Server init

.dockerignore

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+# Git
+.git
+.gitignore
+
+# Python Cache
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+
+# Local Virtual Environments (Crucial to ignore)
+venv
+env
+.env
+.venv
+
+# Local Model Folders (Docker will download a fresh copy on Linux)
+dnabert_local
+*.bin
+*.safetensors
+
+# Mac System Files
+.DS_Store
+
+# Frontend Artifacts (If you have them in the same folder)
+node_modules
+.next
+build
+dist
+
+# Docker
+Dockerfile
+.dockerignore

.gitignore

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+# --- Python ---
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+.venv/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# --- FastAPI / Environment ---
+.env
+.env.local
+
+# --- Node.js / Next.js ---
+node_modules/
+/.next/
+/out/
+.next
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+.pnpm-debug.log*
+
+# --- Project Specific (IMPORTANT) ---
+# Don't push the massive AI model to GitHub
+dnabert_local/
+*.bin
+*.safetensors
+*.pth
+*.pt
+
+# --- Mac OS ---
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# --- IDEs ---
+.vscode/
+.idea/
+*.swp

Dockerfile

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+FROM python:3.10-slim
+
+WORKDIR /app
+
+COPY requirements.txt .
+
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY . .
+
+RUN mkdir -p temp_uploads
+
+EXPOSE 8000
+
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000"]

main.py

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+import os
+import shutil
+from enum import Enum
+from typing import List, Optional
+from datetime import datetime
+
+from fastapi import FastAPI, Depends, HTTPException, UploadFile, File, Form
+from fastapi.responses import FileResponse
+from pydantic import BaseModel
+from sqlalchemy import create_engine, Column, Integer, String, DateTime
+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import sessionmaker, Session
+
+SQLALCHEMY_DATABASE_URL = "sqlite:///./lab.db"
+
+engine = create_engine(
+    SQLALCHEMY_DATABASE_URL, connect_args={"check_same_thread": False}
+)
+SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine)
+
+Base = declarative_base()
+
+class RequestStatus(str, Enum):
+    PENDING = "pending"
+    FILE_UPLOADED = "file uploaded"
+    DONE = "done"
+
+class LabRequest(Base):
+    __tablename__ = "requests"
+
+    id = Column(Integer, primary_key=True, index=True)
+    name = Column(String, index=True)
+    details = Column(String)
+    status = Column(String, default=RequestStatus.PENDING)
+    fastq_file_path = Column(String, nullable=True)
+    report_path = Column(String, nullable=True)
+    created_at = Column(DateTime, default=datetime.utcnow)
+
+Base.metadata.create_all(bind=engine)
+
+class RequestCreate(BaseModel):
+    name: str
+    details: str
+
+class RequestResponse(BaseModel):
+    id: int
+    name: str
+    details: str
+    status: str
+    fastq_file_path: Optional[str] = None
+    report_path: Optional[str] = None
+    created_at: datetime
+
+    class Config:
+        from_attributes = True
+
+app = FastAPI()
+
+UPLOAD_DIR = "temp_uploads"
+os.makedirs(UPLOAD_DIR, exist_ok=True)
+
+def get_db():
+    db = SessionLocal()
+    try:
+        yield db
+    finally:
+        db.close()
+
+@app.post("/request", response_model=RequestResponse)
+def create_request(request: RequestCreate, db: Session = Depends(get_db)):
+    db_request = LabRequest(
+        name=request.name,
+        details=request.details,
+        status=RequestStatus.PENDING
+    )
+    db.add(db_request)
+    db.commit()
+    db.refresh(db_request)
+    return db_request
+
+@app.get("/get-request", response_model=List[RequestResponse])
+def get_requests(db: Session = Depends(get_db)):
+    return db.query(LabRequest).all()
+
+@app.put("/modify-request/{request_id}", response_model=RequestResponse)
+async def modify_request(
+    request_id: int,
+    fastq_file: Optional[UploadFile] = File(None),
+    report_file: Optional[UploadFile] = File(None),
+    db: Session = Depends(get_db)
+):
+    db_request = db.query(LabRequest).filter(LabRequest.id == request_id).first()
+    if not db_request:
+        raise HTTPException(status_code=404, detail="Request not found")
+
+    if fastq_file:
+        file_location = f"{UPLOAD_DIR}/{request_id}_fastq_{fastq_file.filename}"
+        with open(file_location, "wb+") as file_object:
+            shutil.copyfileobj(fastq_file.file, file_object)
+        db_request.fastq_file_path = file_location
+        db_request.status = RequestStatus.FILE_UPLOADED
+
+    if report_file:
+        report_location = f"{UPLOAD_DIR}/{request_id}_report_{report_file.filename}"
+        with open(report_location, "wb+") as file_object:
+            shutil.copyfileobj(report_file.file, file_object)
+        db_request.report_path = report_location
+        db_request.status = RequestStatus.DONE
+    
+    db.commit()
+    db.refresh(db_request)
+    return db_request
+
+@app.get("/download/{filename}")
+async def download_file(filename: str):
+    file_path = os.path.join(UPLOAD_DIR, filename)
+    if os.path.exists(file_path):
+        return FileResponse(file_path, filename=filename)
+    raise HTTPException(status_code=404, detail="File not found")

requirements.txt

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+fastapi
+uvicorn
+sqlalchemy
+python-multipart