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-rw-r--r--wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py78
1 files changed, 38 insertions, 40 deletions
diff --git a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
index 41761944..6dbdf4fc 100644
--- a/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
+++ b/wqflask/tests/unit/wqflask/show_trait/test_export_trait_data.py
@@ -1,3 +1,4 @@
+import datetime
import unittest
from unittest import mock
from wqflask.show_trait.export_trait_data import dict_to_sorted_list
@@ -13,56 +14,53 @@ class AttributesSetter:
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)
+ """Test methods for exporting traits and metadata"""
+ @mock.patch("wqflask.show_trait.export_trait_data.datetime")
@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):
+ def test_get_export_metadata(self, data_mock, trait_mock,date_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_dataset = AttributesSetter({"type": "Publish", "name": "HC_M2_0606_P",
+ "dataset_name": "HC_M2_0606_P"})
+
+ mock_dataset.group = AttributesSetter({"name": "C"})
+ data_mock.create_dataset.return_value = mock_dataset
+
+ trait_data = {
+ "symbol": "Nr3c1",
+ "description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR",
+ "title": "Trait_1 title",
+
+ "authors": "XL_1",
+ "journal": ""
+
+ }
+
+ date_mock.datetime.now.return_value = datetime.datetime(2022, 8, 8, 19, 2, 31, 628813)
+ trait_mock.return_value = AttributesSetter(trait_data)
- 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({
+ "trait_id": "1460303_at",
+ "trait_display_name": "1460303_at",
+ "dataset": "HC_M2_0606_P"
+ })
- 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'], []]
+ expected = [["Phenotype ID:", "1460303_at"],
+ ["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"],
+ ["Group: ", "C"],
+ ["Phenotype: ", 'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'],
+ ["Authors: ", "XL_1"],
+ ["Title: ", "Trait_1 title"],
+ ["Journal: ", "N/A"],
+ ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"],
+ ["Export Date: ", "August 08, 2022"],
+ ["Export Time: ","19:02 GMT"], []]
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):