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-rw-r--r--wqflask/tests/unit/wqflask/correlation/__init__.py0
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py3
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py174
3 files changed, 90 insertions, 87 deletions
diff --git a/wqflask/tests/unit/wqflask/correlation/__init__.py b/wqflask/tests/unit/wqflask/correlation/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/__init__.py
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index db449eb1..44d2e0fc 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -5,8 +5,7 @@ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_ti
class TestCorrelationFunctions(unittest.TestCase):
-
-
+
@mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
index 969a84f5..ffb96dd6 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -2,92 +2,96 @@ import unittest
from unittest import mock
from wqflask.correlation.show_corr_results import get_header_fields
from wqflask.correlation.show_corr_results import generate_corr_json
-from wqflask.correlation.show_corr_results import do_bicor
-class Trait:
- def __init__(self,trait_obj):
- for key,value in trait_obj.items():
- setattr(self,key,value)
+class AttributeSetter:
+ def __init__(self, trait_obj):
+ for key, value in trait_obj.items():
+ setattr(self, key, value)
-class TestShowCorrResults(unittest.TestCase):
- def test_get_header_fields(self):
- expected=[
- ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Sample rho',
- 'N',
- 'Sample p(rho)',
- 'Lit rho',
- 'Tissue rho',
- 'Tissue p(rho)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect'],
-
- ['Index',
- 'ID',
- 'Location',
- 'Sample r',
- 'N',
- 'Sample p(r)']
-
- ]
- result1=get_header_fields("ProbeSet","spearman")
- result2=get_header_fields("Other","Other")
- self.assertEqual(result1,expected[0])
- self.assertEqual(result2,expected[1])
-
-
-
-
- def test_generate_corr_json(self):
- this_trait=Trait({"name":"trait_test"})
- dataset=Trait({"name":"the_name"})
- target_dataset=Trait({"type":"Publish"})
-
- trait_with_publish={
- "description_display":"Trait 2 description",
- "authors":"trait_2 ",
- "pubmed_id":"34n4nn31hn43",
- "lrs_location":"N/A",
- "additive":"",
- "sample_r":100,
- "num_overlap":3.2,
- "view":True,
- "name":"trait_1",
- "pubmed_text":"2016",
- "additive":"",
- "sample_r":10.5,
- "LRS_score_repr":"N/A",
- "LRS_location_repr":"N/A",
- "sample_p":5,
- "num_overlap":"num_1"
-
-
-
- }
- expected_results="""[{"trait_id": "trait_1", "description": "Trait 2 description", "authors": "trait_2 ", "pubmed_id": "34n4nn31hn43", "year": "2016", "lrs_score": "N/A", "lrs_location": "N/A", "additive": "N/A", "sample_r": "10.500", "num_overlap": "num_1", "sample_p": "5.000e+00"}]"""
-
- corr_results=[Trait(trait_with_publish)]
- results=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset=dataset,target_dataset=target_dataset,for_api=True)
- self.assertEqual(results,expected_results)
-
-
-
- def test_generate_corr_json_view_false(self):
- trait=Trait({"view":False})
- corr_results=[trait]
- this_trait=Trait({"name":"trait_test"})
- dataset=Trait({"name":"the_name"})
-
-
- results_where_view_is_false=generate_corr_json(corr_results=corr_results,this_trait=this_trait,dataset={},target_dataset={},for_api=False)
-
- # self.assertEqual(results,[])
- self.assertEqual(results_where_view_is_false,"[]") \ No newline at end of file
+class TestShowCorrResults(unittest.TestCase):
+ def test_get_header_fields(self):
+ expected = [
+ ['Index',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect'],
+
+ ['Index',
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
+
+ ]
+ result1 = get_header_fields("ProbeSet", "spearman")
+ result2 = get_header_fields("Other", "Other")
+ self.assertEqual(result1, expected[0])
+ self.assertEqual(result2, expected[1])
+
+ @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac")
+ def test_generate_corr_json(self, mock_data_hmac):
+ mock_data_hmac.return_value = "hajsdiau"
+
+ dataset = AttributeSetter({"name": "the_name"})
+ this_trait = AttributeSetter(
+ {"name": "trait_test", "dataset": dataset})
+ target_dataset = AttributeSetter({"type": "Publish"})
+ corr_trait_1 = AttributeSetter({
+ "name": "trait_1",
+ "dataset": AttributeSetter({"name": "dataset_1"}),
+ "view": True,
+ "abbreviation": "T1",
+ "description_display": "Trait I description",
+ "authors": "JM J,JYEW",
+ "pubmed_id": "34n4nn31hn43",
+ "pubmed_text": "2016",
+ "pubmed_link": "https://www.load",
+ "lod_score": "",
+ "LRS_location_repr": "BXBS",
+ "additive": "",
+ "sample_r": 10.5,
+ "num_overlap": 2,
+ "sample_p": 5
+
+
+
+
+ })
+ corr_results = [corr_trait_1]
+
+ dataset_type_other = {
+ "location": "cx-3-4",
+ "sample_4": 12.32,
+ "num_overlap": 3,
+ "sample_p": 10.34
+ }
+
+ expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]'
+
+ results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait,
+ dataset=dataset, target_dataset=target_dataset, for_api=True)
+ self.assertEqual(expected_results, results1)
+
+ def test_generate_corr_json_view_false(self):
+ trait = AttributeSetter({"view": False})
+ corr_results = [trait]
+ this_trait = AttributeSetter({"name": "trait_test"})
+ dataset = AttributeSetter({"name": "the_name"})
+
+ results_where_view_is_false = generate_corr_json(
+ corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False)
+ self.assertEqual(results_where_view_is_false, "[]")