local edges and nodes instead of neo4j

KeremKurban · Jun 7, 2024 · 8587272 · 8587272
1 parent 135885f
commit 8587272
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Showing 9 changed files with 348 additions and 76 deletions.
diff --git a/src/citation/flask/server.py b/src/citation/flask/server.py
@@ -1,81 +1,18 @@
-from flask import Flask, jsonify, render_template, request
-from neo4j import GraphDatabase
-import time
-import os
+"""Flask server for the citation graph."""
+from flask import Flask, render_template
 
-app = Flask(__name__, static_folder='../../../static', template_folder='../../../templates')
+app = Flask(
+    __name__,
+    static_folder="../../../static",
+    template_folder="../../../templates",
+)
 
-# Neo4j connection details from environment variables
-uri = os.getenv("NEO4J_URI", "bolt://localhost:7687")
-username = os.getenv("NEO4J_USERNAME", "neo4j")
-password = os.getenv("NEO4J_PASSWORD", "password")
 
-driver = GraphDatabase.driver(uri, auth=(username, password))
-
-def get_nodes_and_links(tx, limit=100):
-    nodes = []
-    links = []
-
-    # Query to get limited nodes with all properties
-    result = tx.run(f"""
-        MATCH (n:Paper)
-        RETURN n
-        LIMIT {limit}
-    """)
-    for record in result:
-        node = record["n"]
-        node_data = {
-            "uid": node["uid"],
-            "label": node["title"] if "title" in node else node.id,
-            "is_bbp": node.get("is_bbp", False),
-        }
-        nodes.append(node_data)
-
-    # Collect node UIDs
-    node_uids = [node["uid"] for node in nodes]
-
-    # Query to get relationships between the limited nodes
-    result = tx.run(f"""
-        MATCH (n:Paper)-[r:CITES]->(m:Paper)
-        WHERE n.uid IN {node_uids} AND m.uid IN {node_uids}
-        RETURN n.uid AS source, m.uid AS target, r
-    """)
-    for record in result:
-        link_data = {
-            "source": record["source"],
-            "target": record["target"],
-        }
-        links.append(link_data)
-
-    return nodes, links
-
-def with_retry(session_func, *args, retries=5, delay=1):
-    for attempt in range(retries):
-        try:
-            with driver.session() as session:
-                return session_func(session, *args)
-        except InterruptedError:
-            if attempt < retries - 1:
-                time.sleep(delay)
-                continue
-            else:
-                raise
-
-@app.route('/nodes')
-def get_nodes():
-    limit = int(request.args.get('limit', 100))  # Get limit from query parameter or default to 100
-    nodes, _ = with_retry(lambda s: s.read_transaction(get_nodes_and_links, limit))
-    return jsonify(nodes)
-
-@app.route('/links')
-def get_links():
-    limit = int(request.args.get('limit', 100))  # Get limit from query parameter or default to 100
-    _, links = with_retry(lambda s: s.read_transaction(get_nodes_and_links, limit))
-    return jsonify(links)
-
-@app.route('/')
+@app.route("/")
 def index():
-    return render_template('index.html')
+    """Render the index page."""
+    return render_template("index.html")
+
 
-if __name__ == '__main__':
-    app.run(debug=True)
+if __name__ == "__main__":
+    app.run(debug=True)
diff --git a/src/citation/flask/server_neo4j.py b/src/citation/flask/server_neo4j.py
@@ -0,0 +1,81 @@
+from flask import Flask, jsonify, render_template, request
+from neo4j import GraphDatabase
+import time
+import os
+
+app = Flask(__name__, static_folder='../../../static', template_folder='../../../templates')
+
+# Neo4j connection details from environment variables
+uri = os.getenv("NEO4J_URI", "bolt://localhost:7687")
+username = os.getenv("NEO4J_USERNAME", "neo4j")
+password = os.getenv("NEO4J_PASSWORD", "password")
+
+driver = GraphDatabase.driver(uri, auth=(username, password))
+
+def get_nodes_and_links(tx, limit=100):
+    nodes = []
+    links = []
+
+    # Query to get limited nodes with all properties
+    result = tx.run(f"""
+        MATCH (n:Paper)
+        RETURN n
+        LIMIT {limit}
+    """)
+    for record in result:
+        node = record["n"]
+        node_data = {
+            "uid": node["uid"],
+            "label": node["title"] if "title" in node else node.id,
+            "is_bbp": node.get("is_bbp", False),
+        }
+        nodes.append(node_data)
+
+    # Collect node UIDs
+    node_uids = [node["uid"] for node in nodes]
+
+    # Query to get relationships between the limited nodes
+    result = tx.run(f"""
+        MATCH (n:Paper)-[r:CITES]->(m:Paper)
+        WHERE n.uid IN {node_uids} AND m.uid IN {node_uids}
+        RETURN n.uid AS source, m.uid AS target, r
+    """)
+    for record in result:
+        link_data = {
+            "source": record["source"],
+            "target": record["target"],
+        }
+        links.append(link_data)
+
+    return nodes, links
+
+def with_retry(session_func, *args, retries=5, delay=1):
+    for attempt in range(retries):
+        try:
+            with driver.session() as session:
+                return session_func(session, *args)
+        except InterruptedError:
+            if attempt < retries - 1:
+                time.sleep(delay)
+                continue
+            else:
+                raise
+
+@app.route('/nodes')
+def get_nodes():
+    limit = int(request.args.get('limit', 100))  # Get limit from query parameter or default to 100
+    nodes, _ = with_retry(lambda s: s.read_transaction(get_nodes_and_links, limit))
+    return jsonify(nodes)
+
+@app.route('/links')
+def get_links():
+    limit = int(request.args.get('limit', 100))  # Get limit from query parameter or default to 100
+    _, links = with_retry(lambda s: s.read_transaction(get_nodes_and_links, limit))
+    return jsonify(links)
+
+@app.route('/')
+def index():
+    return render_template('index.html')
+
+if __name__ == '__main__':
+    app.run(debug=True)
diff --git a/static/links.json b/static/links.json
diff --git a/static/nodes.json b/static/nodes.json
diff --git a/templates/bloom.html b/templates/bloom.html
@@ -0,0 +1,53 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>3D Force Graph</title>
+    <style> 
+        body { margin: 0; } 
+    </style>
+    <script src="//unpkg.com/3d-force-graph"></script>
+    <script type="importmap">{ "imports": { "three": "//unpkg.com/three/build/three.module.js" } }</script>
+</head>
+<body>
+    <div id="3d-graph"></div>
+    <script type="module">
+        import { UnrealBloomPass } from '//unpkg.com/three/examples/jsm/postprocessing/UnrealBloomPass.js';
+
+        const Graph = ForceGraph3D()
+            (document.getElementById('3d-graph'))
+            .backgroundColor('#000003')
+            .nodeLabel('label')
+            .nodeColor(node => node.is_bbp ? 'cyan' : 'red')
+            .nodeVal(node => node.is_bbp ? 10 : 5)  // Set node size based on is_bbp
+            .linkDirectionalParticles(2)  // Add particles to links for visibility
+            .linkDirectionalParticleWidth(0.5)  // Set the width of link particles to make them less bright
+            .linkWidth(1);  // Set the width of links
+
+        // Load data
+        fetch('/static/nodes.json')
+            .then(response => response.json())
+            .then(nodes => {
+                fetch('/static/links.json')
+                    .then(response => response.json())
+                    .then(links => {
+                        // Combine nodes and links into a graph data object
+                        const graphData = { nodes, links };
+
+                        // Apply graph data to the 3D force graph
+                        Graph.graphData(graphData);
+
+                        // Apply UnrealBloomPass for post-processing
+                        const bloomPass = new UnrealBloomPass();
+                        bloomPass.strength = 0.5;
+                        bloomPass.radius = 1;
+                        bloomPass.threshold = 0;
+                        Graph.postProcessingComposer().addPass(bloomPass);
+                    });
+            });
+
+        // Adjust graph dimensions
+        Graph.width(window.innerWidth).height(window.innerHeight);
+    </script>
+</body>
+</html>
diff --git a/templates/index.html b/templates/index.html
@@ -0,0 +1,31 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>3D Force Graph</title>
+    <script src="https://unpkg.com/3d-force-graph"></script>
+</head>
+<body>
+    <div id="3d-graph"></div>
+    <script>
+        // Initialize 3D Force Graph
+        const Graph = ForceGraph3D()
+            (document.getElementById('3d-graph'))
+            .graphData({nodes: [], links: []});
+
+        // Load data
+        fetch('/static/nodes.json')
+            .then(response => response.json())
+            .then(nodes => {
+                fetch('/static/links.json')
+                    .then(response => response.json())
+                    .then(links => {
+                        Graph.graphData({nodes, links});
+                    });
+            });
+
+        // Adjust graph dimensions
+        Graph.width(window.innerWidth).height(window.innerHeight);
+    </script>
+</body>
+</html>
diff --git a/templates/neo4j.html b/templates/neo4j.html
@@ -0,0 +1,50 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>3D Force Graph</title>
+    <style> 
+        body { margin: 0; } 
+    </style>
+    <script src="//unpkg.com/3d-force-graph"></script>
+    <script type="importmap">{ "imports": { "three": "//unpkg.com/three/build/three.module.js" } }</script>
+</head>
+<body>
+    <div id="3d-graph"></div>
+    <script type="module">
+        import { UnrealBloomPass } from '//unpkg.com/three/examples/jsm/postprocessing/UnrealBloomPass.js';
+
+        const Graph = ForceGraph3D()
+            (document.getElementById('3d-graph'))
+            .backgroundColor('#000003')
+            .nodeLabel('label')
+            .nodeColor(node => node.is_bbp ? 'blue' : 'yellow')
+            .nodeVal(node => node.is_bbp ? 10 : 5)  // Set node size based on is_bbp
+            .linkDirectionalParticles(2)  // Add particles to links for visibility
+            .linkDirectionalParticleWidth(0.5)  // Set the width of link particles to make them less bright
+            .linkWidth(1);  // Set the width of links
+
+        // Load data
+        Promise.all([
+            fetch('/nodes').then(response => response.json()),
+            fetch('/links').then(response => response.json())
+        ]).then(([nodes, links]) => {
+            // Combine nodes and links into a graph data object
+            const graphData = { nodes, links };
+
+            // Apply graph data to the 3D force graph
+            Graph.graphData(graphData);
+
+            // Apply UnrealBloomPass for post-processing
+            const bloomPass = new UnrealBloomPass();
+            bloomPass.strength = 4;
+            bloomPass.radius = 1;
+            bloomPass.threshold = 0;
+            Graph.postProcessingComposer().addPass(bloomPass);
+        });
+
+        // Adjust graph dimensions
+        Graph.width(window.innerWidth).height(window.innerHeight);
+    </script>
+</body>
+</html>
diff --git a/templates/neo4j_limit.html b/templates/neo4j_limit.html
@@ -0,0 +1,52 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <title>3D Force Graph</title>
+    <style> 
+        body { margin: 0; } 
+    </style>
+    <script src="//unpkg.com/3d-force-graph"></script>
+    <script type="importmap">{ "imports": { "three": "//unpkg.com/three/build/three.module.js" } }</script>
+</head>
+<body>
+    <div id="3d-graph"></div>
+    <script type="module">
+        import { UnrealBloomPass } from '//unpkg.com/three/examples/jsm/postprocessing/UnrealBloomPass.js';
+
+        const limit = 100;  // Set the limit for number of nodes to fetch
+
+        const Graph = ForceGraph3D()
+            (document.getElementById('3d-graph'))
+            .backgroundColor('#000003')
+            .nodeLabel('label')
+            .nodeColor(node => node.is_bbp ? 'blue' : 'yellow')
+            .nodeVal(node => node.is_bbp ? 10 : 5)  // Set node size based on is_bbp
+            .linkDirectionalParticles(2)  // Add particles to links for visibility
+            .linkDirectionalParticleWidth(0.5)  // Set the width of link particles to make them less bright
+            .linkWidth(1);  // Set the width of links
+
+        // Load data
+        Promise.all([
+            fetch(`/nodes?limit=${limit}`).then(response => response.json()),
+            fetch(`/links?limit=${limit}`).then(response => response.json())
+        ]).then(([nodes, links]) => {
+            // Combine nodes and links into a graph data object
+            const graphData = { nodes, links };
+
+            // Apply graph data to the 3D force graph
+            Graph.graphData(graphData);
+
+            // Apply UnrealBloomPass for post-processing
+            const bloomPass = new UnrealBloomPass();
+            bloomPass.strength = 4;
+            bloomPass.radius = 1;
+            bloomPass.threshold = 0;
+            Graph.postProcessingComposer().addPass(bloomPass);
+        });
+
+        // Adjust graph dimensions
+        Graph.width(window.innerWidth).height(window.innerHeight);
+    </script>
+</body>
+</html>