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authorFrederick Muriuki Muriithi2023-10-06 11:34:54 +0300
committerFrederick Muriuki Muriithi2023-10-06 11:34:54 +0300
commit164da23e29354a74e30db7348d93860f3d5b4ea1 (patch)
treeca297dd418aaa3878fe7e0ab253521f277ed10ac
parente672cf9edc00777a928e492151d06d55e58241e1 (diff)
downloadgenenetwork3-164da23e29354a74e30db7348d93860f3d5b4ea1.tar.gz
Get `CORRELATION_COMMAND` from current_app not `gn3.settings`
The default settings in `gn3.settings` are meant to be overridden thus the code should not be importing the setting from there, rather, the code should get its configurations settings from `flask.current_app.config`.
-rw-r--r--gn3/computations/rust_correlation.py5
1 files changed, 3 insertions, 2 deletions
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index 546da0e..1ae26b8 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -3,15 +3,15 @@
https://github.com/Alexanderlacuna/correlation_rust
"""
-
import subprocess
import json
import csv
import os
+from flask import current_app
+
from gn3.computations.qtlreaper import create_output_directory
from gn3.chancy import random_string
-from gn3.settings import CORRELATION_COMMAND
from gn3.settings import TMPDIR
@@ -54,6 +54,7 @@ def run_correlation(
"""entry function to call rust correlation"""
# pylint: disable=too-many-arguments
+ CORRELATION_COMMAND = current_app.config["CORRELATION_COMMAND"] # make arg?
(tmp_dir, tmp_file) = generate_input_files(dataset)
(output_file, json_file) = generate_json_file(
tmp_dir=tmp_dir, tmp_file=tmp_file, method=method, delimiter=delimiter,