From 17abad9300e4a96a14f94da486ef8307f7d27e06 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 6 Apr 2023 12:31:05 +0300
Subject: 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
---
 gn3/api/async_commands.py | 4 ++--
 gn3/api/correlation.py    | 4 ++--
 gn3/api/heatmaps.py       | 6 +++---
 gn3/api/menu.py           | 6 +++---
 gn3/commands.py           | 5 ++++-
 gn3/db_utils.py           | 9 ---------
 6 files changed, 14 insertions(+), 20 deletions(-)

(limited to 'gn3')

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"""
-- 
cgit v1.2.3