feat: adapt notebook to renku setup

Author: vancauwe

src/neo4j-quickstart/quickstart.ipynb

@@ -28,10 +28,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Define your NEO4J database\n",
-    "\n",
-    "neo4j_database = \"neo4j\"  \n",
-    "\n",
     "# Define your nodes\n",
     "\n",
     "nodes = [\"user\", \"repo\", \"org\"]\n",
@@ -63,21 +59,28 @@
    "source": [
     "import neo4j\n",
     "from utils.neo4jdownloader import Neo4JDownloader\n",
-    "from dotenv import load_dotenv\n",
+    "#from dotenv import load_dotenv\n",
+    "from pathlib import Path\n",
     "import os\n",
     "\n",
-    "load_dotenv()  # Load environment variables from .env file\n",
+    "#load_dotenv()  # Load environment variables from .env file\n",
+    "\n",
+    "def get_downloader():\n",
+    "    secrets_dir = Path(\"/secrets\")\n",
+    "    NEO4J_URI = (secrets_dir / \"neo4j_uri\").read_text()\n",
+    "    NEO4J_USERNAME = (secrets_dir / \"neo4j_user\").read_text()\n",
+    "    NEO4J_PASSWORD = (secrets_dir / \"neo4j_password\").read_text()\n",
+    "    NEO4J_DATABASE = (secrets_dir / \"neo4j_database\").read_text()\n",
     "\n",
-    "def get_downloader(neo4j_database):\n",
-    "    NEO4J_URI = os.environ.get(\"NEO4J_URI\")\n",
-    "    NEO4J_USERNAME = os.environ.get(\"NEO4J_USER\")\n",
-    "    NEO4J_PASSWORD = os.environ.get(\"NEO4J_PASSWORD\")\n",
-    "    NEO4J_DATABASE = neo4j_database\n",
+    "    # NEO4J_URI = os.environ.get(\"NEO4J_URI\")\n",
+    "    # NEO4J_USERNAME = os.environ.get(\"NEO4J_USER\")\n",
+    "    # NEO4J_PASSWORD = os.environ.get(\"NEO4J_PASSWORD\")\n",
+    "    # NEO4J_DATABASE = neo4j_database\n",
     "\n",
     "    return Neo4JDownloader(NEO4J_URI, NEO4J_USERNAME, NEO4J_PASSWORD, NEO4J_DATABASE)\n",
     "\n",
-    "def extract_data(neo4j_database, nodes, relationships):\n",
-    "    downloader = get_downloader(neo4j_database)\n",
+    "def extract_data(nodes, relationships):\n",
+    "    downloader = get_downloader()\n",
     "\n",
     "    try:\n",
     "        nodes_ids, nodes_features = downloader.retrieve_nodes(nodes)\n",
@@ -95,7 +98,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "nodes_ids, nodes_features, edges_indices, edges_attributes = extract_data(neo4j_database, nodes, relationships)\n",
+    "nodes_ids, nodes_features, edges_indices, edges_attributes = extract_data(nodes, relationships)\n",
     "# example of looking at the output\n",
     "# print(nodes_ids[\"org\"])\n",
     "# print(nodes_features[\"org\"])\n",