From a865a2d490722e866c847a996439ed31253fea8a Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Sun, 6 Dec 2020 15:03:27 +0300
Subject: Add svg graph of inputs

* wqflask/wqflask/markdown_routes.py: New import:
"send_from_directory"
(svg_graph): New function that adds route for svg_graph.
* wqflask/wqflask/static/new/css/markdown.css: New style rules for svg
graph.
* wqflask/wqflask/templates/environment.html: Add new section for
displaying svg graph.
---
 wqflask/wqflask/markdown_routes.py          | 8 ++++++++
 wqflask/wqflask/static/new/css/markdown.css | 7 ++++++-
 wqflask/wqflask/templates/environment.html  | 7 +++++++
 3 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py
index 3b60bc96..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(
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..85133ac3 100644
--- a/wqflask/wqflask/templates/environment.html
+++ b/wqflask/wqflask/templates/environment.html
@@ -21,6 +21,13 @@
 </div>
 
 <div id="guix-graph"></div>
+
+<!-- Display the svg graph -->
+
+<div id="guix-svg-graph">
+    <h1>The dependency graph is shown below</h1>
+    <img alt="Dependency graph of the tools needed to build python3-genenetwork2" src="{{url_for('environments_blueprint.svg_graph')}}"/>
+</div>
 {% endif %}
 
 {% endblock %}
-- 
cgit v1.2.3


From efb6a41e7d712407f276e21f9ede3198d7e734dc Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sat, 5 Dec 2020 13:35:43 +0300
Subject: modify tests for run_gemma

---
 .../unit/wqflask/marker_regression/test_gemma_mapping.py      | 11 +++++------
 1 file changed, 5 insertions(+), 6 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..3d00dd7c 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -43,18 +43,18 @@ 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}"}))
+        chromo = AttributeSetter({"chromosomes": this_chromosomes})
+
         dataset_group = MockGroup(
             {"name": "GP1", "genofile": "file_geno"})
         dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name",
@@ -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"))
 
-- 
cgit v1.2.3


From 7e0f91dec563f08671c772e34b85e0edc14195cb Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sat, 5 Dec 2020 13:43:23 +0300
Subject: add pep8 formatting

---
 wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py | 4 ++--
 1 file changed, 2 insertions(+), 2 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 3d00dd7c..b8c13ab4 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -53,12 +53,12 @@ class TestGemmaMapping(unittest.TestCase):
         this_chromosomes={}
         for i in range(1, 5):
             this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
-        chromo = AttributeSetter({"chromosomes": this_chromosomes})
+        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
-- 
cgit v1.2.3


From 7a35308b11a004f1c0899bdb2a2b982597869808 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Sun, 6 Dec 2020 19:33:33 +0300
Subject: Add descriptive paragraph for svg graph

* wqflask/wqflask/templates/environment.html: New paragraph.
---
 wqflask/wqflask/templates/environment.html | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/wqflask/wqflask/templates/environment.html b/wqflask/wqflask/templates/environment.html
index 85133ac3..89e805ce 100644
--- a/wqflask/wqflask/templates/environment.html
+++ b/wqflask/wqflask/templates/environment.html
@@ -26,6 +26,9 @@
 
 <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 %}
-- 
cgit v1.2.3