add fipronil notebook

notebooks/fipronil.ipynb

@@ -0,0 +1,115 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 65,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys, os, io, json\n",
+    "from neo4j import GraphDatabase\n",
+    "from py2neo import Graph\n",
+    "from pathlib import Path\n",
+    "from pandas import DataFrame\n",
+    "import networkx as nx\n",
+    "\n",
+    "graph = Graph(\"bolt://localhost:7687\")\n",
+    "driver = GraphDatabase.driver('bolt://localhost:7687', auth=None)\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Get the neighbourhood of Fipronil as GraphML"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df = DataFrame(graph.run(\"\"\"\n",
+    "WITH $query AS query\n",
+    "CALL apoc.export.graphml.query(query, null, {stream:true, useTypes:true, storeNodeIds:true, readLabels:true})\n",
+    "YIELD file, source, format, nodes, relationships, properties, time, rows, batchSize, batches, done, data\n",
+    "RETURN data;\n",
+    "\"\"\", {'query': \"\"\"\n",
+    "MATCH (other)-[r]-(fipronil:GraphNode)-[:id]->(id:Id { id: \\\"chebi:5063\\\" })\n",
+    "RETURN *\n",
+    "\"\"\"}).data())\n",
+    "\n",
+    "with open('fipronil.graphml', 'w') as f:\n",
+    "    f.write(df['data'][0])\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Loading into networkx and writing Cytoscape JSON"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 79,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "## Helper function to run a Cypher query over a GrEBI graph and return a NetworkX graph from the results\n",
+    "##\n",
+    "def query_to_nx(query):\n",
+    "    results = driver.session().run(query)\n",
+    "    G = nx.MultiDiGraph()\n",
+    "    for node in list(results.graph()._nodes.values()):\n",
+    "        if not 'Id' in node._labels:\n",
+    "            G.add_nodes_from([(node._properties['grebi:nodeId'], dict({\"grebi:type\": list(node._labels)}, **node._properties))])\n",
+    "    for rel in list(results.graph()._relationships.values()):\n",
+    "        if not 'Id' in rel.start_node._labels and not 'Id' in rel.end_node._labels:\n",
+    "            G.add_edges_from([(rel.start_node._properties['grebi:nodeId'], rel.end_node._properties['grebi:nodeId'], rel._properties['edge_id'], dict({\"grebi:type\": rel.type}, **rel._properties))])\n",
+    "    return G\n",
+    "\n",
+    "G = query_to_nx(\"\"\"\n",
+    "MATCH (other)-[r]-(fipronil:GraphNode)-[:id]->(id:Id { id: \\\"chebi:5063\\\" })\n",
+    "RETURN *\n",
+    "\"\"\")\n",
+    "\n",
+    "with open('fipronil.cyjs.json', 'w') as f:\n",
+    "    cydata = nx.cytoscape_data(G)\n",
+    "    for node in cydata['elements']['nodes']:\n",
+    "        node['data']['ids'] = node['data']['id']\n",
+    "        node['data']['id'] = node['data']['grebi:nodeId']\n",
+    "        del node['data']['grebi:nodeId']\n",
+    "    json.dump(cydata, f, indent=2)\n",
+    "\n",
+    "\n",
+    "\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}