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authorBonfaceKilz2020-11-01 13:47:59 +0300
committerGitHub2020-11-01 13:47:59 +0300
commite7045f0219b900eb0d273998bef9a3a550ea8bc5 (patch)
treeaf2f88b9dbda3ff1f633e9829d1d981fee6431f2
parent76468de9d58905e06cb502001470c76918ad6758 (diff)
parent7e2b60d734b426b71f658684b4347d1d7d2ba209 (diff)
downloadgenenetwork2-e7045f0219b900eb0d273998bef9a3a550ea8bc5.tar.gz
Merge pull request #472 from Alexanderlacuna/test-branch
Adding more Test for show_trait module
-rw-r--r--wqflask/tests/wqflask/show_trait/test_export_trait_data.py118
1 files changed, 118 insertions, 0 deletions
diff --git a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py
index 98d599b1..41761944 100644
--- a/wqflask/tests/wqflask/show_trait/test_export_trait_data.py
+++ b/wqflask/tests/wqflask/show_trait/test_export_trait_data.py
@@ -1,10 +1,128 @@
import unittest
+from unittest import mock
from wqflask.show_trait.export_trait_data import dict_to_sorted_list
from wqflask.show_trait.export_trait_data import cmp_samples
+from wqflask.show_trait.export_trait_data import export_sample_table
+from wqflask.show_trait.export_trait_data import get_export_metadata
+
+
+class AttributesSetter:
+ def __init__(self, obj):
+ for key, value in obj.items():
+ setattr(self, key, value)
class TestExportTraits(unittest.TestCase):
"""Test methods related to converting dict to sortedlist"""
+ @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
+ @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+ def test_get_export_metadata_no_publish(self, mock_dataset, mock_trait):
+ """test for exporting metadata with no publish"""
+ mock_dataset_attributes = AttributesSetter(
+ {"type": "no_publish", "dataset_name": "Temp", "name": "Temp"})
+
+ mock_nested_attributes = AttributesSetter({"name": "name"})
+ mock_dataset_attributes.group = mock_nested_attributes
+ mock_dataset.create_dataset.return_value = mock_dataset_attributes
+ mock_trait.return_value = AttributesSetter({"symbol": "", "description_display": "Description",
+ "title": "research1", "journal": "", "authors": ""})
+
+ results = get_export_metadata("random_id", "Temp")
+ expected = [["Record ID: random_id"],
+ ["Trait URL: http://genenetwork.org/show_trait?trait_id=random_id&dataset=Temp"],
+ ["Dataset: Temp"],
+ ["Group: name"], []]
+
+ mock_dataset.create_dataset.assert_called_with("Temp")
+ mock_trait.assert_called_with(
+ dataset=mock_dataset_attributes, name="random_id", cellid=None, get_qtl_info=False)
+ self.assertEqual(results, expected)
+
+ @mock.patch("wqflask.show_trait.export_trait_data.create_trait")
+ @mock.patch("wqflask.show_trait.export_trait_data.data_set")
+ def test_get_export_metadata_with_publish(self, data_mock, trait_mock):
+ """test for exporting metadata with dataset.type=Publish"""
+ mock_dataset_attributes = AttributesSetter({"type": "Publish", "dataset_name": "Temp",
+ "name": "Temp", "description_display": "Description goes here"})
+
+ mock_nested_attributes = AttributesSetter({"name": "name"})
+ mock_dataset_attributes.group = mock_nested_attributes
+ data_mock.create_dataset.return_value = mock_dataset_attributes
+ trait_instance = AttributesSetter({"symbol": "", "description_display": "Description",
+ "title": "research1", "journal": "", "authors": ""})
+ trait_mock.return_value = trait_instance
+
+ results = get_export_metadata(
+ "29ae0615-0d77-4814-97c7-c9e91f6bfd7b", "Temp")
+
+ expected = [['Phenotype ID: 29ae0615-0d77-4814-97c7-c9e91f6bfd7b'],
+ ['Phenotype URL: http://genenetwork.org/show_trait?trait_id=29ae0615-0d77-4814-97c7-c9e91f6bfd7b&dataset=Temp'], [
+ 'Group: name'], ['Phenotype: Description'],
+ ['Authors: N/A'], ['Title: research1'],
+ ['Journal: N/A'], ['Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=Temp'], []]
+
+ self.assertEqual(results, expected)
+
+ @mock.patch("wqflask.show_trait.export_trait_data.dict_to_sorted_list")
+ @mock.patch("wqflask.show_trait.export_trait_data.get_export_metadata")
+ def test_export_sample_table(self, exp_metadata, dict_list):
+ """test for exporting sample table"""
+ targs_obj = {
+ "export_data": """{
+ "primary_samples": [
+ {
+ "other": "germanotta",
+ "name": "Sauroniops",
+ "se":{
+ "name":"S2"
+ },
+ "num_cases":{
+ "k1":"value"
+
+ }
+ }
+ ],
+ "other_samples": [
+ {
+ "se": 1,
+ "num_cases": 4,
+ "value": 6,
+ "name": 3
+ }
+ ]
+ }""",
+ "trait_display_name": "Hair_color",
+ "trait_id": "23177fdc-312e-4084-ad0c-f3eae785fff5",
+ "dataset": {
+ }
+ }
+ exp_metadata.return_value = [
+ ["Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f"], ['Group:gp1'],
+ ["Phenotype:p1"], [
+ "Authors:N/A"],
+ ["Title:research1"],
+ ["Journal:N/A"],
+ ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1"], []]
+ expected = ('Hair_color',
+ [['Phenotype ID:0a2be192-57f5-400b-bbbd-0cf50135995f'],
+ ['Group:gp1'],
+ ['Phenotype:p1'],
+ ['Authors:N/A'],
+ ['Title:research1'],
+ ['Journal:N/A'],
+ ['Dataset Link: '
+ 'http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=name1'],
+ [],
+ ['Name', 'Value', 'SE', 'N'],
+ ['Sauroniops', 'germanotta'],
+ [3, 6, 1, 4]])
+
+ dict_list.side_effect = [['Sauroniops', 'germanotta'], [3, 6, 1, 4]]
+
+ self.assertEqual(export_sample_table(targs_obj), expected)
+ exp_metadata.assert_called_with(
+ "23177fdc-312e-4084-ad0c-f3eae785fff5", {})
+ self.assertEqual(dict_list.call_count, 2)
def test_dict_to_sortedlist(self):
"""test for conversion of dict to sorted list"""