] = '%3.1f' % line[10]
+                    if line[11] != "" and line[11] != None:
+                        this_trait['LRS_score_repr'] = round(line[10], 1)
                     this_trait['additive'] = "N/A"
-                    if line[13] != "":
-                        this_trait['additive'] = line[13]
+                    if line[14] != "" and line[14] != None:
+                        this_trait['additive'] = round(line[14], 3)
 
                     #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
                     #trait_id = line[4]
                     #with Bench("Building trait object"):
-                    #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=False, get_sample_info=False)
+                    trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
+                    max_lrs_text = "N/A"
+                    if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
+                        max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+                    this_trait['max_lrs_text'] = max_lrs_text
+
                     self.trait_list.append(this_trait)
 
         elif self.type == "phenotype":
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 59901404..09d5e1e3 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -14,7 +14,7 @@ div.sample_group {
   left: 100px;
 }
 
-table.dataTable thead th{
+table.dataTable thead th, table.dataTable tfoot th{
   border-right: 1px solid white;
   color: white;
   background-color: #369;
@@ -27,7 +27,7 @@ table.dataTable thead .sorting_desc {
   background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
 }
 
-table.dataTable thead th {
+table.dataTable thead th, table.dataTable tfoot {
   padding: 4px 18px 4px 10px;
 }
 
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index ff5c56f1..5433f2c5 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -7,7 +7,7 @@
 {% block content %}
 <!-- Start of body -->
 
-    <div class="container">
+    <div class="container" style="width: 2000px;">
 
         <p>You searched for {{ terms }}.</p>
         <p>To study a record, click on its Record ID below.<br />Check records below and click Add button to add to selection.</p>
@@ -30,59 +30,9 @@
             <br />
             <div style="width: 100%;">
               <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
-                <thead>
-                  <tr>
-                    <th></th>
-                    <th data-export="Index">Index</th>
-                    <th data-export="Record">Record ID</th>
-                    <th data-export="Species">Species</th> 
-                    <th data-export="Group">Group</th> 
-                    <th data-export="Tissue">Tissue</th> 
-                    <th data-export="Dataset">Dataset</th> 
-                    <th data-export="Symbol">Symbol</th> 
-                    <th data-export="Description">Description</th> 
-                    <th data-export="Location">Location</th>
-                    <th data-export="Mean">Mean</th>
-                    <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
-                    <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
-                  </tr>
-                </thead> 
                 <tbody>
-                  {% for this_trait in trait_list %}
-                  <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset }}">
-                    <td align="center" style="padding: 0px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset)) }}"></td>
-                    <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
-                    <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset)}}">{{ this_trait.name }}</a></td>
-                    <td data-export="{{ this_trait.species }}">{{ this_trait.species }}</td>
-                    <td data-export="{{ this_trait.group }}">{{ this_trait.group }}</td>
-                    <td data-export="{{ this_trait.tissue }}">{{ this_trait.tissue }}</td>
-                    <td data-export="{{ this_trait.dataset }}">{{ this_trait.dataset }}</td>
-                    <td data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</td>
-                    <td data-export="{{ this_trait.description }}">{{ this_trait.description }}</td>
-                    <td data-export="{{ this_trait.location_repr }}" align="right">{{ this_trait.location_repr }}</td>
-                    <td data-export="{{ '%0.3f' % this_trait.mean|float }}" align="right">{{ '%0.3f' % this_trait.mean|float }}</td>
-                    <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
-                    <td data-export="{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ '%0.3f' % this_trait.additive|float }}{% else %}N/A{% endif %}</td>
-                  </tr>
-                  {% endfor %}
+                  <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
                 </tbody>
-                <tfoot>
-                  <tr>
-                    <th></th>
-                    <th>Index</th>
-                    <th>Record ID</th>
-                    <th>Species</th> 
-                    <th>Group</th> 
-                    <th>Tissue</th> 
-                    <th>Dataset</th> 
-                    <th>Symbol</th> 
-                    <th>Description</th> 
-                    <th>Location</th>
-                    <th>Mean</th>
-                    <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
-                    <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
-                  </tr>
-                </tfoot> 
               </table>
             </div>
         </div>
@@ -100,7 +50,11 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-	
+
+    <script type='text/javascript'>
+      var the_rows = {{ trait_list|safe }};
+    </script>
+
     <script type="text/javascript" charset="utf-8">
         $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
         {
@@ -119,49 +73,138 @@
 
             console.time("Creating table");
             $('#trait_table').DataTable( {
-                "createdRow": function ( row, data, index ) {
+                'createdRow': function ( row, data, index ) {
+                    $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
+                    $('td', row).eq(1).attr("align", "right");
+                    $('td', row).slice(10,14).attr("align", "right");
                     $('td', row).eq(8).attr('title', $('td', row).eq(8).text());
-                    if ($('td', row).eq(8).text().length > 50) {
-                        $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 50));
+                    if ($('td', row).eq(8).text().length > 45) {
+                        $('td', row).eq(8).text($('td', row).eq(8).text().substring(0, 45));
                         $('td', row).eq(8).text($('td', row).eq(8).text() + '...')
                     }
+                    $('td', row).eq(5).attr('title', $('td', row).eq(5).text());
+                    if ($('td', row).eq(5).text().length > 25) {
+                        $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 25));
+                        $('td', row).eq(5).text($('td', row).eq(5).text() + '...')
+                    }
+                    $('td', row).eq(6).attr('title', $('td', row).eq(6).text());
+                    if ($('td', row).eq(6).text().length > 35) {
+                        $('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 35));
+                        $('td', row).eq(6).text($('td', row).eq(6).text() + '...')
+                    }
                 },
-                "paging": false,
-                "columns": [
-                    { "orderDataType": "dom-checkbox" },
-                    { "type": "natural", "width": "3%" },
-                    { "type": "natural", "width": "6%" },
-                    { "type": "natural", "width": "8%" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural", "width": "7%" },
-                    { "type": "natural", "width": "4%" },
-                    { "type": "natural", "width": "5%" },
-                    { "type": "natural", "width": "5%" }
-                ],
-                "columnDefs": [
+                'data': the_rows,
+                'columns': [
+                    { 
+                      'data': null,
+                      'orderDataType': "dom-checkbox",
+                      'render': function(data, type, row, meta) {
+                        return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
+                      }
+                    },
+                    {
+                      'title': "Index",
+                      'type': "natural", 
+                      'data': "index"
+                    },
+                    { 
+                      'title': "Record ID",
+                      'type': "natural", 
+                      'data': null,
+                      'render': function(data, type, row, meta) {
+                        return '<a href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.name + '</a>'
+                      }
+                    },
+                    { 
+                      'title': "Species",
+                      'type': "natural", 
+                      'data': "species"
+                    },
+                    { 
+                      'title': "Group",
+                      'type': "natural",
+                      'data': "group"
+                    },
+                    { 
+                      'title': "Tissue",
+                      'type': "natural",
+                      'data': "tissue"
+                    },
+                    { 
+                      'title': "Dataset",
+                      'type': "natural",
+                      'data': "dataset_fullname"
+                    },
+                    { 
+                      'title': "Symbol",
+                      'type': "natural",
+                      'data': "symbol"
+                    },
+                    { 
+                      'title': "Description",
+                      'type': "natural",
+                      'data': "description"
+                    },
+                    { 
+                      'title': "Location",
+                      'type': "natural", 
+                      'data': "location_repr"
+                    },
                     {
-                        "targets": 0,
-                        "orderable": false,
-                        "orderDataType": "dom-checkbox"
+                      'title': "Mean",
+                      'type': "natural", 
+                      'data': "mean"
+                    },
+                    { 
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'type': "natural", 
+                      'data': "LRS_score_repr"
+                    },
+                    { 
+                      'title': "Max LRS Location",
+                      'type': "natural", 
+                      'data': "max_lrs_text"
+                    },
+                    { 
+                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'type': "natural", 
+                      'data': "additive"
                     }
                 ],
-                "order": [[1, "asc" ]],
-                "sDom": "tir",
-                "autoWidth": false,
-                "deferRender": true,
-                "bSortClasses": false,
-                "scrollY": "600px",
-                "scrollCollapse": true,
-                "scroller": true,
-                "scrollX": true,
-                "paging": false,
-                "orderClasses": true
+                'order': [[1, "asc" ]],
+                'sDom': "tir",
+                'autoWidth': true,
+                'deferRender': true,
+                'paging': false,
+                'orderClasses': true,
+                'processing': true,
+                'language': {
+                  'loadingRecords': '&nbsp;',
+                  'processing': 'Loading...'
+                }
             } );
 
+            $('#trait_table').append(
+              '<tfoot>' + 
+                '<tr>' +
+                  '<th></th>' +
+                  '<th>Index</th>' +
+                  '<th>Record ID</th>' +
+                  '<th>Species</th> ' +
+                  '<th>Group</th>' +
+                  '<th>Tissue</th>' +
+                  '<th>Dataset</th>' + 
+                  '<th>Symbol</th>' + 
+                  '<th>Description</th>' + 
+                  '<th>Location</th>' +
+                  '<th>Mean</th>' +
+                  '<th>Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>' +
+                  '<th>Max LRS Location</th>' + 
+                  '<th>Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>' +
+                '</tr>' + 
+              '</tfoot>'
+            );
+
             console.timeEnd("Creating table");
 
         });
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 96675306..566ea7ca 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -112,25 +112,27 @@
         </a>
         {% if this_trait.dataset.type == 'ProbeSet' %}
         {% if this_trait.symbol != None %}
-        <a href="http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
+        <a target="_blank" href="http://www.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
         <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
         </a>
         {% endif %}
         {% if UCSC_BLAT_URL != "" %}
-        <a href="{{ UCSC_BLAT_URL }}">
+        <a target="_blank" href="{{ UCSC_BLAT_URL }}">
         <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
         </a>
         {% endif %}
         {% if this_trait.symbol != None %}
-        <a href="http://genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
+        <a target="_blank" href="http://genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
         <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
         </a>
-        <a href="http://genenetwork.org/webqtl/main.py?FormID=SnpBrowserResultPage&submitStatus=1&diffAlleles=True&customStrain=True&geneName={{ this_trait.symbol }}">
+        {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
+        <a href="./snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
         <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
         </a>
         {% endif %}
+        {% endif %}
         {% if show_probes == "True" %}
-        <a href="http://genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
+        <a target="_blank" href="http://genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
         <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
         </a>
         {% endif %}
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 8ae763fa..87cbab84 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -183,7 +183,7 @@
     <div style="margin-top: 20px;">
     {% if filtered_results is defined %}
     {% if filtered_results|length > limit_number %}
-    There are more than 5000 results. Consider limiting your search to a smaller range.
+    There are more than 10000 results. Consider limiting your search to a smaller range.
     {% else %}
     <table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
       <thead>