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authorAlexanderlacuna2020-11-28 15:00:00 +0300
committerBonfaceKilz2021-01-06 01:26:38 +0300
commit3eda2b13e10937cbd661d6d411286c5b84bcd7cf (patch)
tree92423017e03d089b30adfe1f9f3ed7c21dd28cdd
parentdf2c3f9ee43dd055f7766eedee32d76090ad80b2 (diff)
downloadgenenetwork2-3eda2b13e10937cbd661d6d411286c5b84bcd7cf.tar.gz
add correlation test
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py21
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py95
2 files changed, 116 insertions, 0 deletions
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
new file mode 100644
index 00000000..db449eb1
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -0,0 +1,21 @@
+import unittest
+from unittest import mock
+from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values
+from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+
+
+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"""
+ mock_class_instance = mock_class.return_value
+ mock_class_instance.gene_symbols = ["k1", "k2", "k3"]
+ mock_class_instance.get_symbol_values_pairs.return_value = {
+ "k1": ["v1", "v2", "v3"], "k2": ["v2", "v3"], "k3": ["k3"]}
+ results = get_trait_symbol_and_tissue_values(
+ symbol_list=["k1", "k2", "k3"])
+ mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3'])
+ self.assertEqual({"k1": ["v1", "v2", "v3"], "k2": [
+ "v2", "v3"], "k3": ["k3"]}, results)
diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
new file mode 100644
index 00000000..4e63207e
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py
@@ -0,0 +1,95 @@
+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 TestShowCorrResults(unittest.TestCase):
+
+ def test_process_samples(self):
+ pass
+ 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