Integrate correlation API

- add new api for gn2-gn3 sample r integration
- delete map for sample list to values
- add db util file
- add python msql-client dependency
- add db for fetching lit correlation results
- add unittests for db utils
- add tests for db_utils
- modify api for fetching lit correlation results
- refactor Mock Database Connector and unittests
- add sql url parser
- add SQL URI env variable
- refactor code for db utils
- modify return data for lit correlation
- refactor tissue correlation endpoint
- replace db_instance with conn

1 files changed, 37 insertions, 0 deletions

diff --git a/tests/unit/test_db_utils.py b/tests/unit/test_db_utils.py
new file mode 100644
index 0000000..0f2de9e
--- /dev/null
+++ b/tests/unit/test_db_utils.py
@@ -0,0 +1,37 @@
+"""module contains test for db_utils"""
+
+from unittest import TestCase
+from unittest import mock
+
+from types import SimpleNamespace
+
+from gn3.db_utils import database_connector
+from gn3.db_utils import parse_db_url
+
+
+class TestDatabase(TestCase):
+    """class contains testd for db connection functions"""
+
+    @mock.patch("gn3.db_utils.mdb")
+    @mock.patch("gn3.db_utils.parse_db_url")
+    def test_database_connector(self, mock_db_parser, mock_sql):
+        """test for creating database connection"""
+        mock_db_parser.return_value = ("localhost", "guest", "4321", "users")
+        callable_cursor = lambda: SimpleNamespace(execute=3)
+        cursor_object = SimpleNamespace(cursor=callable_cursor)
+        mock_sql.connect.return_value = cursor_object
+        mock_sql.close.return_value = None
+        results = database_connector()
+
+        mock_sql.connect.assert_called_with(
+            "localhost", "guest", "4321", "users")
+        self.assertIsInstance(
+            results, tuple, "database not created successfully")
+
+    @mock.patch("gn3.db_utils.SQL_URI",
+                "mysql://username:4321@localhost/test")
+    def test_parse_db_url(self):
+        """test for parsing db_uri env variable"""
+        results = parse_db_url()
+        expected_results = ("localhost", "username", "4321", "test")
+        self.assertEqual(results, expected_results)