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"""
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FastAPI Main Application
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Backend API for Cancer@Home
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"""
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from fastapi import FastAPI, HTTPException
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from fastapi.middleware.cors import CORSMiddleware
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from fastapi.staticfiles import StaticFiles
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from fastapi.responses import HTMLResponse
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from strawberry.fastapi import GraphQLRouter
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from pathlib import Path
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import uvicorn
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from backend.neo4j.graphql_schema import schema
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from backend.neo4j.db_manager import DatabaseManager
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from backend.boinc.client import BOINCClient, BOINCTaskManager
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from backend.gdc.client import GDCClient
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from backend.pipeline import (
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FASTQProcessor,
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BLASTRunner,
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VariantCaller
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)
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app = FastAPI(
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title="Cancer@Home v2",
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description="Distributed cancer genomics research platform",
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version="2.0.0"
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)
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app.add_middleware(
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CORSMiddleware,
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allow_origins=["*"],
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allow_credentials=True,
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allow_methods=["*"],
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allow_headers=["*"],
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)
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graphql_app = GraphQLRouter(schema)
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app.include_router(graphql_app, prefix="/graphql")
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frontend_path = Path("frontend/dist")
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if frontend_path.exists():
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app.mount("/static", StaticFiles(directory=str(frontend_path)), name="static")
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@app.get("/", response_class=HTMLResponse)
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async def root():
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"""Serve main dashboard"""
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html_file = Path("frontend/index.html")
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if html_file.exists():
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with open(html_file, 'r') as f:
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return f.read()
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return """
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<!DOCTYPE html>
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<html>
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<head>
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<title>Cancer@Home v2</title>
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<style>
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body {
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font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
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margin: 0;
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padding: 0;
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background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
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color: white;
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}
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.container {
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max-width: 1200px;
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margin: 0 auto;
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padding: 40px 20px;
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}
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h1 {
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font-size: 3em;
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margin-bottom: 20px;
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}
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.card {
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background: rgba(255, 255, 255, 0.1);
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border-radius: 10px;
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padding: 30px;
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margin: 20px 0;
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backdrop-filter: blur(10px);
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}
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.links {
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display: grid;
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grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
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gap: 20px;
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margin-top: 30px;
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}
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.link-card {
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background: rgba(255, 255, 255, 0.15);
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border-radius: 8px;
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padding: 20px;
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text-decoration: none;
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color: white;
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transition: transform 0.2s;
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}
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.link-card:hover {
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transform: translateY(-5px);
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background: rgba(255, 255, 255, 0.25);
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}
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.link-card h3 {
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margin-top: 0;
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}
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</style>
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</head>
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<body>
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<div class="container">
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<h1>🧬 Cancer@Home v2</h1>
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<div class="card">
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<h2>Welcome to Cancer@Home</h2>
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<p>A distributed computing platform for cancer genomics research</p>
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</div>
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<div class="links">
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<a href="/api/docs" class="link-card">
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<h3>📚 API Documentation</h3>
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<p>Interactive API docs with Swagger UI</p>
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</a>
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<a href="/graphql" class="link-card">
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<h3>🔍 GraphQL Playground</h3>
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<p>Query cancer data with GraphQL</p>
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</a>
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<a href="http://localhost:7474" class="link-card">
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<h3>📊 Neo4j Browser</h3>
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<p>Visualize graph database</p>
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</a>
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<a href="/api/health" class="link-card">
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<h3>💚 Health Check</h3>
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<p>Check system status</p>
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</a>
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</div>
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</div>
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</body>
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</html>
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"""
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@app.get("/api/health")
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async def health_check():
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"""Health check endpoint"""
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db = DatabaseManager()
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try:
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db.execute_query("RETURN 1")
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neo4j_status = "healthy"
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except Exception as e:
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neo4j_status = f"unhealthy: {str(e)}"
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finally:
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db.close()
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return {
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"status": "healthy",
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"neo4j": neo4j_status,
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"version": "2.0.0"
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}
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@app.get("/api/boinc/tasks")
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async def get_boinc_tasks(status: str = None):
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"""Get BOINC tasks"""
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client = BOINCClient()
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tasks = client.list_tasks(status=status)
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return {"tasks": [vars(t) for t in tasks]}
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@app.post("/api/boinc/submit")
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async def submit_boinc_task(workunit_type: str, input_file: str):
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"""Submit new BOINC task"""
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manager = BOINCTaskManager()
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if workunit_type == "variant_calling":
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task_id = manager.submit_variant_calling(input_file)
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elif workunit_type == "blast_search":
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task_id = manager.submit_blast_search(input_file)
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else:
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task_id = manager.client.submit_task(workunit_type, input_file)
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return {"task_id": task_id, "status": "submitted"}
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@app.get("/api/boinc/statistics")
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async def get_boinc_statistics():
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"""Get BOINC statistics"""
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client = BOINCClient()
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stats = client.get_statistics()
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return stats
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@app.get("/api/gdc/projects")
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async def get_gdc_projects():
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"""Get available GDC projects"""
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projects = [
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{"id": "TCGA-BRCA", "name": "Breast Cancer", "cases": 1098},
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{"id": "TCGA-LUAD", "name": "Lung Adenocarcinoma", "cases": 585},
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{"id": "TCGA-COAD", "name": "Colon Adenocarcinoma", "cases": 461},
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{"id": "TCGA-GBM", "name": "Glioblastoma", "cases": 617},
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{"id": "TARGET-AML", "name": "Acute Myeloid Leukemia", "cases": 238},
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]
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return {"projects": projects}
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@app.get("/api/gdc/files/{project_id}")
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async def search_gdc_files(project_id: str, limit: int = 10):
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"""Search GDC files for a project"""
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client = GDCClient()
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files = client.get_project_files(project_id, limit=limit)
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return {"files": [vars(f) for f in files]}
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@app.post("/api/gdc/download")
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async def download_gdc_file(file_id: str):
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"""Download a file from GDC"""
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client = GDCClient()
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file_path = client.download_file(file_id)
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if file_path:
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return {"status": "success", "file_path": str(file_path)}
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else:
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raise HTTPException(status_code=500, detail="Download failed")
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@app.post("/api/pipeline/fastq/qc")
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async def run_fastq_qc(file_path: str):
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"""Run FASTQ quality control"""
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processor = FASTQProcessor()
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stats = processor.calculate_statistics(Path(file_path))
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return {"statistics": stats}
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@app.post("/api/pipeline/blast")
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async def run_blast(query_file: str):
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"""Run BLAST search"""
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runner = BLASTRunner()
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output_file = runner.run_blastn(Path(query_file))
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if output_file:
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hits = runner.parse_results(output_file)
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return {
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"status": "success",
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"output_file": str(output_file),
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"total_hits": len(hits),
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"hits": hits[:10]
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}
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else:
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raise HTTPException(status_code=500, detail="BLAST search failed")
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@app.post("/api/pipeline/variants")
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async def call_variants(alignment_file: str, reference_genome: str):
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"""Call variants from alignment"""
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caller = VariantCaller()
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vcf_file = caller.call_variants(
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Path(alignment_file),
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Path(reference_genome)
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)
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variants = caller.filter_variants(vcf_file)
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return {
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"status": "success",
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"vcf_file": str(vcf_file),
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"total_variants": len(variants),
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"variants": [vars(v) for v in variants]
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}
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@app.get("/api/neo4j/summary")
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async def get_database_summary():
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"""Get database summary statistics"""
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db = DatabaseManager()
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query = """
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MATCH (g:Gene) WITH count(g) as genes
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MATCH (m:Mutation) WITH genes, count(m) as mutations
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MATCH (p:Patient) WITH genes, mutations, count(p) as patients
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MATCH (c:CancerType) WITH genes, mutations, patients, count(c) as cancer_types
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RETURN genes, mutations, patients, cancer_types
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"""
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result = db.execute_query(query)
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db.close()
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return result[0] if result else {}
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@app.get("/api/neo4j/genes/{symbol}")
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async def get_gene_info(symbol: str):
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"""Get gene information"""
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db = DatabaseManager()
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from backend.neo4j.db_manager import GeneRepository
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repo = GeneRepository(db)
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gene = repo.get_gene_by_symbol(symbol)
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if gene:
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mutations = repo.get_gene_mutations(gene['gene_id'])
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db.close()
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return {
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"gene": gene,
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"mutations": mutations,
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"mutation_count": len(mutations)
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}
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db.close()
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raise HTTPException(status_code=404, detail="Gene not found")
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if __name__ == "__main__":
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uvicorn.run(app, host="0.0.0.0", port=5000)
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