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-rw-r--r--wqflask/base/trait.py22
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py8
-rw-r--r--wqflask/wqflask/static/new/css/colorbox.css238
-rw-r--r--wqflask/wqflask/templates/base.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/correlation_matrix.html2
-rw-r--r--wqflask/wqflask/templates/correlation_page.html41
-rw-r--r--wqflask/wqflask/templates/ctl_results.html8
-rw-r--r--wqflask/wqflask/templates/heatmap.html2
-rw-r--r--wqflask/wqflask/templates/mapping_results.html9
-rw-r--r--wqflask/wqflask/templates/network_graph.html8
-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/show_trait.html37
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html30
16 files changed, 369 insertions, 48 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ec8c40a0..50bd8874 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -25,19 +25,19 @@ def create_trait(**kw):
assert bool(kw.get('dataset')) != bool(
kw.get('dataset_name')), "Needs dataset ob. or name"
- if kw.get('name'):
- if kw.get('dataset_name'):
- if kw.get('dataset_name') != "Temp":
- dataset = create_dataset(kw.get('dataset_name'))
- else:
- dataset = kw.get('dataset')
+ assert bool(kw.get('name')), "Needs trait name"
+ if kw.get('dataset_name'):
if kw.get('dataset_name') != "Temp":
- if dataset.type == 'Publish':
- permissions = check_resource_availability(
- dataset, kw.get('name'))
- else:
- permissions = check_resource_availability(dataset)
+ dataset = create_dataset(kw.get('dataset_name'))
+ else:
+ dataset = kw.get('dataset')
+
+ if dataset.type == 'Publish':
+ permissions = check_resource_availability(
+ dataset, kw.get('name'))
+ else:
+ permissions = check_resource_availability(dataset)
if "view" in permissions['data']:
the_trait = GeneralTrait(**kw)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c474e0e0..891fcc66 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -426,6 +426,8 @@ class RunMapping(object):
marker['display_pos'] = "N/A"
self.qtl_results.append(marker)
+ total_markers = len(self.qtl_results)
+
with Bench("Exporting Results"):
export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
@@ -489,13 +491,15 @@ class RunMapping(object):
perm_results = self.perm_output,
significant = significant_for_browser,
browser_files = browser_files,
- selected_chr = this_chr
+ selected_chr = this_chr,
+ total_markers = total_markers
)
else:
self.js_data = dict(
chr_lengths = chr_lengths,
browser_files = browser_files,
- selected_chr = this_chr
+ selected_chr = this_chr,
+ total_markers = total_markers
)
def run_rqtl_plink(self):
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/templates/base.html b/wqflask/wqflask/templates/base.html
index faa59deb..95a2c39e 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" />
@@ -254,7 +254,7 @@
<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>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ccec495b..50e1a792 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -44,7 +44,7 @@
GeneWeaver
</button>
- <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+ <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
BNW
</button>
diff --git a/wqflask/wqflask/templates/comparison_bar_chart.html b/wqflask/wqflask/templates/comparison_bar_chart.html
index f791457f..b27a6b06 100644
--- a/wqflask/wqflask/templates/comparison_bar_chart.html
+++ b/wqflask/wqflask/templates/comparison_bar_chart.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Comparison Bar Chart{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
{% endblock %}
{% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 4e150618..96ad9c35 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -4,7 +4,7 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..3cca7495 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -49,7 +49,7 @@
GeneWeaver
</button>
- <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+ <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
BNW
</button>
@@ -345,8 +345,15 @@
'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
'type': "natural-minus-na",
'width': "40px",
- 'data': "sample_r",
- 'orderSequence': [ "desc", "asc"]
+ 'data': null,
+ 'orderSequence': [ "desc", "asc"],
+ 'render': function(data, type, row, meta) {
+ if (data.sample_r != "N/A") {
+ return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+ } else {
+ return data.sample_r
+ }
+ }
},
{
'title': "N",
@@ -357,7 +364,7 @@
},
{
'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
- 'type': "natural-minus-na",
+ 'type': "scientific",
'width': "65px",
'data': "sample_p",
'orderSequence': [ "desc", "asc"]
@@ -459,8 +466,15 @@
'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
'type': "natural-minus-na",
'width': "40px",
- 'data': "sample_r",
- 'orderSequence': [ "desc", "asc"]
+ 'data': null,
+ 'orderSequence': [ "desc", "asc"],
+ 'render': function(data, type, row, meta) {
+ if (data.sample_r != "N/A") {
+ return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+ } else {
+ return data.sample_r
+ }
+ }
},
{
'title': "N",
@@ -471,7 +485,7 @@
},
{
'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
- 'type': "natural-minus-na",
+ 'type': "scientific",
'width': "65px",
'data': "sample_p",
'orderSequence': [ "desc", "asc"]
@@ -506,8 +520,15 @@
'title': "Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}",
'type': "natural-minus-na",
'width': "40px",
- 'data': "sample_r",
- 'orderSequence': [ "desc", "asc"]
+ 'data': null,
+ 'orderSequence': [ "desc", "asc"],
+ 'render': function(data, type, row, meta) {
+ if (data.sample_r != "N/A") {
+ return "<a target\"_blank\" href=\"corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2=" + data.dataset + "&trait_1={{ this_trait.name }}&trait_2=" + data.trait_id + "\">" + data.sample_r + "</a>"
+ } else {
+ return data.sample_r
+ }
+ }
},
{
'title': "N",
@@ -518,7 +539,7 @@
},
{
'title': "Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})",
- 'type': "natural-minus-na",
+ 'type': "scientific",
'width': "65px",
'data': "sample_p",
'orderSequence': [ "desc", "asc"]
diff --git a/wqflask/wqflask/templates/ctl_results.html b/wqflask/wqflask/templates/ctl_results.html
index 5b8a4cc2..6f009183 100644
--- a/wqflask/wqflask/templates/ctl_results.html
+++ b/wqflask/wqflask/templates/ctl_results.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
- <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}">
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
<style>
/* The Cytoscape Web container must have its dimensions set. */
@@ -67,10 +67,10 @@
<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="/js/cytoscape/cytoscape.min.js"></script>
- <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script>
<!-- should be using cytoscape-popper for tips, see docs -->
- <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script>
<!--
Loads flash - who wants that?
diff --git a/wqflask/wqflask/templates/heatmap.html b/wqflask/wqflask/templates/heatmap.html
index 497838dd..b16de42e 100644
--- a/wqflask/wqflask/templates/heatmap.html
+++ b/wqflask/wqflask/templates/heatmap.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Heatmap{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
{% endblock %}
{% block content %} <!-- Start of body -->
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9542c29d..70df1dde 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -4,7 +4,7 @@
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
- <link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='purescript-genome-browser/css/purescript-genetics-browser.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" />
@@ -359,7 +359,7 @@
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.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="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script>
<script>
js_data = {{ js_data | safe }}
@@ -388,8 +388,11 @@
"targets": 0,
"orderable": false
} ],
+ "language": {
+ "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records",
+ },
"order": [[1, "asc" ]],
- "sDom": "RZtir",
+ "sDom": "iRZtir",
"iDisplayLength": -1,
"autoWidth": false,
"deferRender": true,
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 06937293..2941cb80 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block css %}
<link rel="stylesheet" type="text/css" href="/static/new/css/network_graph.css" />
- <link rel="stylesheet" type="text/css" href="/js/cytoscape-panzoom/cytoscape.js-panzoom.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='cytoscape-panzoom/cytoscape.js-panzoom.css') }}">
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='qtip2/jquery.qtip.min.css') }}">
<style>
/* The Cytoscape Web container must have its dimensions set. */
@@ -143,10 +143,10 @@
<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="/js/cytoscape/cytoscape.min.js"></script>
- <script language="javascript" type="text/javascript" src="/js/cytoscape-panzoom/cytoscape-panzoom.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape/cytoscape.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-panzoom/cytoscape-panzoom.js') }}"></script>
<!-- should be using cytoscape-popper for tips, see docs -->
- <script language="javascript" type="text/javascript" src="/js/cytoscape-qtip/cytoscape-qtip.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='cytoscape-qtip/cytoscape-qtip.js') }}"></script>
<!--
Loads flash - who wants that?
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index a706403b..38dca514 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -4,7 +4,7 @@
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
{% endblock %}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 87c97c50..6be60f64 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -92,7 +92,7 @@
GeneWeaver
</button>
- <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian Network" >
+ <button id="send_to_bnw" class="btn btn-primary submit_special" data-url="/bnw_page" title="Bayesian network software for causal modeling and reasoning, with an intuitive interface to incorporate biological knowledge and a complete pipeline from data to model to prediction" >
BNW
</button>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 25aa6230..7c32fe55 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -5,10 +5,9 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/box_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='d3-tip/d3-tip.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/noUiSlider/nouislider.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='nouislider/nouislider.min.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
@@ -147,9 +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 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="/static/new/packages/noUiSlider/nouislider.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>
@@ -221,6 +219,33 @@
primary_table.search($(this).val()).draw();
} );
+ $('.toggle-vis').on('click', function (e) {
+ e.preventDefault();
+
+ function toggle_column(column) {
+ //ZS: Toggle column visibility
+ column.visible( ! column.visible() );
+ if (column.visible()){
+ $(this).removeClass("active");
+ } else {
+ $(this).addClass("active");
+ }
+ }
+
+ // Get the column API object
+ var target_cols = $(this).attr('data-column').split(",")
+ for (let i = 0; i < target_cols.length; i++){
+ console.log("THE COL:", target_cols[i])
+ var column = primary_table.column( target_cols[i] );
+ toggle_column(column);
+
+ {% if sample_groups|length != 1 %}
+ var column2 = other_table.column( target_cols[i] );
+ toggle_column(column2);
+ {% endif %}
+ }
+ } );
+
{% if sample_groups|length != 1 %}
$('#other_searchbox').on( 'keyup', function () {
other_table.search($(this).val()).draw();
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 2e730248..4ad11a5e 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,36 @@
<div>
{% for sample_type in sample_groups %}
<div class="sample-table-container">
+ {% if loop.index == 1 %}
+ <b>Show/Hide Columns:</b>
+ <br>
+ <button class="toggle-vis" data-column="1">ID</button>
+ <button class="toggle-vis" data-column="2">Sample</button>
+ <button class="toggle-vis" data-column="3">Value</button>
+ {% if sample_groups[0].se_exists %}
+ <button class="toggle-vis" data-column="4,5">SE</button>
+ {% if has_num_cases %}
+ <button class="toggle-vis" data-column="6">N</button>
+ {% set attr_start_pos = 7 %}
+ {% else %}
+ {% set attr_start_pos = 6 %}
+ {% endif %}
+ {% else %}
+ {% if has_num_cases %}
+ <button class="toggle-vis" data-column="4">N</button>
+ {% set attr_start_pos = 5 %}
+ {% else %}
+ {% set attr_start_pos = 4 %}
+ {% endif %}
+ {% endif %}
+ {% if sample_groups[0].attributes %}
+ {% for attribute in sample_groups[0].attributes %}
+ <button class="toggle-vis" data-column="{{ loop.index + attr_start_pos - 1 }}">{{ sample_groups[0].attributes[attribute].name }}</button>
+ {% endfor %}
+ {% endif %}
+ <br>
+ <br>
+ {% endif %}
<div class="sample-table-search-container">
<input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control sample-table-search" placeholder="Search This Table For ...">
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 01:15:03 +0000