""" FastAPI Main Application Backend API for Cancer@Home """ from fastapi import FastAPI, HTTPException from fastapi.middleware.cors import CORSMiddleware from fastapi.staticfiles import StaticFiles from fastapi.responses import HTMLResponse from strawberry.fastapi import GraphQLRouter from pathlib import Path import uvicorn from backend.neo4j.graphql_schema import schema from backend.neo4j.db_manager import DatabaseManager from backend.boinc.client import BOINCClient, BOINCTaskManager from backend.gdc.client import GDCClient from backend.pipeline import ( FASTQProcessor, BLASTRunner, VariantCaller ) # Initialize FastAPI app = FastAPI( title="Cancer@Home v2", description="Distributed cancer genomics research platform", version="2.0.0" ) # CORS middleware app.add_middleware( CORSMiddleware, allow_origins=["*"], allow_credentials=True, allow_methods=["*"], allow_headers=["*"], ) # GraphQL endpoint graphql_app = GraphQLRouter(schema) app.include_router(graphql_app, prefix="/graphql") # Serve frontend static files frontend_path = Path("frontend/dist") if frontend_path.exists(): app.mount("/static", StaticFiles(directory=str(frontend_path)), name="static") @app.get("/", response_class=HTMLResponse) async def root(): """Serve main dashboard""" html_file = Path("frontend/index.html") if html_file.exists(): with open(html_file, 'r') as f: return f.read() # Fallback HTML return """ Cancer@Home v2

🧬 Cancer@Home v2

Welcome to Cancer@Home

A distributed computing platform for cancer genomics research

📚 API Documentation

Interactive API docs with Swagger UI

🔍 GraphQL Playground

Query cancer data with GraphQL

📊 Neo4j Browser

Visualize graph database

💚 Health Check

Check system status

""" @app.get("/api/health") async def health_check(): """Health check endpoint""" db = DatabaseManager() try: db.execute_query("RETURN 1") neo4j_status = "healthy" except Exception as e: neo4j_status = f"unhealthy: {str(e)}" finally: db.close() return { "status": "healthy", "neo4j": neo4j_status, "version": "2.0.0" } # BOINC API Endpoints @app.get("/api/boinc/tasks") async def get_boinc_tasks(status: str = None): """Get BOINC tasks""" client = BOINCClient() tasks = client.list_tasks(status=status) return {"tasks": [vars(t) for t in tasks]} @app.post("/api/boinc/submit") async def submit_boinc_task(workunit_type: str, input_file: str): """Submit new BOINC task""" manager = BOINCTaskManager() if workunit_type == "variant_calling": task_id = manager.submit_variant_calling(input_file) elif workunit_type == "blast_search": task_id = manager.submit_blast_search(input_file) else: task_id = manager.client.submit_task(workunit_type, input_file) return {"task_id": task_id, "status": "submitted"} @app.get("/api/boinc/statistics") async def get_boinc_statistics(): """Get BOINC statistics""" client = BOINCClient() stats = client.get_statistics() return stats # GDC API Endpoints @app.get("/api/gdc/projects") async def get_gdc_projects(): """Get available GDC projects""" projects = [ {"id": "TCGA-BRCA", "name": "Breast Cancer", "cases": 1098}, {"id": "TCGA-LUAD", "name": "Lung Adenocarcinoma", "cases": 585}, {"id": "TCGA-COAD", "name": "Colon Adenocarcinoma", "cases": 461}, {"id": "TCGA-GBM", "name": "Glioblastoma", "cases": 617}, {"id": "TARGET-AML", "name": "Acute Myeloid Leukemia", "cases": 238}, ] return {"projects": projects} @app.get("/api/gdc/files/{project_id}") async def search_gdc_files(project_id: str, limit: int = 10): """Search GDC files for a project""" client = GDCClient() files = client.get_project_files(project_id, limit=limit) return {"files": [vars(f) for f in files]} @app.post("/api/gdc/download") async def download_gdc_file(file_id: str): """Download a file from GDC""" client = GDCClient() file_path = client.download_file(file_id) if file_path: return {"status": "success", "file_path": str(file_path)} else: raise HTTPException(status_code=500, detail="Download failed") # Pipeline API Endpoints @app.post("/api/pipeline/fastq/qc") async def run_fastq_qc(file_path: str): """Run FASTQ quality control""" processor = FASTQProcessor() stats = processor.calculate_statistics(Path(file_path)) return {"statistics": stats} @app.post("/api/pipeline/blast") async def run_blast(query_file: str): """Run BLAST search""" runner = BLASTRunner() output_file = runner.run_blastn(Path(query_file)) if output_file: hits = runner.parse_results(output_file) return { "status": "success", "output_file": str(output_file), "total_hits": len(hits), "hits": hits[:10] # Return first 10 hits } else: raise HTTPException(status_code=500, detail="BLAST search failed") @app.post("/api/pipeline/variants") async def call_variants(alignment_file: str, reference_genome: str): """Call variants from alignment""" caller = VariantCaller() vcf_file = caller.call_variants( Path(alignment_file), Path(reference_genome) ) variants = caller.filter_variants(vcf_file) return { "status": "success", "vcf_file": str(vcf_file), "total_variants": len(variants), "variants": [vars(v) for v in variants] } # Neo4j Query Endpoints @app.get("/api/neo4j/summary") async def get_database_summary(): """Get database summary statistics""" db = DatabaseManager() query = """ MATCH (g:Gene) WITH count(g) as genes MATCH (m:Mutation) WITH genes, count(m) as mutations MATCH (p:Patient) WITH genes, mutations, count(p) as patients MATCH (c:CancerType) WITH genes, mutations, patients, count(c) as cancer_types RETURN genes, mutations, patients, cancer_types """ result = db.execute_query(query) db.close() return result[0] if result else {} @app.get("/api/neo4j/genes/{symbol}") async def get_gene_info(symbol: str): """Get gene information""" db = DatabaseManager() from backend.neo4j.db_manager import GeneRepository repo = GeneRepository(db) gene = repo.get_gene_by_symbol(symbol) if gene: mutations = repo.get_gene_mutations(gene['gene_id']) db.close() return { "gene": gene, "mutations": mutations, "mutation_count": len(mutations) } db.close() raise HTTPException(status_code=404, detail="Gene not found") if __name__ == "__main__": uvicorn.run(app, host="0.0.0.0", port=5000)