Replace APP_DEFAULTS dict with actual conf params

5 files changed, 16 insertions, 20 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())
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index deabcc4..e434dab 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -20,13 +20,11 @@ class GemmaAPITest(unittest.TestCase):
     """Test cases for the Gemma API"""
     def setUp(self):
         self.app = create_app({
-            "APP_DEFAULTS": {
-                "GENODIR": os.path.abspath(
-                    os.path.join(os.path.dirname(__file__),
-                                 "test_data/")),
-                "TMPDIR": "/tmp",
-                "REDIS_JOB_QUEUE": "GN3::job-queue",
-                "GEMMA_WRAPPER_CMD": "gemma-wrapper"}}).test_client()
+            "GENODIR": os.path.abspath(
+                os.path.join(os.path.dirname(__file__),
+                             "test_data/")),
+            "REDIS_JOB_QUEUE": "GN3::job-queue",
+            "GEMMA_WRAPPER_CMD": "gemma-wrapper"}).test_client()
 
     @mock.patch("gn3.api.gemma.run_cmd")
     def test_get_version(self, mock_run_cmd):