Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/add-glossary-page

1 files changed, 242 insertions, 0 deletions

diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
new file mode 100644
index 00000000..24150738
--- /dev/null
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -0,0 +1,242 @@
+"""test for wqflask/show_trait/test_show_trait.py"""
+import unittest
+from unittest import mock
+from wqflask import app
+from wqflask.show_trait.show_trait import check_if_attr_exists
+from wqflask.show_trait.show_trait import get_ncbi_summary
+from wqflask.show_trait.show_trait import has_num_cases
+from wqflask.show_trait.show_trait import get_table_widths
+from wqflask.show_trait.show_trait import get_categorical_variables
+from wqflask.show_trait.show_trait import get_trait_units
+from wqflask.show_trait.show_trait import get_nearest_marker
+from wqflask.show_trait.show_trait import get_genotype_scales
+from wqflask.show_trait.show_trait import requests
+
+
+class TraitObject:
+    def __init__(self, obj):
+        for key, value in obj.items():
+            setattr(self, key, value)
+
+
+class TestTraits(unittest.TestCase):
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    def test_check_if_attr_exists_truthy(self):
+        """"test if attributes exists with true return"""
+        trait_obj = TraitObject({"id_type": "id"})
+        trait_obj2 = TraitObject({"sample_name": ['samp1']})
+        results = check_if_attr_exists(trait_obj, "id_type")
+        result2 = check_if_attr_exists(trait_obj2, "sample_name")
+        self.assertIsInstance(trait_obj, TraitObject)
+        self.assertTrue(results)
+        self.assertTrue(result2)
+
+    def test_check_if_attr_exists_empty_attr(self):
+        """test if attributes exists with false return"""
+        trait_obj = TraitObject({"sample": ""})
+        trait_obj2 = TraitObject({"group": None})
+        result = check_if_attr_exists(trait_obj, "sample")
+        result2 = check_if_attr_exists(trait_obj, "group")
+        self.assertFalse(result)
+        self.assertFalse(result2)
+
+    def test_check_if_attr_exists_falsey(self):
+        """check if attribute exists with empty attributes"""
+        trait_obj = TraitObject({})
+        results = check_if_attr_exists(trait_obj, "any")
+        self.assertFalse(results)
+
+    @mock.patch("wqflask.show_trait.show_trait.requests.get")
+    @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+    def test_get_ncbi_summary_request_success(self, mock_exists, mock_get):
+        """test for getting ncbi summary with 
+        successful request"""
+        trait = TraitObject({"geneid": "id"})
+        mock_exists.return_value = True
+        content_json_string = """{
+          "result":{
+            "id":{
+              "summary":"this is a summary of the geneid"
+            }
+          }
+        }
+        """
+        get_return_obj = TraitObject({"content": content_json_string})
+        mock_get.return_value = get_return_obj
+        results = get_ncbi_summary(trait)
+        mock_exists.assert_called_once()
+        mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
+
+        self.assertEqual(results, "this is a summary of the geneid")
+
+    @mock.patch("wqflask.show_trait.show_trait.requests.get")
+    @mock.patch("wqflask.show_trait.show_trait.check_if_attr_exists")
+    def test_get_ncbi_summary_request_fail(self, mock_exists, mock_get_fail):
+        """test for getting ncbi summary with request fail"""
+        trait = TraitObject({"geneid": "id"})
+        mock_exists.return_value = True
+        mock_get_fail.side_effect = Exception("an error occurred")
+        content_json_string = """{
+          "result":{
+            "id":{
+              "summary":"this is a summary of the geneid"
+            }
+          }
+        }
+        """
+        results = get_ncbi_summary(trait)
+        self.assertEqual(results, None)
+
+    def test_hash_num_cases_is_probeset(self):
+        """test for hash num_cases with dataset.type set to Probeset"""
+        create_dataset = TraitObject({"type": "ProbeSet"})
+        create_trait = TraitObject({"dataset": create_dataset})
+        self.assertFalse(has_num_cases(create_trait))
+
+    def test_hash_num_cases_no_probeset(self):
+        """test for hash num cases with dataset.type not Probeset"""
+        create_dataset = TraitObject({"type": "Temp"})
+        construct_data = {
+            "nm1": TraitObject({"num_cases": False}),
+            "nm2": TraitObject({"num_cases": True}),
+            "nm3": TraitObject({"num_cases": False})
+        }
+        construct_data2 = {
+            "nm1": TraitObject({"num_cases": False}),
+            "nm2": TraitObject({"num_cases": False}),
+            "nm3": TraitObject({"num_cases": False})
+        }
+        create_trait = TraitObject(
+            {"dataset": create_dataset, "data": construct_data})
+        create_trait2 = TraitObject(
+            {"dataset": create_dataset, "data": construct_data2})
+
+        results = has_num_cases(create_trait)
+        self.assertTrue(has_num_cases(create_trait))
+        self.assertFalse(has_num_cases(create_trait2))
+
+    def test_get_table_widths(self):
+        """test for getting table widths"""
+        sample_groups = [TraitObject({'se_exists': True, "attributes": ["attr1", "attr2", "attr3"]}
+                                     ), TraitObject(
+            {"se_exists": False, "attributes": ["at1", "at2"]
+             })]
+
+        results_with_numcase = get_table_widths(sample_groups, True)
+        result_no_numcase = get_table_widths(sample_groups, False)
+
+        results_one_sample = get_table_widths(
+            [TraitObject({"se_exists": True, "attributes": []})], True)
+        expected_with_numcase = (450, "750px")
+        expected_no_numcase = (450, "670px")
+        expected_one_sample = (250, "540px")
+        self.assertEqual(results_with_numcase, expected_with_numcase)
+        self.assertEqual(result_no_numcase, expected_no_numcase)
+        self.assertEqual(results_one_sample,
+                         expected_one_sample)
+
+    def test_get_categorical_variables_no_sample_attributes(self):
+        """test for getting categorical variable names with no samples"""
+        trait = TraitObject({})
+        sample_list = TraitObject({"se_exists": True, "attributes": []})
+        self.assertEqual(get_categorical_variables(trait, sample_list), [])
+
+    def test_get_categorical_variables_with_sample_attributes(self):
+        """test for getting categorical variable names with no samples"""
+        this_trait = TraitObject({"data": {
+            "Gene1": TraitObject({"extra_attributes": {"ex1": "ex1value"}}),
+            "Gene2": TraitObject({"extra_attributes": {"ex2": "ex2value"}}),
+            "Gene3": TraitObject({"extra_attributes": {"ex3": "ex3value"}})
+        }})
+        sample_list = TraitObject({"attributes": {
+            "sample_attribute_1": TraitObject({"name": "ex1"}),
+            "sample_attribute_2": TraitObject({"name": "ex2"}),
+            "sample_attribute_3": TraitObject({"name": "ex3"}),
+            "sample_attribute_4": TraitObject({"name": "not_in_extra_attributes"})
+        }})
+        results = get_categorical_variables(this_trait, sample_list)
+        self.assertEqual(
+            ["ex1", "ex2", "ex3", "not_in_extra_attributes"], results)
+
+    def test_get_trait_units(self):
+        """test for getting trait units"""
+        trait = TraitObject(
+            {"description_fmt": "[this is a description] another test [N/A]"})
+        trait_no_unit_type = TraitObject({"description_fmt": ""})
+        results = get_trait_units(trait)
+        results_no_unit = get_trait_units(trait_no_unit_type)
+        self.assertEqual(results, "this is a descriptionN/A")
+        self.assertEqual(results_no_unit, "Value")
+
+    @mock.patch("wqflask.show_trait.show_trait.g")
+    def test_get_nearest_marker(self, mock_db):
+        """test for getting nearest marker with non-empty db"""
+
+        mock_db.db.execute.return_value.fetchall.return_value = [
+            ["Geno1", "Geno2"], ["Geno3"]]
+
+        trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+        group_name = TraitObject({"name": "group_name"})
+        this_db = TraitObject({"group": group_name})
+        results_with_item_db = get_nearest_marker(trait, this_db)
+        called_with_value = """SELECT Geno.Name
+               FROM Geno, GenoXRef, GenoFreeze
+               WHERE Geno.Chr = 'test_chr' AND
+                     GenoXRef.GenoId = Geno.Id AND
+                     GenoFreeze.Id = GenoXRef.GenoFreezeId AND
+                     GenoFreeze.Name = 'group_nameGeno'
+               ORDER BY ABS( Geno.Mb - test_mb) LIMIT 1"""
+
+        mock_db.db.execute.assert_called_with(called_with_value)
+
+        self.assertEqual(results_with_item_db, "Geno1")
+
+    @mock.patch("wqflask.show_trait.show_trait.g")
+    def test_get_nearest_marker_empty_db(self, mock_db):
+        """test for getting nearest marker with empty db"""
+        mock_db.db.execute.return_value.fetchall.return_value = []
+        trait = TraitObject({"locus_chr": "test_chr", "locus_mb": "test_mb"})
+        group_name = TraitObject({"name": "group_name"})
+        this_db = TraitObject({"group": group_name})
+        results_empty_db = get_nearest_marker(trait, this_db)
+        mock_db.db.execute.assert_called_once()
+        self.assertEqual(results_empty_db, "")
+
+    @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+    def test_get_genotype_scales_with_genofile_is_list(self, mock_get_scales):
+        """test for getting genotype scales with genofile as list """
+        # where genofile is instance of list
+        genofiles_list = [{"filename": "file1", "location": "~/data/files/f1"},
+                          {"filename": "file2", "location": "~/data/files/f2"},
+                          {"filename": "file3", "location": "~/data/files/f3"}]
+
+        mock_get_scales.side_effect = [[["morgan", "cM"]],
+                                       [["morgan", "cM"]],
+                                       [["physic", "Mb"]]]
+
+        results = get_genotype_scales(genofiles_list)
+        expected_results = {
+            "~/data/files/f1": [["morgan", "cM"]],
+            "~/data/files/f2": [["morgan", "cM"]],
+            "~/data/files/f3": [["physic", "Mb"]]
+        }
+
+        multiple_calls = [mock.call('~/data/files/f1'), mock.call('~/data/files/f2'),
+                          mock.call('~/data/files/f3')]
+        mock_get_scales.assert_has_calls(multiple_calls)
+        self.assertEqual(results, expected_results)
+
+    @mock.patch("wqflask.show_trait.show_trait.get_scales_from_genofile")
+    def test_genotype_scales_with_genofile_other(self, mock_get_scales):
+        """test for getting genotype scales with genofile as a string"""
+        file_location = "~/another_file_location"
+        mock_get_scales.return_value = [["physic", "Mb"]]
+        expected_results = {f"{file_location}": [["physic", "Mb"]]}
+        self.assertEqual(get_genotype_scales(file_location), expected_results)
+        mock_get_scales.assert_called_once_with(file_location)