Merge pull request #448 from zsloan/misc_rob_changes

Misc rob changes
author: zsloan 2020-09-29 16:48:24 -0500
committer: GitHub 2020-09-29 16:48:24 -0500
commit: b06657d216fb8e0d94125ec77beb3fdf6e0c7e8a (patch)
tree: 066e541cd115aea69f18630e12c3fd780eb70304 /wqflask/wqflask
parent: d34258bed3ef13350499414100401df3bf08a105 (diff)
parent: 5a5dd3daf638cd95358bf102fd8d8c2023d44aae (diff)
download: genenetwork2-b06657d216fb8e0d94125ec77beb3fdf6e0c7e8a.tar.gz
9 files changed, 43 insertions, 46 deletions
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 338302af..92deab20 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -46,4 +46,9 @@ table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
 table.dataTable.cell-border tbody tr th:first-child,
 table.dataTable.cell-border tbody tr td:first-child {
   border-left: 1px solid #ccc;
+}
+
+.glyphicon {
+  position: relative;
+  top: 2px;
 }
 \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 685d6291..61134a88 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,7 +93,7 @@ $(function() {
 
   });
 
-  add = function() {
+  add_to_collection = function() {
     var traits;
     traits = $("#trait_table input:checked").map(function() {
       return $(this).val();
@@ -250,7 +250,7 @@ $(function() {
   $("#select_all").click(select_all);
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
-  $("#add").click(add);
+  $("#add").click(add_to_collection);
   $("#submit_bnw").click(submit_bnw);
   $("#export_traits").click(export_traits);
   $('.trait_checkbox, .btn').click(change_buttons);
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index e6802cc4..b44538cf 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -21,6 +21,14 @@
     {% block css %}
     {% endblock %}
 
+    <style>
+        table.dataTable thead .sorting_asc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
+        }
+        table.dataTable thead .sorting_desc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
+        }
+    </style>
 </head>
 
 <body style="width: 100%">
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 825dfb84..62b6abb5 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
         or add to an existing collection.</p>
     </div>
     <div class="modal-body" style="margin-left: 20px;">
-        <form action="/collections/new" data-validate="parsley" id="add_form">
+        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
             {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
             {% else %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index dce814dd..ca8aece3 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -16,8 +16,6 @@
         </h1>
         <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
 
-        <!--<hr style="height: 1px; background-color: #A9A9A9;">-->
-
         <div>
           <form id="collection_form" action="/delete" method="post">
             <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
@@ -77,7 +75,7 @@
             <input type="hidden" name="database_name" id="database_name" value="None">
             <input type="hidden" name="export_data" id="export_data" value="">
             <input type="hidden" name="file_name" id="file_name" value="collection_table">
-            <button class="btn btn-default" id="export_traits">Download CSV</button>
+            <button class="btn btn-default" id="export_traits">Download</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
             <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -99,9 +97,9 @@
                             <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#L" target="_blank"><sup>?</sup></a></th>
-                            <th data-export="Max LRS Location">Max LRS Location</th>
-                            <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th>
+                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Peak Location">Peak Location</th>
+                            <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
                     </thead>
 
@@ -144,7 +142,7 @@
                             <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
                             {% endif %}
                             <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
-                            {% if this_trait.additive|float > 0 %}
+                            {% if this_trait.additive|float != 0 %}
                             <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
                             {% else %}
                             <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 282e752d..487c6980 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -127,7 +127,7 @@
               <input type="hidden" name="export_data" id="export_data" value="">
               <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
               <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+              <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button>
               <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
               <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
               <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -315,20 +315,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
                       'width': "120px",
@@ -390,20 +390,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "additive",
@@ -412,7 +412,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "location"
                     }{% endif %}
                 ],
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 8b3e4907..4aced50c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -215,43 +215,27 @@
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-        <a href="#redirect">
-        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
-        </a>
+        <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.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>
+        <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
         {% endif %}
         {% if 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>
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
         {% endif %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.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>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button>
         {% 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>
+        <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
         {% endif %}
         {% endif %}
         {% if show_probes == "True" %}
-        <a target="_blank" href="http://gn1.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>
+        <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.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', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
-        </a>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
-        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
-            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
-        </a>
+            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button>
         {% endif %}
     </div>
 </div>
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 05a2be73..a8ed91b1 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -5,7 +5,7 @@
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
         </div>
         <div style="padding-left: 10px; display: inline;">
-          <input type="button" class="btn btn-default export" value="Export">
+          <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
           <select class="select optional span2 export_format">
             <option value="excel">Excel</option>
             <option value="csv">CSV</option>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 974081d3..7bdb3ef9 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -76,11 +76,13 @@
                             <i class="icon-signal"></i> Sort By Value
                             </button>
                         </div>
+                        <!--
                         <div class="btn-group">
-                            <button type="button" class="btn btn-default" id="color_by_trait">
+                            <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
                                 <i class="icon-tint"></i> Color by Trait
                             </button>
                         </div>
+                        -->
                         <div id="bar_chart_container">
                             <div id="bar_chart"></div>
                         </div>
author	zsloan	2020-09-29 16:48:24 -0500
committer	GitHub	2020-09-29 16:48:24 -0500
commit	b06657d216fb8e0d94125ec77beb3fdf6e0c7e8a (patch)
tree	066e541cd115aea69f18630e12c3fd780eb70304 /wqflask/wqflask
parent	d34258bed3ef13350499414100401df3bf08a105 (diff)
parent	5a5dd3daf638cd95358bf102fd8d8c2023d44aae (diff)
download	genenetwork2-b06657d216fb8e0d94125ec77beb3fdf6e0c7e8a.tar.gz