Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

9 files changed, 36 insertions, 14 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/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>