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import io
import json
import os
import sys
import tempfile
import uuid
import zipfile
from contextlib import redirect_stdout
from pathlib import Path
from fastapi import FastAPI, File, Form, UploadFile
from fastapi.responses import FileResponse, JSONResponse, StreamingResponse
from fastapi.staticfiles import StaticFiles
app = FastAPI()
# In-memory job store
jobs: dict = {}
@app.post("/api/process")
async def process(
model_files: list[UploadFile] = File(...),
mapping_files: list[UploadFile] = File(...),
expr_file: UploadFile = File(...),
batch_count: int = Form(1000),
):
job_id = str(uuid.uuid4())
jobs[job_id] = {
"status": "running",
"progress": 0,
"messages": [],
"output_zip": None,
"error": None,
"file_count": batch_count,
"species_count": len(model_files),
}
# Save uploaded files to temp dir
tmp = tempfile.mkdtemp()
model_paths = []
for f in model_files:
content = await f.read()
path = os.path.join(tmp, f.filename)
with open(path, "wb") as out:
out.write(content)
model_paths.append(path)
mapping_paths = []
for f in mapping_files:
content = await f.read()
path = os.path.join(tmp, f.filename)
with open(path, "wb") as out:
out.write(content)
mapping_paths.append(path)
expr_content = await expr_file.read()
expr_path = os.path.join(tmp, expr_file.filename)
with open(expr_path, "wb") as out:
out.write(expr_content)
species_prefixes = [Path(f.filename).stem.split("_")[0] for f in model_files]
asyncio.create_task(
run_bootstrap(job_id, model_paths, mapping_paths, expr_path, species_prefixes, batch_count, tmp)
)
return {"job_id": job_id}
async def run_bootstrap(job_id, model_paths, mapping_paths, expr_path, species_prefixes, batch_count, tmp):
job = jobs[job_id]
def add_msg(text, type_=""):
job["messages"].append({"text": text, "type": type_})
try:
add_msg(f"Starting bootstrap for: {', '.join(species_prefixes)}", "info")
job["progress"] = 10
output_dir = os.path.join(tmp, "output")
os.makedirs(output_dir, exist_ok=True)
captured = io.StringIO()
def run_sync():
sys.path.insert(0, "/app")
from utils.bootstrap_genes import bootstrap_genes
with redirect_stdout(captured):
bootstrap_genes(
model_pre_filenames=model_paths,
mapping_filenames=mapping_paths,
species_prefixes=species_prefixes,
combined_geneExpr_filename=expr_path,
geneExpr_folder=output_dir,
batch_count=batch_count,
)
job["progress"] = 20
loop = asyncio.get_event_loop()
await loop.run_in_executor(None, run_sync)
job["progress"] = 80
# Relay only key status lines — skip all Warning lines
for line in captured.getvalue().strip().split("\n"):
line = line.strip()
if not line or line.startswith("Warning"):
continue
if "Write to" in line:
add_msg("Writing output files…", "ok")
elif line.startswith("Read") or line.startswith("Species") or line.startswith("Bootstrap"):
add_msg(line, "info")
add_msg("Compressing output files…", "info")
job["progress"] = 90
zip_path = os.path.join(tmp, "geneExpr_bootstrapped.zip")
output_files = sorted([f for f in os.listdir(output_dir) if f.endswith(".csv")])
with zipfile.ZipFile(zip_path, "w", zipfile.ZIP_DEFLATED) as zf:
for fname in output_files:
zf.write(os.path.join(output_dir, fname), arcname=fname)
job["output_zip"] = zip_path
job["file_count"] = batch_count
job["species_count"] = len(species_prefixes)
job["progress"] = 100
job["status"] = "done"
add_msg(f"Done! {batch_count} files generated.", "ok")
except Exception as e:
import traceback
job["status"] = "error"
job["error"] = str(e)
add_msg(f"Error: {e}", "err")
print(traceback.format_exc(), flush=True)
@app.get("/api/progress/{job_id}")
async def progress_stream(job_id: str):
async def event_stream():
last_idx = 0
while True:
job = jobs.get(job_id)
if not job:
yield f"data: {json.dumps({'status': 'error', 'error': 'Job not found'})}\n\n"
break
new_msgs = job["messages"][last_idx:]
last_idx = len(job["messages"])
for msg in new_msgs:
payload = {
"message": msg["text"],
"type": msg["type"],
"progress": job["progress"],
"label": msg["text"],
}
yield f"data: {json.dumps(payload)}\n\n"
if job["status"] == "done":
yield f"data: {json.dumps({'status': 'done', 'progress': 100, 'file_count': job.get('file_count'), 'species_count': job.get('species_count')})}\n\n"
break
elif job["status"] == "error":
yield f"data: {json.dumps({'status': 'error', 'error': job.get('error', 'Unknown error')})}\n\n"
break
if not new_msgs:
yield f"data: {json.dumps({'progress': job['progress'], 'label': 'Processing…'})}\n\n"
await asyncio.sleep(1)
return StreamingResponse(
event_stream(),
media_type="text/event-stream",
headers={"Cache-Control": "no-cache", "X-Accel-Buffering": "no"},
)
@app.get("/api/download/{job_id}")
async def download(job_id: str):
job = jobs.get(job_id, {})
zip_path = job.get("output_zip")
if not zip_path or not os.path.exists(zip_path):
return JSONResponse({"error": "File not found"}, status_code=404)
return FileResponse(
zip_path,
filename="geneExpr_bootstrapped.zip",
media_type="application/zip",
)
# Serve frontend — must be last
app.mount("/", StaticFiles(directory="/app/frontend", html=True), name="frontend")
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