Lint some test files

2 files changed, 223 insertions, 123 deletions

diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 50df2bb4..53e1b9a2 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -20,12 +20,7 @@ class MockDataset(AttributeSetter):
         return None
 
     def retrieve_genes(self, id=None):
-        return {
-            "TT-1": "GH-1",
-            "TT-2": "GH-2",
-            "TT-3": "GH-3"
-
-        }
+        return {"TT-1": "GH-1", "TT-2": "GH-2", "TT-3": "GH-3"}
 
 
 class TestCorrelations(unittest.TestCase):
@@ -37,18 +32,10 @@ class TestCorrelations(unittest.TestCase):
         self.app_context.pop()
 
     def test_init_corr_params(self):
-        start_vars = {
-            "return_count": "3",
-            "type": "T1",
-            "method": "spearman"
-        }
+        start_vars = {"return_count": "3", "type": "T1", "method": "spearman"}
 
         corr_params_results = init_corr_params(start_vars=start_vars)
-        expected_results = {
-            "return_count": 3,
-            "type": "T1",
-            "method": "spearman"
-        }
+        expected_results = {"return_count": 3, "type": "T1", "method": "spearman"}
 
         self.assertEqual(corr_params_results, expected_results)
 
@@ -57,74 +44,100 @@ class TestCorrelations(unittest.TestCase):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
         with conn.cursor() as cursor:
-            cursor.fetchone.side_effect = [
-                ("MG-1",), ("MG-2",)]
-
-            self.assertEqual(convert_to_mouse_gene_id(
-                species="Other", gene_id=""), None)
-            self.assertEqual(convert_to_mouse_gene_id(
-                species="mouse", gene_id="MG-4"), "MG-4")
-            self.assertEqual(convert_to_mouse_gene_id(
-                species="rat", gene_id="R1"), "MG-1")
-            self.assertEqual(convert_to_mouse_gene_id(
-                species="human", gene_id="H1"), "MG-2")
+            cursor.fetchone.side_effect = [("MG-1",), ("MG-2",)]
+
+            self.assertEqual(
+                convert_to_mouse_gene_id(species="Other", gene_id=""), None
+            )
+            self.assertEqual(
+                convert_to_mouse_gene_id(species="mouse", gene_id="MG-4"), "MG-4"
+            )
+            self.assertEqual(
+                convert_to_mouse_gene_id(species="rat", gene_id="R1"), "MG-1"
+            )
+            self.assertEqual(
+                convert_to_mouse_gene_id(species="human", gene_id="H1"), "MG-2"
+            )
 
     @mock.patch("wqflask.api.correlation.database_connection")
     @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
     def test_do_literature_correlation_for_all_traits(
-            self,
-            mock_convert_to_mouse_geneid, mock_db):
-        mock_convert_to_mouse_geneid.side_effect = [
-            "MG-1", "MG-2;", "MG-3", "MG-4"]
-
-        trait_geneid_dict = {
-            "TT-1": "GH-1",
-            "TT-2": "GH-2",
-            "TT-3": "GH-3"
+        self, mock_convert_to_mouse_geneid, mock_db
+    ):
+        mock_convert_to_mouse_geneid.side_effect = ["MG-1", "MG-2;", "MG-3", "MG-4"]
 
-        }
+        trait_geneid_dict = {"TT-1": "GH-1", "TT-2": "GH-2", "TT-3": "GH-3"}
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
         with conn.cursor() as cursor:
-            cursor.fetchone.side_effect = [
-                ("V1", ), ("V2", ), ("V3", )]
+            cursor.fetchone.side_effect = [("V1",), ("V2",), ("V3",)]
             this_trait = AttributeSetter({"geneid": "GH-1"})
             target_dataset = AttributeSetter(
-                {"group": AttributeSetter({"species": "rat"})})
+                {"group": AttributeSetter({"species": "rat"})}
+            )
             results = do_literature_correlation_for_all_traits(
-                this_trait=this_trait, target_dataset=target_dataset,
-                trait_geneid_dict=trait_geneid_dict, corr_params={})
-            expected_results = {'TT-1': ['GH-1', 0],
-                                'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+                this_trait=this_trait,
+                target_dataset=target_dataset,
+                trait_geneid_dict=trait_geneid_dict,
+                corr_params={},
+            )
+            expected_results = {
+                "TT-1": ["GH-1", 0],
+                "TT-2": ["GH-2", "V1"],
+                "TT-3": ["GH-3", "V2"],
+            }
             self.assertEqual(results, expected_results)
 
     @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
     def test_get_sample_r_and_p_values(self, mock_normalize):
 
         group = AttributeSetter(
-            {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]})
+            {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]}
+        )
         target_dataset = AttributeSetter({"group": group})
 
         target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
-        trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
-                      "S3": AttributeSetter(
-            {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
-            "S6": AttributeSetter({"value": 5.0})}
+        trait_data = {
+            "S1": AttributeSetter({"value": 2.3}),
+            "S2": AttributeSetter({"value": 1.1}),
+            "S3": AttributeSetter({"value": 6.3}),
+            "S4": AttributeSetter({"value": 3.6}),
+            "S5": AttributeSetter({"value": 4.1}),
+            "S6": AttributeSetter({"value": 5.0}),
+        }
         this_trait = AttributeSetter({"data": trait_data})
-        mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
-                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
-        mock_normalize.side_effect = [([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
-                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
-                                      ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
-                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
-                                      ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)]
-
-        results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
-        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
-        results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
-        }, target_vals=target_vals, target_dataset=target_dataset, type="spearman")
-        results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
-        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+        mock_normalize.return_value = (
+            [2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+            [3.4, 6.2, 4.1, 3.4, 1.2, 5.6],
+            6,
+        )
+        mock_normalize.side_effect = [
+            ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+            ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+            ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3),
+        ]
+
+        results_pearsonr = get_sample_r_and_p_values(
+            this_trait=this_trait,
+            this_dataset={},
+            target_vals=target_vals,
+            target_dataset=target_dataset,
+            type="pearson",
+        )
+        results_spearmanr = get_sample_r_and_p_values(
+            this_trait=this_trait,
+            this_dataset={},
+            target_vals=target_vals,
+            target_dataset=target_dataset,
+            type="spearman",
+        )
+        results_num_overlap = get_sample_r_and_p_values(
+            this_trait=this_trait,
+            this_dataset={},
+            target_vals=target_vals,
+            target_dataset=target_dataset,
+            type="pearson",
+        )
         expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
         expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
         for i, val in enumerate(expected_pearsonr):
@@ -137,18 +150,26 @@ class TestCorrelations(unittest.TestCase):
     def test_calculate_results(self, literature_correlation):
 
         literature_correlation.return_value = {
-            'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+            "TT-1": ["GH-1", 0],
+            "TT-2": ["GH-2", 3],
+            "TT-3": ["GH-3", 1],
+        }
 
-        this_dataset = MockDataset(
-            {"group": AttributeSetter({"species": "rat"})})
-        target_dataset = MockDataset(
-            {"group": AttributeSetter({"species": "rat"})})
+        this_dataset = MockDataset({"group": AttributeSetter({"species": "rat"})})
+        target_dataset = MockDataset({"group": AttributeSetter({"species": "rat"})})
         this_trait = AttributeSetter({"geneid": "GH-1"})
         corr_params = {"type": "literature"}
         sorted_results = calculate_results(
-            this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params)
-        expected_results = {'TT-2': ['GH-2', 3],
-                            'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+            this_trait=this_trait,
+            this_dataset=this_dataset,
+            target_dataset=target_dataset,
+            corr_params=corr_params,
+        )
+        expected_results = {
+            "TT-2": ["GH-2", 3],
+            "TT-3": ["GH-3", 1],
+            "TT-1": ["GH-1", 0],
+        }
 
         self.assertTrue(isinstance(sorted_results, OrderedDict))
         self.assertEqual(dict(sorted_results), expected_results)
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 46a74231..a09d1538 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -17,48 +17,110 @@ class TestSnpBrowser(unittest.TestCase):
         self.app_context.pop()
 
     def test_get_header_list(self):
-        empty_columns = {"snp_source": "false", "conservation_score": "true", "gene_name": "false",
-                         "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
+        empty_columns = {
+            "snp_source": "false",
+            "conservation_score": "true",
+            "gene_name": "false",
+            "transcript": "false",
+            "exon": "false",
+            "domain_2": "true",
+            "function": "false",
+            "function_details": "true",
+        }
         strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
-        expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
-                              'Domain 1', 'Domain 2', 'Details'],
-                             ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
-                            ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
-                             'conservation_score', 'domain_1', 'domain_2',
-                             'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
+        expected_results = (
+            [
+                [
+                    "Index",
+                    "SNP ID",
+                    "Chr",
+                    "Mb",
+                    "Alleles",
+                    "ConScore",
+                    "Domain 1",
+                    "Domain 2",
+                    "Details",
+                ],
+                ["S1", "S2", "S3", "S4", "S5"],
+            ],
+            5,
+            [
+                "index",
+                "snp_name",
+                "chr",
+                "mb_formatted",
+                "alleles",
+                "conservation_score",
+                "domain_1",
+                "domain_2",
+                "function_details",
+                "S1",
+                "S2",
+                "S3",
+                "S4",
+                "S5",
+            ],
+        )
 
         results_with_snp = get_header_list(
-            variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
+            variant_type="SNP",
+            strains=strains,
+            species="Mouse",
+            empty_columns=empty_columns,
+        )
         results_with_indel = get_header_list(
-            variant_type="InDel", strains=strains, species="rat", empty_columns=[])
+            variant_type="InDel", strains=strains, species="rat", empty_columns=[]
+        )
         expected_results_with_indel = (
-            ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
-             'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
-            ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
-             'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
+            [
+                "Index",
+                "ID",
+                "Type",
+                "InDel Chr",
+                "Mb Start",
+                "Mb End",
+                "Strand",
+                "Size",
+                "Sequence",
+                "Source",
+            ],
+            0,
+            [
+                "index",
+                "indel_name",
+                "indel_type",
+                "indel_chr",
+                "indel_mb_s",
+                "indel_mb_e",
+                "indel_strand",
+                "indel_size",
+                "indel_sequence",
+                "source_name",
+            ],
+        )
 
         self.assertEqual(expected_results, results_with_snp)
         self.assertEqual(expected_results_with_indel, results_with_indel)
 
     @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_get_gene_id(self, mock_db):
-        db_query_value = ("SELECT geneId FROM GeneList WHERE "
-                          "SpeciesId = %s AND geneSymbol = %s")
+        db_query_value = (
+            "SELECT geneId FROM GeneList WHERE " "SpeciesId = %s AND geneSymbol = %s"
+        )
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
         with conn.cursor() as cursor:
-            cursor.fetchone.return_value = (("517d729f-aa13-4413"
-                                             "-a885-40a3f7ff768a"),)
+            cursor.fetchone.return_value = (
+                ("517d729f-aa13-4413" "-a885-40a3f7ff768a"),
+            )
 
             results = get_gene_id(
-                species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83",
-                gene_name="INSR")
+                species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR"
+            )
             cursor.execute.assert_called_once_with(
-                db_query_value,
-                ("c9c0f59e-1259-4cba-91e6-831ef1a99c83",
-                 "INSR"))
-            self.assertEqual(results,
-                             "517d729f-aa13-4413-a885-40a3f7ff768a")
+                db_query_value, ("c9c0f59e-1259-4cba-91e6-831ef1a99c83", "INSR")
+            )
+            self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
 
     @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_gene_id_name_dict(self, mock_db):
@@ -68,25 +130,37 @@ class TestSnpBrowser(unittest.TestCase):
         with conn.cursor() as cursor:
             cursor.fetchall.side_effect = [
                 [],
-                [("fsdf43-fseferger-f22", "GH1"),
-                 ("1sdf43-fsewferger-f22", "GH2"),
-                 ("fwdj43-fstferger-f22", "GH3")]]
-            self.assertEqual("", get_gene_id_name_dict(
-                species_id="fregb343bui43g4",
-                gene_name_list=no_gene_names))
+                [
+                    ("fsdf43-fseferger-f22", "GH1"),
+                    ("1sdf43-fsewferger-f22", "GH2"),
+                    ("fwdj43-fstferger-f22", "GH3"),
+                ],
+            ]
+            self.assertEqual(
+                "",
+                get_gene_id_name_dict(
+                    species_id="fregb343bui43g4", gene_name_list=no_gene_names
+                ),
+            )
             gene_name_list = ["GH1", "GH2", "GH3"]
             no_results = get_gene_id_name_dict(
-                species_id="ret3-32rf32", gene_name_list=gene_name_list)
+                species_id="ret3-32rf32", gene_name_list=gene_name_list
+            )
             results_found = get_gene_id_name_dict(
-                species_id="ret3-32rf32", gene_name_list=gene_name_list)
-            expected_found = {'GH1': 'fsdf43-fseferger-f22',
-                              'GH2': '1sdf43-fsewferger-f22',
-                              'GH3': 'fwdj43-fstferger-f22'}
+                species_id="ret3-32rf32", gene_name_list=gene_name_list
+            )
+            expected_found = {
+                "GH1": "fsdf43-fseferger-f22",
+                "GH2": "1sdf43-fsewferger-f22",
+                "GH3": "fwdj43-fstferger-f22",
+            }
             db_query_value = (
                 "SELECT geneId, geneSymbol FROM GeneList WHERE "
-                "SpeciesId = %s AND geneSymbol in (%s, %s, %s)")
+                "SpeciesId = %s AND geneSymbol in (%s, %s, %s)"
+            )
             cursor.execute.assert_called_with(
-                db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3"))
+                db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3")
+            )
             self.assertEqual(results_found, expected_found)
             self.assertEqual(no_results, {})
 
@@ -95,26 +169,31 @@ class TestSnpBrowser(unittest.TestCase):
         conn = mock.MagicMock()
         mock_db.return_value.__enter__.return_value = conn
         with conn.cursor() as cursor:
-            cursor.fetchone.side_effect = [
-                ("fsdf-232sdf-sdf", "GHA"), ""]
+            cursor.fetchone.side_effect = [("fsdf-232sdf-sdf", "GHA"), ""]
             results_found = check_if_in_gene(
-                species_id="517d729f-aa13-4413-a885-40a3f7ff768a",
-                chr_="CH1", mb=12.09)
+                species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09
+            )
             self.assertEqual(results_found, ["fsdf-232sdf-sdf", "GHA"])
             db_query_value = (
                 "SELECT geneId, geneSymbol FROM GeneList "
                 "WHERE SpeciesId = %s AND chromosome = %s "
-                "AND (txStart < %s AND txEnd > %s)")
+                "AND (txStart < %s AND txEnd > %s)"
+            )
             gene_not_found = check_if_in_gene(
-                species_id="517d729f-aa13-4413-a885-40a3f7ff768a",
-                chr_="CH1", mb=12.09)
+                species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09
+            )
             cursor.execute.assert_has_calls(
-                [mock.call(db_query_value,
-                           ("517d729f-aa13-4413-a885-40a3f7ff768a",
-                            "CH1", 12.09, 12.09)),
-                 mock.call(db_query_value,
-                           ("517d729f-aa13-4413-a885-40a3f7ff768a",
-                            "CH1", 12.09, 12.09))])
+                [
+                    mock.call(
+                        db_query_value,
+                        ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09),
+                    ),
+                    mock.call(
+                        db_query_value,
+                        ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09),
+                    ),
+                ]
+            )
             self.assertEqual(gene_not_found, "")
 
     @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
@@ -124,4 +203,4 @@ class TestSnpBrowser(unittest.TestCase):
         with conn.cursor() as cursor:
             cursor.execute.return_value.fetchall.return_value = []
             results = get_browser_sample_lists(species_id="12")
-            self.assertEqual(results, {'mouse': [], 'rat': []})
+            self.assertEqual(results, {"mouse": [], "rat": []})