Replace "g.db" object with a proper database connection

* wqflask/tests/unit/wqflask/api/test_correlation.py: Use proper
database connection instead of the db connection attached at "g.db".
* wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py: Ditto.
* wqflask/wqflask/api/correlation.py: Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py: Ditto.

2 files changed, 113 insertions, 88 deletions

diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 1089a36f..57986e80 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -52,28 +52,28 @@ class TestCorrelations(unittest.TestCase):
 
         self.assertEqual(corr_params_results, expected_results)
 
-    @mock.patch("wqflask.api.correlation.g")
+    @mock.patch("wqflask.api.correlation.database_connection")
     def test_convert_to_mouse_gene_id(self, mock_db):
-
-        results = convert_to_mouse_gene_id(species="Other", gene_id="")
-        self.assertEqual(results, None)
-
-        rat_species_results = convert_to_mouse_gene_id(
-            species="rat", gene_id="GH1")
-
-        mock_db.db.execute.return_value.fetchone.side_effect = [
-            AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})]
-
-        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.g")
+        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")
+
+    @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):
+    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"]
 
@@ -83,19 +83,22 @@ class TestCorrelations(unittest.TestCase):
             "TT-3": "GH-3"
 
         }
-        mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter(
-            {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})]
-
-        this_trait = AttributeSetter({"geneid": "GH-1"})
-
-        target_dataset = AttributeSetter(
-            {"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']}
-        self.assertEqual(results, expected_results)
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            cursor.fetchone.side_effect = [
+                AttributeSetter({"value": "V1"}),
+                AttributeSetter({"value": "V2"}),
+                AttributeSetter({"value": "V3"})]
+            this_trait = AttributeSetter({"geneid": "GH-1"})
+            target_dataset = AttributeSetter(
+                {"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']}
+            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):
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 89442c47..46a74231 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -40,66 +40,88 @@ class TestSnpBrowser(unittest.TestCase):
         self.assertEqual(expected_results, results_with_snp)
         self.assertEqual(expected_results_with_indel, results_with_indel)
 
-    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_get_gene_id(self, mock_db):
-        mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
-        db_query_value = """
-                SELECT
-                        geneId
-                FROM
-                        GeneList
-                WHERE
-                        SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'
-            """
-        results = get_gene_id(
-            species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
-        mock_db.db.execute.assert_called_once_with(db_query_value)
-        self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
+        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"),)
 
-    @mock.patch("wqflask.snp_browser.snp_browser.g")
+            results = get_gene_id(
+                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")
+
+    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_gene_id_name_dict(self, mock_db):
         no_gene_names = []
-        self.assertEqual("", get_gene_id_name_dict(
-            species_id="fregb343bui43g4", gene_name_list=no_gene_names))
-        gene_name_list = ["GH1", "GH2", "GH3"]
-        mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"),
-                                                                     ("fwdj43-fstferger-f22", "GH3")]]
-        no_results = get_gene_id_name_dict(
-            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'}
-        db_query_value = """
-                SELECT
-                        geneId, geneSymbol
-                FROM
-                        GeneList
-                WHERE
-                        SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')
-            """
-        mock_db.db.execute.assert_called_with(db_query_value)
-        self.assertEqual(results_found, expected_found)
-        self.assertEqual(no_results, {})
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        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))
+            gene_name_list = ["GH1", "GH2", "GH3"]
+            no_results = get_gene_id_name_dict(
+                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'}
+            db_query_value = (
+                "SELECT geneId, geneSymbol FROM GeneList WHERE "
+                "SpeciesId = %s AND geneSymbol in (%s, %s, %s)")
+            cursor.execute.assert_called_with(
+                db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3"))
+            self.assertEqual(results_found, expected_found)
+            self.assertEqual(no_results, {})
 
-    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_check_if_in_gene(self, mock_db):
-        mock_db.db.execute.return_value.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)
-        db_query_value = """SELECT geneId, geneSymbol
-                   FROM GeneList
-                   WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND
-                        (txStart < 12.09 AND txEnd > 12.09); """
-        gene_not_found = check_if_in_gene(
-            species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
-        mock_db.db.execute.assert_called_with(db_query_value)
-        self.assertEqual(gene_not_found, "")
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        with conn.cursor() as cursor:
+            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)
+            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)")
+            gene_not_found = check_if_in_gene(
+                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))])
+            self.assertEqual(gene_not_found, "")
 
-    @mock.patch("wqflask.snp_browser.snp_browser.g")
+    @mock.patch("wqflask.snp_browser.snp_browser.database_connection")
     def test_get_browser_sample_lists(self, mock_db):
-        mock_db.db.execute.return_value.fetchall.return_value = []
-
-        results = get_browser_sample_lists(species_id="12")
-        self.assertEqual(results, {'mouse': [], 'rat': []})
+        conn = mock.MagicMock()
+        mock_db.return_value.__enter__.return_value = conn
+        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': []})