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authorzsloan2020-12-09 15:17:09 -0600
committerzsloan2020-12-09 15:17:09 -0600
commit0823820162a371b38756c18ae8d6d3d25fcdfcb1 (patch)
tree9fc1a317f24bef31259a2b810e8cdf9f5fa926fc
parentcdba483dfae360b99a77551b82d27f2d5b6c7b08 (diff)
parent69f3e56b1d0425f35cd9baa75b3cf3a42c876305 (diff)
downloadgenenetwork2-0823820162a371b38756c18ae8d6d3d25fcdfcb1.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing
-rw-r--r--test/requests/link_checker.py13
-rw-r--r--wqflask/wqflask/static/new/css/colorbox.css238
-rw-r--r--wqflask/wqflask/static/new/css/marker_regression.css4
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/auto_hide_column.js21
-rw-r--r--wqflask/wqflask/templates/admin/create_group.html2
-rw-r--r--wqflask/wqflask/templates/admin/group_manager.html2
-rw-r--r--wqflask/wqflask/templates/admin/ind_user_manager.html2
-rw-r--r--wqflask/wqflask/templates/admin/manage_user.html2
-rw-r--r--wqflask/wqflask/templates/admin/search_for_groups.html2
-rw-r--r--wqflask/wqflask/templates/admin/set_group_privileges.html2
-rw-r--r--wqflask/wqflask/templates/admin/view_group.html2
-rw-r--r--wqflask/wqflask/templates/base.html7
-rw-r--r--wqflask/wqflask/templates/collections/list.html4
-rw-r--r--wqflask/wqflask/templates/collections/not_logged_in.html4
-rw-r--r--wqflask/wqflask/templates/collections/view.html2
-rw-r--r--wqflask/wqflask/templates/comparison_bar_chart.html2
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html4
-rw-r--r--wqflask/wqflask/templates/correlation_page.html2
-rw-r--r--wqflask/wqflask/templates/ctl_results.html2
-rw-r--r--wqflask/wqflask/templates/docedit.html2
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html2
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html2
-rw-r--r--wqflask/wqflask/templates/mapping_results.html2
-rw-r--r--wqflask/wqflask/templates/network_graph.html3
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html2
-rw-r--r--wqflask/wqflask/templates/search_result_page.html2
-rw-r--r--wqflask/wqflask/templates/set_group_privileges.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html7
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html2
30 files changed, 309 insertions, 38 deletions
diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 1a9eb695..36aeea83 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -103,6 +103,7 @@ def check_packaged_js_files(args_obj, parser):
"/js/DataTablesExtensions/colResize/dataTables.colResize.js",
"/js/DataTablesExtensions/colReorder/js/dataTables.colReorder.js",
"/js/DataTablesExtensions/buttons/js/buttons.colVis.min.js",
+ "/js/DataTablesExtensions/scroller/js/scroller.dataTables.min.js",
"/js/DataTables/js/jquery.dataTables.js",
"/css/DataTablesExtensions/scroller/css/scroller.dataTables.min.css",
# Datatables plugins:
@@ -116,6 +117,16 @@ def check_packaged_js_files(args_obj, parser):
"/js/nvd3/nv.d3.min.css",
"/js/qtip2/jquery.qtip.min.js",
"/js/js_alt/md5.min.js",
+ "/js/js_alt/jstat.min.js",
+ "/js/js_alt/parsley.min.js",
+ "/js/js_alt/timeago.min.js",
+ "/js/plotly/plotly.min.js",
+ "/js/ckeditor/ckeditor.js",
+ "/js/jszip/jszip.min.js",
+ "/js/jscolor/jscolor.js",
+ "/js/DataTables/js/jquery.js",
+ "/css/DataTables/css/jquery.dataTables.css",
+ "/js/colorbox/jquery.colorbox-min.js",
"/css/nouislider/nouislider.min.css",
"/js/nouislider/nouislider.js",
"/js/purescript-genome-browser/js/purescript-genetics-browser.js",
@@ -125,6 +136,8 @@ def check_packaged_js_files(args_obj, parser):
"/js/cytoscape-panzoom/cytoscape.js-panzoom.css",
"/js/cytoscape-qtip/cytoscape-qtip.js",
"/css/d3-tip/d3-tip.css",
+ "/js/DataTables/images/sort_asc_disabled.png",
+ "/js/DataTables/images/sort_desc_disabled.png",
]
print("Checking links")
diff --git a/wqflask/wqflask/static/new/css/colorbox.css b/wqflask/wqflask/static/new/css/colorbox.css
new file mode 100644
index 00000000..8b9fb388
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/colorbox.css
@@ -0,0 +1,238 @@
+/*
+ Colorbox Core Style:
+ The following CSS is consistent between example themes and should not be altered.
+*/
+#colorbox,
+#cboxOverlay,
+#cboxWrapper {
+ position: absolute;
+ top: 0;
+ left: 0;
+ z-index: 9999;
+ overflow: hidden;
+}
+
+#cboxOverlay {
+ position: fixed;
+ width: 100%;
+ height: 100%;
+}
+
+#cboxMiddleLeft,
+#cboxBottomLeft {
+ clear: left;
+}
+
+#cboxContent {
+ position: relative;
+}
+
+#cboxLoadedContent {
+ overflow: auto;
+ -webkit-overflow-scrolling: touch;
+}
+
+#cboxTitle {
+ margin: 0;
+}
+
+#cboxLoadingOverlay,
+#cboxLoadingGraphic {
+ position: absolute;
+ top: 0;
+ left: 0;
+ width: 100%;
+ height: 100%;
+}
+
+#cboxPrevious,
+#cboxNext,
+#cboxClose,
+#cboxSlideshow {
+ cursor: pointer;
+}
+
+.cboxPhoto {
+ float: left;
+ margin: auto;
+ border: 0;
+ display: block;
+ max-width: none;
+ -ms-interpolation-mode: bicubic;
+}
+
+.cboxIframe {
+ width: 100%;
+ height: 100%;
+ display: block;
+ border: 0;
+}
+
+#colorbox,
+#cboxContent,
+#cboxLoadedContent {
+ box-sizing: content-box;
+ -moz-box-sizing: content-box;
+ -webkit-box-sizing: content-box;
+}
+
+/*
+ User Style:
+ Change the following styles to modify the appearance of Colorbox. They are
+ ordered & tabbed in a way that represents the nesting of the generated HTML.
+*/
+#cboxOverlay {
+ background: #fff;
+}
+
+#colorbox {
+ outline: 0;
+}
+
+#cboxTopLeft {
+ width: 25px;
+ height: 25px;
+ background: url(images/border1.png) no-repeat 0 0;
+}
+
+#cboxTopCenter {
+ height: 25px;
+ background: url(images/border1.png) repeat-x 0 -50px;
+}
+
+#cboxTopRight {
+ width: 25px;
+ height: 25px;
+ background: url(images/border1.png) no-repeat -25px 0;
+}
+
+#cboxBottomLeft {
+ width: 25px;
+ height: 25px;
+ background: url(images/border1.png) no-repeat 0 -25px;
+}
+
+#cboxBottomCenter {
+ height: 25px;
+ background: url(images/border1.png) repeat-x 0 -75px;
+}
+
+#cboxBottomRight {
+ width: 25px;
+ height: 25px;
+ background: url(images/border1.png) no-repeat -25px -25px;
+}
+
+#cboxMiddleLeft {
+ width: 25px;
+ background: url(images/border2.png) repeat-y 0 0;
+}
+
+#cboxMiddleRight {
+ width: 25px;
+ background: url(images/border2.png) repeat-y -25px 0;
+}
+
+#cboxContent {
+ background: #fff;
+ overflow: hidden;
+}
+
+.cboxIframe {
+ background: #fff;
+}
+
+#cboxError {
+ padding: 50px;
+ border: 1px solid #ccc;
+}
+
+#cboxLoadedContent {
+ margin-bottom: 20px;
+}
+
+#cboxTitle {
+ position: absolute;
+ bottom: 0px;
+ left: 0;
+ text-align: center;
+ width: 100%;
+ color: #999;
+}
+
+#cboxCurrent {
+ position: absolute;
+ bottom: 0px;
+ left: 100px;
+ color: #999;
+}
+
+#cboxLoadingOverlay {
+ background: #fff url(images/loading.gif) no-repeat 5px 5px;
+}
+
+/* these elements are buttons, and may need to have additional styles reset to avoid unwanted base styles */
+#cboxPrevious,
+#cboxNext,
+#cboxSlideshow,
+#cboxClose {
+ border: 0;
+ padding: 0;
+ margin: 0;
+ overflow: visible;
+ width: auto;
+ background: none;
+}
+
+/* avoid outlines on :active (mouseclick), but preserve outlines on :focus (tabbed navigating) */
+#cboxPrevious:active,
+#cboxNext:active,
+#cboxSlideshow:active,
+#cboxClose:active {
+ outline: 0;
+}
+
+#cboxSlideshow {
+ position: absolute;
+ bottom: 0px;
+ right: 42px;
+ color: #444;
+}
+
+#cboxPrevious {
+ position: absolute;
+ bottom: 0px;
+ left: 0;
+ color: #444;
+}
+
+#cboxNext {
+ position: absolute;
+ bottom: 0px;
+ left: 63px;
+ color: #444;
+}
+
+#cboxClose {
+ position: absolute;
+ bottom: 0;
+ right: 0;
+ display: block;
+ color: #444;
+}
+
+/*
+ The following fixes a problem where IE7 and IE8 replace a PNG's alpha transparency with a black fill
+ when an alpha filter (opacity change) is set on the element or ancestor element. This style is not applied to or needed in IE9.
+ See: http://jacklmoore.com/notes/ie-transparency-problems/
+*/
+.cboxIE #cboxTopLeft,
+.cboxIE #cboxTopCenter,
+.cboxIE #cboxTopRight,
+.cboxIE #cboxBottomLeft,
+.cboxIE #cboxBottomCenter,
+.cboxIE #cboxBottomRight,
+.cboxIE #cboxMiddleLeft,
+.cboxIE #cboxMiddleRight {
+ filter: progid:DXImageTransform.Microsoft.gradient(startColorstr=#00FFFFFF, endColorstr=#00FFFFFF);
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index e0a5ceea..9f56b63d 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -48,10 +48,10 @@ table.dataTable thead th{
}
table.dataTable thead .sorting_asc {
- background-image: url("../packages/DataTables/images/sort_asc_disabled.png");
+ background-image: url("/js/DataTables/images/sort_asc_disabled.png");
}
table.dataTable thead .sorting_desc {
- background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
+ background-image: url("/js/DataTables/images/sort_desc_disabled.png");
}
table.dataTable thead th {
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 39c6ba53..27404801 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -25,10 +25,10 @@ table.dataTable thead th, table.dataTable tfoot th{
}
table.dataTable thead .sorting_asc {
- background-image: url("../packages/DataTables/images/sort_asc_disabled.png");
+ background-image: url("/js/DataTables/images/sort_asc_disabled.png");
}
table.dataTable thead .sorting_desc {
- background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
+ background-image: url("/js/DataTables/images/sort_desc_disabled.png");
}
table.dataTable thead th, table.dataTable tfoot {
diff --git a/wqflask/wqflask/static/new/javascript/auto_hide_column.js b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
new file mode 100644
index 00000000..1a4dc039
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/auto_hide_column.js
@@ -0,0 +1,21 @@
+ function filterDatatable(datatable){
+ let invalidColumns=[]
+ let columnCount=datatable.columns().header().length;
+ let numberOfRows=datatable.rows().count();
+ for (let col=0; col<columnCount; col++){
+ colObj = datatable.column(col).nodes().to$();
+ allNAs = true;
+ for (let i=0;i<numberOfRows;i++){
+ cellContent = colObj[i].childNodes[0].data
+ if (cellContent != "N/A" && cellContent != ""){
+ allNAs = false;
+ break;
+ }
+ }
+ if (allNAs){
+ invalidColumns.push(col)
+ }
+ }
+ return datatable.columns(invalidColumns).visible(false);
+
+ } \ No newline at end of file
diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 5a6929fb..38ae834c 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -80,7 +80,7 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index c8ed6851..c0b99e75 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -2,7 +2,7 @@
{% block title %}Group Manager{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/admin/ind_user_manager.html b/wqflask/wqflask/templates/admin/ind_user_manager.html
index e859b442..b821e5d5 100644
--- a/wqflask/wqflask/templates/admin/ind_user_manager.html
+++ b/wqflask/wqflask/templates/admin/ind_user_manager.html
@@ -103,7 +103,7 @@
{% block js %}
- <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script>
<script>
$('body').timeago();
</script>
diff --git a/wqflask/wqflask/templates/admin/manage_user.html b/wqflask/wqflask/templates/admin/manage_user.html
index 7afe075f..3ef90b90 100644
--- a/wqflask/wqflask/templates/admin/manage_user.html
+++ b/wqflask/wqflask/templates/admin/manage_user.html
@@ -2,7 +2,7 @@
{% block title %}View and Edit Group{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
index f304a172..0e1ec720 100644
--- a/wqflask/wqflask/templates/admin/search_for_groups.html
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -63,7 +63,7 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html
index bc52788f..04842453 100644
--- a/wqflask/wqflask/templates/admin/set_group_privileges.html
+++ b/wqflask/wqflask/templates/admin/set_group_privileges.html
@@ -2,7 +2,7 @@
{% block title %}Set Group Privileges{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html
index 9e3cce7b..26692fe8 100644
--- a/wqflask/wqflask/templates/admin/view_group.html
+++ b/wqflask/wqflask/templates/admin/view_group.html
@@ -2,7 +2,7 @@
{% block title %}View and Edit Group{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index faa59deb..bb618294 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -17,7 +17,7 @@
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
- <link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/colorbox.css" />
<!--<link rel="stylesheet" type="text/css" href="/static/new/css/main.css" />-->
<link rel="stylesheet" type="text/css" href="/static/new/css/parsley.css" />
@@ -254,10 +254,11 @@
<script type="text/javascript" src="/static/new/js_external/json2.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.9.1/jquery-ui.min.js" type="text/javascript"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/colorbox/jquery.colorbox.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='colorbox/jquery.colorbox-min.js') }}"></script>
<!--<script type="text/javascript" src="/static/new/javascript/login.js"></script>-->
- <script type="text/javascript" src="/static/new/js_external/parsley.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/parsley.min.js') }}"></script>
+
{% block js %}
{% endblock %}
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 9e0c0f07..2ff7b2fd 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -66,10 +66,10 @@
{% endblock %}
{% block js %}
- <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.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="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.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/buttons/js/dataTables.buttons.min.js') }}"></script>
<script>
diff --git a/wqflask/wqflask/templates/collections/not_logged_in.html b/wqflask/wqflask/templates/collections/not_logged_in.html
index a4c8747e..49b0e07d 100644
--- a/wqflask/wqflask/templates/collections/not_logged_in.html
+++ b/wqflask/wqflask/templates/collections/not_logged_in.html
@@ -5,7 +5,7 @@
{{ header("Not logged in") }}
- <div id "collections_holder" class="container">
+ <div id="collections_holder" class="container">
<div class="page-header">
<h1>Please log in in order to use this feature.</h1>
</div>
@@ -16,7 +16,7 @@
{% endblock %}
{% block js %}
- <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/timeago.min.js') }}"></script>
<script>
$('body').timeago();
</script>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 50e1a792..99a6f2de 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -162,7 +162,7 @@
{% endblock %}
{% 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='jszip/jszip.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.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>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index b27a6b06..e3dd03d5 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -32,7 +32,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
- <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+ <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/comparison_bar_chart.js"></script>
{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 1133fcd2..a0436ade 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -349,11 +349,11 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
- <script language="javascript" type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jscolor/jscolor.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.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="/static/new/javascript/get_traits_from_collection.js"></script>-->
- <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+ <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 3cca7495..7acccc25 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -171,7 +171,7 @@
<script 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="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index f90ee20c..6f009183 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -64,7 +64,7 @@
gn2_url = "{{ gn2_url | safe }}"
</script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/docedit.html b/wqflask/wqflask/templates/docedit.html
index b87c5b41..50bb96c0 100644
--- a/wqflask/wqflask/templates/docedit.html
+++ b/wqflask/wqflask/templates/docedit.html
@@ -16,7 +16,7 @@
{{content|safe}}
</textarea>
<button class="submit_changes" style="margin-top: 20px;">Submit Changes</button>
- <script src="/static/packages/ckeditor/ckeditor.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='ckeditor/ckeditor.js') }}"></script>
<script type="text/javascript">
CKEDITOR.replace('ckcontent', {
height: '650px',
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index d5bc4141..6fd0abe8 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.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="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.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/colReorder/js/dataTables.colReorder.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index ccd4a9d9..0dc6fe5f 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.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="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.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/colReorder/js/dataTables.colReorder.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 70df1dde..86aa74b0 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -350,7 +350,7 @@
<script type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
<script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script>
<script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
- <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+ <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
{% if manhattan_plot == True and selectedChr == -1 %}
<script type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
{% endif %}
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 3c2ec601..2941cb80 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -139,8 +139,7 @@
elements_list = {{ elements | safe }}
gn2_url = "{{ gn2_url | safe }}"
</script>
-
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='qtip2/jquery.qtip.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index d64bb4b4..38dca514 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -64,7 +64,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.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/scientific.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 6be60f64..3be2e395 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -183,7 +183,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.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="/static/new/js_external/jszip.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.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/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>
diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/wqflask/wqflask/templates/set_group_privileges.html
index 98b0cc12..a0a53292 100644
--- a/wqflask/wqflask/templates/set_group_privileges.html
+++ b/wqflask/wqflask/templates/set_group_privileges.html
@@ -2,7 +2,7 @@
{% block title %}Set Group Privileges{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index bacab9f4..b02f8140 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -132,9 +132,9 @@
<script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
<script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
<script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script>
- <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
+ <script type="text/javascript" src="{{ url_for('js', filename='js_alt/jstat.min.js') }}"></script>
<script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
- <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
+ <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
@@ -146,9 +146,8 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/scroller.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='nouislider/nouislider.js') }}"></script>
-
<script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 4f25e90a..ba72ff27 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -38,7 +38,7 @@
</div>
<div class="form-group">
- <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+ <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
<div class="col-xs-4 controls">
<select name="corr_return_results" class="form-control">
{% for return_result in corr_tools.return_results_menu %}