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authorFrederick Muriuki Muriithi2023-04-06 12:31:05 +0300
committerFrederick Muriuki Muriithi2023-04-06 12:31:05 +0300
commit17abad9300e4a96a14f94da486ef8307f7d27e06 (patch)
tree38fe3bfd36be9a821adfc67b83fbbd587ceb8b5e /gn3/api
parent3d873435f0d464864d4d691d6be4db40931fac05 (diff)
downloadgenenetwork3-17abad9300e4a96a14f94da486ef8307f7d27e06.tar.gz
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
Diffstat (limited to 'gn3/api')
-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
4 files changed, 10 insertions, 10 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))