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authorzsloan2020-10-01 12:52:30 -0500
committerzsloan2020-10-01 12:52:30 -0500
commit832ebc46a0e7a6f7c3faef5eb36f1104a66fd626 (patch)
tree08050a3761191935b5111bd97f935cd0af0d5ae7
parent8a01dca227aa03e794ced5f99513355f2a035f2f (diff)
parent5a91ed3bce93934a224d8fbbb7053a1980dd216c (diff)
downloadgenenetwork2-832ebc46a0e7a6f7c3faef5eb36f1104a66fd626.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into corr_matrix_error_fix
Diffstat
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css5
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js14
-rw-r--r--wqflask/wqflask/templates/base.html8
-rw-r--r--wqflask/wqflask/templates/collections/add.html2
-rw-r--r--wqflask/wqflask/templates/collections/view.html26
-rw-r--r--wqflask/wqflask/templates/correlation_page.html20
-rw-r--r--wqflask/wqflask/templates/search_result_page.html29
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html32
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html4
10 files changed, 71 insertions, 71 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..86660126 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);
@@ -261,6 +261,12 @@ $(function() {
let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
+ function extract_inner_text(the_string){
+ var span = document.createElement('span');
+ span.innerHTML = the_string;
+ return span.textContent || span.innerText;
+ }
+
function sort_NAs(a, b, sort_function){
if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
return 0;
@@ -276,10 +282,10 @@ $(function() {
$.extend( $.fn.dataTableExt.oSort, {
"natural-minus-na-asc": function (a, b) {
- return sort_NAs(a, b, naturalAsc)
+ return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc)
},
"natural-minus-na-desc": function (a, b) {
- return sort_NAs(a, b, naturalDesc)
+ return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc)
}
});
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..bc487a59 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>
@@ -166,13 +164,13 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
- <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+ <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript">
@@ -187,10 +185,14 @@
console.time("Creating table");
$('#trait_table').dataTable( {
"columns": [
- { "type": "natural", "width": 10 },
+ {
+ "orderDataType": "dom-checkbox",
+ "orderSequence": [ "desc", "asc"],
+ "width": 10
+ },
{ "type": "natural", "width": 50 },
{ "type": "natural" },
- { "type": "natural", "width": 120 },
+ { 'type': "natural-minus-na", "width": 120 },
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural", "width": 130 },
@@ -199,10 +201,6 @@
{ "type": "natural", "width": 130 },
{ "type": "natural" }
],
- "columnDefs": [ {
- "targets": 0,
- "orderable": false
- } ],
"order": [[1, "asc" ]],
buttons: [
{
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index e597bea9..bb2a697f 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -175,9 +175,13 @@
<TD data-export="N/A">N/A</TD>
{% endif %}
<td data-export="{{ trait.pubmed_text }}">
+ {% if trait.pubmed_text != "N/A" %}
<a href="{{ trait.pubmed_link }}">
{{ trait.pubmed_text }}
</a>
+ {% else %}
+ {{ trait.pubmed_text }}
+ {% endif %}
</td>
<td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
<td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
@@ -365,9 +369,9 @@
{ "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
{ "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
{ "type": "scientific" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" }
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" }
],
"createdRow": function ( row, data, index ) {
$('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -419,13 +423,13 @@
{ "type": "natural" },
{ "type": "natural", "width": "20%" },
{ "type": "natural", "width": "12%" },
- { "orderDataType": "dom-innertext" },
+ { "type": "natural-minus-na" },
{ "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
{ "type": "natural" },
{ "type": "scientific" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" }
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" }
],
"order": [[9, "asc" ]],
"sDom": "Btir",
@@ -461,7 +465,7 @@
{ "type": "natural" },
{ "type": "natural" },
{ "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
- { "type": "natural" },
+ { "type": "natural-minus-na" },
{ "type": "scientific" }
],
"order": [[6, "asc" ]],
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 282e752d..e2e1aa46 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>
@@ -274,10 +274,9 @@
},
{
'title': "Record",
- 'type': "natural",
+ 'type': "natural-minus-na",
'data': null,
'width': "60px",
- 'orderDataType': "dom-inner-text",
'render': function(data, type, row, meta) {
return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
}
@@ -315,20 +314,20 @@
'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",
@@ -367,17 +366,11 @@
author_string = data.authors
}
return author_string
- // try {
- // return decodeURIComponent(escape(author_string))
- // } catch(err){
- // return author_string
- // }
}
},
{
'title': "Year",
'type': "natural-minus-na",
- 'orderDataType': "dom-inner-text",
'data': null,
'width': "80px",
'render': function(data, type, row, meta) {
@@ -390,20 +383,20 @@
'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 +405,7 @@
{
'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>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 23:36:56 +0000