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-rw-r--r--wqflask/base/trait.py22
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py13
-rw-r--r--wqflask/wqflask/markdown_routes.py10
-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/static/new/css/markdown.css7
-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/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.html4
-rw-r--r--wqflask/wqflask/templates/collections/list.html2
-rw-r--r--wqflask/wqflask/templates/collections/view.html4
-rw-r--r--wqflask/wqflask/templates/comparison_bar_chart.html4
-rw-r--r--wqflask/wqflask/templates/corr_scatterplot.html4
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html2
-rw-r--r--wqflask/wqflask/templates/correlation_page.html43
-rw-r--r--wqflask/wqflask/templates/ctl_results.html10
-rw-r--r--wqflask/wqflask/templates/docedit.html2
-rw-r--r--wqflask/wqflask/templates/environment.html10
-rw-r--r--wqflask/wqflask/templates/facilities.html2
-rw-r--r--wqflask/wqflask/templates/glossary.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/heatmap.html2
-rw-r--r--wqflask/wqflask/templates/links.html2
-rw-r--r--wqflask/wqflask/templates/mapping_results.html11
-rw-r--r--wqflask/wqflask/templates/network_graph.html11
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html4
-rw-r--r--wqflask/wqflask/templates/policies.html2
-rw-r--r--wqflask/wqflask/templates/references.html2
-rw-r--r--wqflask/wqflask/templates/search_result_page.html4
-rw-r--r--wqflask/wqflask/templates/set_group_privileges.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html39
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html30
37 files changed, 427 insertions, 85 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/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 5b621264..b8c13ab4 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -43,22 +43,22 @@ class TestGemmaMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc")
@mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/")
@mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output")
- @mock.patch("wqflask.marker_regression.gemma_mapping.logger")
@mock.patch("wqflask.marker_regression.gemma_mapping.flat_files")
@mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file")
@mock.patch("wqflask.marker_regression.run_mapping.random.choice")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")
@mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
- def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco):
+ def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco):
"""add tests for run_gemma where first run is set to true"""
- chromosomes = []
+ this_chromosomes={}
for i in range(1, 5):
- chromosomes.append(AttributeSetter({"name": f"CH{i}"}))
- chromo = AttributeSetter({"chromosomes": chromosomes})
+ this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+ chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
+
dataset_group = MockGroup(
{"name": "GP1", "genofile": "file_geno"})
dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name",
- "species": AttributeSetter({"chromosomes": chromo})})
+ "species": AttributeSetter({"chromosomes": chromosomes})})
trait = AttributeSetter({"name": "trait1"})
samples = []
mock_gen_pheno_txt.return_value = None
@@ -76,7 +76,6 @@ class TestGemmaMapping(unittest.TestCase):
mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR")
mock_os.path.isfile.assert_called_once_with(
('/home/user/imgfile_output.assoc.txt'))
- self.assertEqual(mock_logger.debug.call_count, 2)
self.assertEqual(mock_flat_files.call_count, 4)
self.assertEqual(results, ([], "GP1_GWA_RRRRRR"))
diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py
index 183f4caa..ebf75807 100644
--- a/wqflask/wqflask/markdown_routes.py
+++ b/wqflask/wqflask/markdown_routes.py
@@ -9,6 +9,7 @@ import sys
from bs4 import BeautifulSoup
+from flask import send_from_directory
from flask import Blueprint
from flask import render_template
@@ -99,6 +100,13 @@ def environments():
200)
+@environments_blueprint.route('/svg-dependency-graph')
+def svg_graph():
+ directory, file_name, _ = get_file_from_python_search_path(
+ "wqflask/dependency-graph.svg").partition("dependency-graph.svg")
+ return send_from_directory(directory, file_name)
+
+
@links_blueprint.route("/")
def links():
return render_template(
@@ -109,7 +117,7 @@ def links():
@policies_blueprint.route("/")
def policies():
return render_template(
- "links.html",
+ "policies.html",
rendered_markdown=render_markdown("general/policies/policies.md")), 200
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/static/new/css/markdown.css b/wqflask/wqflask/static/new/css/markdown.css
index 38d664e2..859fe7fc 100644
--- a/wqflask/wqflask/static/new/css/markdown.css
+++ b/wqflask/wqflask/static/new/css/markdown.css
@@ -62,7 +62,8 @@
}
.graph-legend,
-#guix-graph {
+#guix-graph,
+#guix-svg-graph{
width: 90%;
margin: 10px auto;
}
@@ -71,6 +72,10 @@
border: solid 2px black;
}
+#guix-svg-graph img {
+ width: 100%;
+}
+
#markdown table {
width: 100%;
}
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/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..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/list.html b/wqflask/wqflask/templates/collections/list.html
index 9e0c0f07..b04672ec 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -69,7 +69,7 @@
<script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.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/view.html b/wqflask/wqflask/templates/collections/view.html
index ccec495b..99a6f2de 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>
@@ -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 f791457f..e3dd03d5 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 -->
@@ -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_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..7acccc25 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>
@@ -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>
@@ -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 e374eb4e..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. */
@@ -64,13 +64,13 @@
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="/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/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/environment.html b/wqflask/wqflask/templates/environment.html
index 5fe01dad..89e805ce 100644
--- a/wqflask/wqflask/templates/environment.html
+++ b/wqflask/wqflask/templates/environment.html
@@ -21,6 +21,16 @@
</div>
<div id="guix-graph"></div>
+
+<!-- Display the svg graph -->
+
+<div id="guix-svg-graph">
+ <h1>The dependency graph is shown below</h1>
+
+ <p>To explore this image SVG you may want to open it in new browser page and zoom in. Or use an SVG viewing application.</p>
+
+ <img alt="Dependency graph of the tools needed to build python3-genenetwork2" src="{{url_for('environments_blueprint.svg_graph')}}"/>
+</div>
{% endif %}
{% endblock %}
diff --git a/wqflask/wqflask/templates/facilities.html b/wqflask/wqflask/templates/facilities.html
index a022b657..56b127f9 100644
--- a/wqflask/wqflask/templates/facilities.html
+++ b/wqflask/wqflask/templates/facilities.html
@@ -10,7 +10,7 @@
<div class="github-btn-container">
<div class="github-btn">
- <a href="https://github.com/genenetwork/gn-docs">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/help/facilities.md">
Edit Text
<img src="/static/images/edit.png">
</a>
diff --git a/wqflask/wqflask/templates/glossary.html b/wqflask/wqflask/templates/glossary.html
index 752c4b12..aaee7c5a 100644
--- a/wqflask/wqflask/templates/glossary.html
+++ b/wqflask/wqflask/templates/glossary.html
@@ -10,7 +10,7 @@
<div class="github-btn-container">
<div class="github-btn">
- <a href="https://github.com/genenetwork/gn-docs">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/glossary/glossary.md">
Edit Text
<img src="/static/images/edit.png">
</a>
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/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/links.html b/wqflask/wqflask/templates/links.html
index 072e8429..6e91adae 100644
--- a/wqflask/wqflask/templates/links.html
+++ b/wqflask/wqflask/templates/links.html
@@ -10,7 +10,7 @@
<div class="github-btn-container">
<div class="github-btn ">
- <a href="https://github.com/genenetwork/gn-docs">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/links/links.md">
Edit Text
<img src="/static/images/edit.png">
</a>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 9542c29d..86aa74b0 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" />
@@ -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 %}
@@ -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 be3d0402..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. */
@@ -139,15 +139,14 @@
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>
- <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 f1646af7..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 %}
@@ -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/policies.html b/wqflask/wqflask/templates/policies.html
index 4e0985d3..e36c9e08 100644
--- a/wqflask/wqflask/templates/policies.html
+++ b/wqflask/wqflask/templates/policies.html
@@ -10,7 +10,7 @@
<div class="github-btn-container">
<div class="github-btn ">
- <a href="https://github.com/genenetwork/gn-docs">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/policies/policies.md">
Edit Text
<img src="/static/images/edit.png">
</a>
diff --git a/wqflask/wqflask/templates/references.html b/wqflask/wqflask/templates/references.html
index f723a1e8..04e60361 100644
--- a/wqflask/wqflask/templates/references.html
+++ b/wqflask/wqflask/templates/references.html
@@ -6,7 +6,7 @@
{% block content %}
<div class="github-btn-container">
<div class="github-btn">
- <a href="https://github.com/genenetwork/gn-docs">
+ <a href="https://github.com/genenetwork/gn-docs/blob/master/general/references/references.md">
Edit Text
<img src="/static/images/edit.png">
</a>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 87c97c50..3be2e395 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>
@@ -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 7b74a3f6..9fd75d16 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 %}
@@ -135,7 +134,7 @@
<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="/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>
@@ -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 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="/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>