Update [Config File] : Add user input and infos regarding config file overwriting

Author: Guillaume V.

examples/freesurfer/freesurfer_longitudinal_processing/freesurfer_longitudinal.ipynb

@@ -106,7 +106,11 @@
   {
    "metadata": {},
    "cell_type": "markdown",
-   "source": "**User variables**: should be checked and supplied at each execution. This cell will create a user_config.py file, please modify the values of the file created and not those here",
+   "source": [
+    "**User variables**: should be checked and supplied at each execution. This cell will create a user_config.py file. Please modify the variable values by editing the user_config.py file after it is created.\n",
+    "\n",
+    "⚠️ We strongly advise you not to modify the values directly in this cell in order to avoid conflicts when updating the notebook."
+   ],
    "id": "dd7f54bce66f9e9f"
   },
   {
@@ -134,7 +138,16 @@
     "LICENSE_PATH = Path('~/PATH/LICENSE_NAME.txt').expanduser() # Your pipeline license path, will be copied into VIP input_dirs automatically\n",
     "\"\"\"\n",
     "\n",
-    "CONFIG_PATH.write_text(user_config)"
+    "if CONFIG_PATH.exists():\n",
+    "    answer = input(\"The user_config.py file already exists. Overwrite config ? (y/N): \")\n",
+    "    if answer != \"y\":\n",
+    "        print(\"File not created, as user_config.py already exists.\")\n",
+    "    else:\n",
+    "        CONFIG_PATH.write_text(user_config)\n",
+    "        print(\"User_config.py overwritten with default values.\")\n",
+    "else:\n",
+    "    CONFIG_PATH.write_text(user_config)\n",
+    "    print(\"User_config.py created with default values.\")\n"
    ],
    "id": "c7f8787950ccc948",
    "outputs": [],
@@ -316,7 +329,7 @@
     "}\n",
     "\n",
     "session = VipSession.init(\n",
-    "    api_key=VIP_KEY,\n",
+    "    api_key=cfg.VIP_KEY,\n",
     "    input_dir=str(cfg.LOCAL_DATASET_PATH),\n",
     "    output_dir= str(FS_CROSS_OUTPUT_DIR),\n",
     "    pipeline_id=PIPELINE_ALL_ID,\n",
@@ -343,7 +356,7 @@
    "cell_type": "code",
    "source": [
     "# Connect back to session if needed\n",
-    "VipSession.init(api_key=VIP_KEY)\n",
+    "VipSession.init(api_key=cfg.VIP_KEY)\n",
     "session = VipSession(output_dir=str(FS_CROSS_OUTPUT_DIR))\n",
     "\n",
     "# Download outputs to the output_dir\n",
@@ -483,7 +496,7 @@
     "}\n",
     "\n",
     "session = VipSession.init(\n",
-    "    api_key=VIP_KEY,\n",
+    "    api_key=cfg.VIP_KEY,\n",
     "    input_dir=str(FS_BASE_INPUT_DIR),\n",
     "    output_dir= str(FS_BASE_OUTPUT_DIR),\n",
     "    pipeline_id=PIPELINE_BASE_ID,\n",
@@ -510,7 +523,7 @@
    "cell_type": "code",
    "source": [
     "# Connect back to session if needed\n",
-    "VipSession.init(api_key=VIP_KEY)\n",
+    "VipSession.init(api_key=cfg.VIP_KEY)\n",
     "session = VipSession(output_dir=str(FS_BASE_OUTPUT_DIR))\n",
     "\n",
     "# Download outputs to the output_dir\n",
@@ -596,7 +609,7 @@
     "print(f\"Submitting {len(subjects)} LONG jobs for subjects: {', '.join(subjects)}\")\n",
     "\n",
     "session = VipSession.init(\n",
-    "    api_key=VIP_KEY,\n",
+    "    api_key=cfg.VIP_KEY,\n",
     "    input_dir=str(FS_BASE_OUTPUT_DIR.parent),  # LONG pipeline uses data from BASE inputs and outputs\n",
     "    output_dir=str(FS_LONG_OUTPUT_DIR),\n",
     "    pipeline_id=PIPELINE_LONG_ID,\n",
@@ -623,7 +636,7 @@
    "cell_type": "code",
    "source": [
     "# Connect back to session if needed\n",
-    "VipSession.init(api_key=VIP_KEY)\n",
+    "VipSession.init(api_key=cfg.VIP_KEY)\n",
     "session = VipSession(output_dir=str(FS_LONG_OUTPUT_DIR))\n",
     "\n",
     "# Download outputs to the output_dir\n",