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-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/static/new/css/markdown.css7
-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/set_group_privileges.html2
-rw-r--r--wqflask/wqflask/templates/admin/view_group.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/links.html2
-rw-r--r--wqflask/wqflask/templates/policies.html2
-rw-r--r--wqflask/wqflask/templates/references.html2
-rw-r--r--wqflask/wqflask/templates/set_group_privileges.html2
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
15 files changed, 42 insertions, 20 deletions
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/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/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/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/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/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/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/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..25aa6230 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -147,7 +147,7 @@
<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="/static/new/packages/noUiSlider/nouislider.js"></script>
<script type="text/javascript" src="/static/new/javascript/initialize_show_trait_tables.js"></script>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:56:30 +0000