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-rw-r--r--gn3/api/async_commands.py4
-rw-r--r--gn3/api/correlation.py4
-rw-r--r--gn3/api/heatmaps.py6
-rw-r--r--gn3/api/menu.py6
-rw-r--r--gn3/commands.py5
-rw-r--r--gn3/db_utils.py9
6 files changed, 14 insertions, 20 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"""