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-rw-r--r--gn3/api/gemma.py6
-rw-r--r--gn3/api/general.py2
-rw-r--r--gn3/file_utils.py1
-rw-r--r--gn3/settings.py15
4 files changed, 11 insertions, 13 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 7c76f2f..a351ab1 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -19,7 +19,7 @@ gemma = Blueprint("gemma", __name__)
@gemma.route("/version")
def get_version():
"""Display the installed version of gemma-wrapper"""
- gemma_cmd = current_app.config['APP_DEFAULTS'].get('GEMMA_WRAPPER_CMD')
+ gemma_cmd = current_app.config["GEMMA_WRAPPER_CMD"]
return jsonify(
run_cmd(f"{gemma_cmd} -v | head -n 1"))
@@ -34,7 +34,7 @@ file output is returned.
"""
data = request.get_json()
- app_defaults = current_app.config.get('APP_DEFAULTS')
+ app_defaults = current_app.config
__hash = generate_hash_of_string(
f"{data.get('genofile_name')}_"
''.join(data.get("values", "")))
@@ -52,7 +52,7 @@ file output is returned.
if data.get("loco"):
gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}"
k_computation_cmd = generate_gemma_computation_cmd(
- gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD") + "_haha",
+ gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"),
gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"},
gemma_kwargs=gemma_kwargs,
output_file=(f"{app_defaults.get('TMPDIR')}/gn2/"
diff --git a/gn3/api/general.py b/gn3/api/general.py
index 91a113c..d05d6f4 100644
--- a/gn3/api/general.py
+++ b/gn3/api/general.py
@@ -25,7 +25,7 @@ week. If a TOKEN is not provided, generate a token for the new user.
status = 201
results = extract_uploaded_file(
gzipped_file=file_,
- target_dir=current_app.config["APP_DEFAULTS"].get("TMPDIR"),
+ target_dir=current_app.config["TMPDIR"],
token=token)
if results.get("status") > 0:
status = 500
diff --git a/gn3/file_utils.py b/gn3/file_utils.py
index ca80373..d5177b0 100644
--- a/gn3/file_utils.py
+++ b/gn3/file_utils.py
@@ -9,7 +9,6 @@ import tarfile
from functools import partial
from typing import Dict
from werkzeug.utils import secure_filename
-from gn3.settings import APP_DEFAULTS
def get_dir_hash(directory: str) -> str:
diff --git a/gn3/settings.py b/gn3/settings.py
index ddff766..f5988bb 100644
--- a/gn3/settings.py
+++ b/gn3/settings.py
@@ -3,11 +3,10 @@
import tempfile
import os
-APP_DEFAULTS = {
- "BCRYPT_SALT": "$2b$12$mxLvu9XRLlIaaSeDxt8Sle", # Change this!
- "GEMMA_WRAPPER_CMD": os.environ.get("GEMMA_WRAPPER", "gemma-wrapper"),
- "TMPDIR": os.environ.get("TMPDIR", tempfile.gettempdir()),
- "GENODIR": "",
- "REDIS_URI": "redis://localhost:6379/0",
- "REDIS_JOB_QUEUE": "GN3::job-queue"
-}
+BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle" # Change this!
+DATA_DIR = ""
+GEMMA_WRAPPER_CMD = os.environ.get("GEMMA_WRAPPER", "gemma-wrapper")
+GENODIR = ""
+REDIS_URI = "redis://localhost:6379/0"
+REDIS_JOB_QUEUE = "GN3::job-queue"
+TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir())