Remove deprecated `gn3.db_utils.database_connector` function

Remove the deprecated function and fix a myriad of bugs that arise from
removing the function.

Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils

11 files changed, 59 insertions, 79 deletions

diff --git a/gn3/api/async_commands.py b/gn3/api/async_commands.py
index c0cf4bb..da146b8 100644
--- a/gn3/api/async_commands.py
+++ b/gn3/api/async_commands.py
@@ -11,6 +11,6 @@ def command_state(command_id):
         state = rconn.hgetall(name=command_id)
         if not state:
             return jsonify(
-                status=404,
-                error="The command id provided does not exist.")
+                error="The command id provided does not exist.",
+                status="error"), 404
         return jsonify(dict(state.items()))
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py
index 6e70899..eb4cc7d 100644
--- a/gn3/api/correlation.py
+++ b/gn3/api/correlation.py
@@ -9,7 +9,7 @@ from flask import request
 from flask import current_app
 
 from gn3.settings import SQL_URI
-from gn3.db_utils import database_connector
+from gn3.db_utils import database_connection
 from gn3.commands import run_sample_corr_cmd
 from gn3.responses.pcorrs_responses import build_response
 from gn3.commands import run_async_cmd, compose_pcorrs_command
@@ -64,7 +64,7 @@ def compute_lit_corr(species=None, gene_id=None):
     might be needed for actual computing of the correlation results
     """
 
-    with database_connector() as conn:
+    with database_connection(current_app.config["SQL_URI"]) as conn:
         target_traits_gene_ids = request.get_json()
         target_trait_gene_list = list(target_traits_gene_ids.items())
 
diff --git a/gn3/api/heatmaps.py b/gn3/api/heatmaps.py
index 80c8ca8..26c165f 100644
--- a/gn3/api/heatmaps.py
+++ b/gn3/api/heatmaps.py
@@ -5,9 +5,9 @@ Module to hold the entrypoint functions that generate heatmaps
 import io
 from flask import jsonify
 from flask import request
-from flask import Blueprint
+from flask import Blueprint, current_app
 from gn3.heatmaps import build_heatmap
-from gn3.db_utils import database_connector
+from gn3.db_utils import database_connection
 
 heatmaps = Blueprint("heatmaps", __name__)
 
@@ -24,7 +24,7 @@ def clustered_heatmaps():
         return jsonify({
             "message": "You need to provide at least two trait names."
         }), 400
-    with database_connector() as conn:
+    with database_connection(current_app.config["SQL_URI"]) as conn:
         def parse_trait_fullname(trait):
             name_parts = trait.split(":")
             return f"{name_parts[1]}::{name_parts[0]}"
diff --git a/gn3/api/menu.py b/gn3/api/menu.py
index cc77ab8..58b761e 100644
--- a/gn3/api/menu.py
+++ b/gn3/api/menu.py
@@ -1,14 +1,14 @@
 """API for data used to generate menus"""
 
-from flask import jsonify, Blueprint
+from flask import jsonify, Blueprint, current_app
 
 from gn3.db.menu import gen_dropdown_json
-from gn3.db_utils import database_connector
+from gn3.db_utils import database_connection
 
 menu = Blueprint("menu", __name__)
 
 @menu.route("/generate/json")
 def generate_json():
     """Get the menu in the JSON format"""
-    with database_connector() as conn:
+    with database_connection(current_app.config["SQL_URI"]) as conn:
         return jsonify(gen_dropdown_json(conn))
diff --git a/gn3/commands.py b/gn3/commands.py
index 0e78fd2..a90e895 100644
--- a/gn3/commands.py
+++ b/gn3/commands.py
@@ -14,6 +14,8 @@ from typing import Tuple
 from typing import Union
 from typing import Sequence
 from uuid import uuid4
+
+from flask import current_app
 from redis.client import Redis  # Used only in type hinting
 
 from gn3.chancy import random_string
@@ -80,7 +82,8 @@ def compose_pcorrs_command(
 
     prefix_cmd = (
         f"{sys.executable}", "-m", "scripts.partial_correlations",
-        primary_trait, ",".join(control_traits), __parse_method__(method))
+        primary_trait, ",".join(control_traits), __parse_method__(method),
+        current_app.config["SQL_URI"])
     if (
             kwargs.get("target_database") is not None
             and kwargs.get("target_traits") is None):
diff --git a/gn3/db_utils.py b/gn3/db_utils.py
index 4827358..e9db10f 100644
--- a/gn3/db_utils.py
+++ b/gn3/db_utils.py
@@ -17,15 +17,6 @@ def parse_db_url(sql_uri: str) -> Tuple:
         parsed_db.path[1:], parsed_db.port)
 
 
-# This function is deprecated. Use database_connection instead.
-def database_connector(sql_uri: str = "") -> mdb.Connection:
-    """function to create db connector"""
-    host, user, passwd, db_name, db_port = parse_db_url(
-        sql_uri or current_app.config["SQL_URI"])
-
-    return mdb.connect(host, user, passwd, db_name, port=(db_port or 3306))
-
-
 # pylint: disable=missing-class-docstring, missing-function-docstring, too-few-public-methods
 class Connection(Protocol):
     """Type Annotation for MySQLdb's connection object"""
diff --git a/scripts/partial_correlations.py b/scripts/partial_correlations.py
index 1fbab78..aab8f08 100644
--- a/scripts/partial_correlations.py
+++ b/scripts/partial_correlations.py
@@ -4,7 +4,7 @@ import json
 import traceback
 from argparse import ArgumentParser
 
-from gn3.db_utils import database_connector
+from gn3.db_utils import database_connection
 from gn3.responses.pcorrs_responses import OutputEncoder
 from gn3.computations.partial_correlations import (
     partial_correlations_with_target_db,
@@ -108,6 +108,10 @@ def process_cli_arguments():
         help="The correlation method to use",
         type=str,
         choices=("pearsons", "spearmans"))
+    parser.add_argument(
+        "sql_uri",
+        help="The uri to use to connect to the database",
+        type=str)
     against_db_parser(against_traits_parser(
         parser.add_subparsers(
             title="subcommands",
@@ -119,7 +123,7 @@ def main():
     """Entry point for the script"""
     args = process_cli_arguments()
 
-    with database_connector() as conn:
+    with database_connection(args.sql_uri) as conn:
         print(json.dumps(run_pcorrs(conn, args), cls=OutputEncoder))
 
 
diff --git a/tests/integration/conftest.py b/tests/integration/conftest.py
index c953d84..795c42d 100644
--- a/tests/integration/conftest.py
+++ b/tests/integration/conftest.py
@@ -4,7 +4,7 @@ import MySQLdb
 
 from gn3.app import create_app
 from gn3.chancy import random_string
-from gn3.db_utils import parse_db_url, database_connector
+from gn3.db_utils import parse_db_url, database_connection
 
 @pytest.fixture(scope="session")
 def client():
@@ -18,17 +18,18 @@ def client():
 
 
 @pytest.fixture(scope="session")
-def db_conn():
+def db_conn(client):
     """Create a db connection fixture for tests"""
     # 01) Generate random string to append to all test db artifacts for the session
+    live_db_uri = client.application.config["SQL_URI"]
     rand_str = random_string(15)
-    live_db_details = parse_db_url()
+    live_db_details = parse_db_url(live_db_uri)
     test_db_name = f"test_{live_db_details[3]}_{rand_str}"
     #
     # 02) Create new test db
     #     Use context manager to ensure the live connection is automatically
     #     closed on exit
-    with database_connector() as live_db_conn:
+    with database_connection(live_db_uri) as live_db_conn:
         with live_db_conn.cursor() as live_db_cursor:
             live_db_cursor.execute(f"CREATE DATABASE {test_db_name}")
             #
diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py
index c1d518d..51769b5 100644
--- a/tests/integration/test_correlation.py
+++ b/tests/integration/test_correlation.py
@@ -65,15 +65,15 @@ class CorrelationIntegrationTest(TestCase):
 
     @pytest.mark.integration_test
     @mock.patch("gn3.api.correlation.compute_all_lit_correlation")
-    @mock.patch("gn3.api.correlation.database_connector")
-    def test_lit_correlation(self, database_connector, mock_compute_corr):
+    @mock.patch("gn3.api.correlation.database_connection")
+    def test_lit_correlation(self, database_connection, mock_compute_corr):
         """Test api/correlation/lit_corr/{species}/{gene_id}"""
 
         mock_compute_corr.return_value = []
 
-        database_connector.return_value = mock.Mock()
-        database_connector.return_value.__enter__ = mock.Mock()
-        database_connector.return_value.__exit__ = mock.Mock()
+        database_connection.return_value = mock.Mock()
+        database_connection.return_value.__enter__ = mock.Mock()
+        database_connection.return_value.__exit__ = mock.Mock()
 
         post_data = {"1426678_at": "68031",
                      "1426679_at": "68036",
diff --git a/tests/performance/perf_query.py b/tests/performance/perf_query.py
index e534e9b..cdac9a9 100644
--- a/tests/performance/perf_query.py
+++ b/tests/performance/perf_query.py
@@ -7,7 +7,7 @@ from inspect import getmembers
 from inspect import isfunction
 
 from functools import wraps
-from gn3.db_utils import database_connector
+from gn3.db_utils import database_connection
 
 
 def timer(func):
@@ -26,9 +26,10 @@ def timer(func):
 
 
 def query_executor(query: str,
+                   sql_uri: str,
                    fetch_all: bool = True):
     """function to execute a query"""
-    with database_connector() as conn:
+    with database_connection(sql_uri) as conn:
         with conn.cursor() as cursor:
             cursor.execute(query)
 
@@ -58,22 +59,22 @@ def fetch_probeset_query(dataset_name: str):
 
 
 @timer
-def perf_hc_m2_dataset():
+def perf_hc_m2_dataset(sql_uri: str):
     """test the default dataset HC_M2_0606_P"""
 
     dataset_name = "HC_M2_0606_P"
     print(f"Performance test for {dataset_name}")
 
-    query_executor(fetch_probeset_query(dataset_name=dataset_name))
+    query_executor(fetch_probeset_query(dataset_name=dataset_name), sql_uri)
 
 
 @timer
-def perf_umutaffyexon_dataset():
+def perf_umutaffyexon_dataset(sql_uri):
     """largest dataset in gn"""
 
     dataset_name = "UMUTAffyExon_0209_RMA"
     print(f"Performance test for {dataset_name}")
-    query_executor(fetch_probeset_query(dataset_name=dataset_name))
+    query_executor(fetch_probeset_query(dataset_name=dataset_name), sql_uri)
 
 
 def fetch_perf_functions():
@@ -102,6 +103,7 @@ def fetch_cmd_args():
 
 
 if __name__ == '__main__':
+    # Figure out how to pass the database uri here... Maybe use click.
     func_list = fetch_cmd_args()
     for func_obj in func_list:
         func_obj()
diff --git a/tests/unit/test_db_utils.py b/tests/unit/test_db_utils.py
index a319692..0211107 100644
--- a/tests/unit/test_db_utils.py
+++ b/tests/unit/test_db_utils.py
@@ -1,49 +1,28 @@
 """module contains test for db_utils"""
-
-from unittest import TestCase
 from unittest import mock
-from types import SimpleNamespace
 
 import pytest
 
 import gn3
-from gn3.db_utils import database_connector
-from gn3.db_utils import parse_db_url
-
-@pytest.fixture(scope="class")
-def setup_app(request, fxtr_app):
-    """Setup the fixtures for the class."""
-    request.cls.app = fxtr_app
-
-class TestDatabase(TestCase):
-    """class contains testd for db connection functions"""
-
-    @pytest.mark.unit_test
-    @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", None)
-        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()
-
+from gn3.db_utils import parse_db_url, database_connection
+
+@pytest.mark.unit_test
+@mock.patch("gn3.db_utils.mdb")
+@mock.patch("gn3.db_utils.parse_db_url")
+def test_database_connection(mock_db_parser, mock_sql):
+    """test for creating database connection"""
+    print(f"MOCK SQL: {mock_sql}")
+    print(f"MOCK DB PARSER: {mock_db_parser}")
+    mock_db_parser.return_value = ("localhost", "guest", "4321", "users", None)
+
+    with database_connection("mysql://guest:4321@localhost/users") as conn:
         mock_sql.connect.assert_called_with(
-            "localhost", "guest", "4321", "users", port=3306)
-        self.assertIsInstance(
-            results, SimpleNamespace, "database not created successfully")
-
-    @pytest.mark.unit_test
-    @pytest.mark.usefixtures("setup_app")
-    def test_parse_db_url(self):
-        """test for parsing db_uri env variable"""
-        print(self.__dict__)
-        with self.app.app_context(), mock.patch.dict(# pylint: disable=[no-member]
-                gn3.db_utils.current_app.config,
-                {"SQL_URI": "mysql://username:4321@localhost/test"},
-                clear=True):
-            results = parse_db_url()
-            expected_results = ("localhost", "username", "4321", "test", None)
-            self.assertEqual(results, expected_results)
+            db="users", user="guest", passwd="4321", host="localhost",
+            port=3306)
+
+@pytest.mark.unit_test
+def test_parse_db_url():
+    """test for parsing db_uri env variable"""
+    results = parse_db_url("mysql://username:4321@localhost/test")
+    expected_results = ("localhost", "username", "4321", "test", None)
+    assert results == expected_results