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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/gemma_mapping.py8
-rw-r--r--wqflask/wqflask/static/new/css/markdown.css7
-rw-r--r--wqflask/wqflask/templates/correlation_page.html39
-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
12 files changed, 80 insertions, 39 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/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 02f91a32..61e4897c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -31,7 +31,8 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
this_chromosomes = this_dataset.species.chromosomes.chromosomes
- this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes]
+ this_chromosomes_name=[this_chromosomes[chromosome].name for chromosome in this_chromosomes]
+
chr_list_string=",".join(this_chromosomes_name)
if covariates != "":
@@ -45,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
genofile_name,
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
+
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -77,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -93,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
else:
gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename)
-
- logger.debug("gemma_command:" + gemma_command)
os.system(gemma_command)
else:
gwa_output_filename = output_files
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/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 06ee9056..68566ee5 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -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/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>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 21:07:27 +0000