Neo4j

neo4j/README.md

@@ -0,0 +1,24 @@
+# Neo4J ADCY5
+This directory in the repository explains how to setup and create the Neo4J database.
+
+## Quickstart
+
+1. Run the command `python main.py` to create the JSON file which performs data collection accross the internet.
+2. Run the command `python ParseJson.py` creates the CSV.
+3. Open the `load.cql` file to create the query from the `output.csv` to run on the cloud Neo4J.
+
+## Cloud Storage
+The data is located on https://console.neo4j.io/ and you can find the authentication, urls, and secrets in `keys.txt`.
+
+## Install
+- Run `./install.sh`
+- Run the command `./neo4j-community-5.17.0/bin/neo4j status` to see the status of the Neo4J database.
+
+## Visualize
+
+Run this query to produce a visualization.
+
+```cypher
+MATCH (v:Variant)-[:CONTRIBUTED_BY]->(c:Contributor)
+RETURN v, c
+```

neo4j/app.py

@@ -0,0 +1,33 @@
+from flask import Flask, request, Response
+import requests
+from flask_cors import CORS  # Import CORS
+
+app = Flask(__name__)
+CORS(app)  # Enable CORS on the Flask app
+NEO4J_URL = "http://localhost:7474/browser"  # Default URL where Neo4j browser is running
+
+@app.route('/', defaults={'path': ''}, methods=["GET", "POST", "PUT", "DELETE", "PATCH"])
+@app.route('/<path:path>', methods=["GET", "POST", "PUT", "DELETE", "PATCH"])
+def proxy(path):
+    global NEO4J_URL
+    if request.method == "GET":
+        resp = requests.get(f'{NEO4J_URL}/{path}', stream=True)
+    elif request.method == "POST":
+        resp = requests.post(f'{NEO4J_URL}/{path}', json=request.json, stream=True)
+    elif request.method == "PUT":
+        resp = requests.put(f'{NEO4J_URL}/{path}', json=request.json, stream=True)
+    elif request.method == "DELETE":
+        resp = requests.delete(f'{NEO4J_URL}/{path}', stream=True)
+    elif request.method == "PATCH":
+        resp = requests.patch(f'{NEO4J_URL}/{path}', json=request.json, stream=True)
+    else:
+        return 'Unsupported HTTP method', 405
+
+    excluded_headers = ['content-encoding', 'content-length', 'transfer-encoding', 'connection']
+    headers = [(name, value) for (name, value) in resp.raw.headers.items()
+               if name.lower() not in excluded_headers]
+    response = Response(resp.content, resp.status_code, headers)
+    return response
+
+if __name__ == '__main__':
+    app.run(port=8888, debug=True)

neo4j/install.sh

@@ -0,0 +1,3 @@
+wget https://neo4j.com/artifact.php?name=neo4j-community-5.17.0-unix.tar.gz
+tar -xf artifact.php\?name\=neo4j-community-5.17.0-unix.tar.gz
+./neo4j-community-5.17.0/bin/neo4j start

neo4j/keys.txt

@@ -0,0 +1,6 @@
+# Wait 60 seconds before connecting using these details, or login to https://console.neo4j.io to validate the Aura Instance is available
+NEO4J_URI=neo4j+s://a8b1f4fd.databases.neo4j.io
+NEO4J_USERNAME=neo4j
+NEO4J_PASSWORD=43SNNN1z7WxtGO95-8uwA0qSLLRk6AgL52OyrbjFVDg
+AURA_INSTANCEID=a8b1f4fd
+AURA_INSTANCENAME=Instance01

neo4j/load.cql

@@ -0,0 +1,9 @@
+LOAD CSV WITH HEADERS FROM 'file:///output.csv' AS row
+WITH row WHERE row.Contributors IS NOT NULL
+MERGE (v:Variant {name: row.`Allelic variant list`})
+MERGE (r:Reference {citation: row.`Reference list`})
+MERGE (l:Link {url: row.`External links`})
+MERGE (c:Contributor {name: row.Contributors})
+MERGE (v)-[:HAS_REFERENCE]->(r)
+MERGE (r)-[:HAS_LINK]->(l)
+MERGE (v)-[:CONTRIBUTED_BY]->(c);