Refactor: Unified pipeline execution, simplified UI, and fixed Docker config
- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency. - Backend: Changed output format to ZIP and added auto-cleanup of intermediate files. - Backend: Fixed language parameter passing in API and tasks. - Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views. - Frontend: Implemented simulated progress bar for better UX. - Frontend: Restored One-click load button and added result file structure documentation. - Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml. - Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.
This commit is contained in:
zly
@@ -1,118 +0,0 @@
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# Build stage: Install dependencies using pixi
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FROM ghcr.io/prefix-dev/pixi:latest AS builder
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WORKDIR /app
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# Copy project files
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COPY pixi.toml .
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COPY pyproject.toml .
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COPY scripts/ scripts/
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COPY bttoxin/ bttoxin/
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COPY web/ web/
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COPY Data/ Data/
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COPY frontend/ frontend/
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# Install all pixi environments
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RUN pixi install
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# Create shell hook for webbackend environment
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RUN pixi shell-hook -e webbackend > /shell-hook.sh
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RUN echo 'exec "$@"' >> /shell-hook.sh
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# ===========================
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# Stage 1: Build frontend
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# ===========================
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FROM node:20 AS frontend-builder
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WORKDIR /app
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COPY --from=builder /app/frontend ./
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RUN npm install -g pnpm && pnpm install && pnpm build
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# ===========================
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# Stage 2: Production (Nginx + Backend)
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# ===========================
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FROM ubuntu:24.04 AS production
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WORKDIR /app
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# Install Nginx and runtime dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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nginx \
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curl \
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&& rm -rf /var/lib/apt/lists/*
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# Copy pixi executable from builder
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COPY --from=builder /usr/local/bin/pixi /usr/local/bin/pixi
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RUN chmod +x /usr/local/bin/pixi
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# Copy backend environment from builder
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COPY --from=builder /app/.pixi /app/.pixi
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COPY --from=builder /shell-hook.sh /shell-hook.sh
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# Copy backend code
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COPY --from=builder /app/web /app/web
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COPY --from=builder /app/Data /app/Data
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COPY --from=builder /app/bttoxin /app/bttoxin
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COPY --from=builder /app/scripts /app/scripts
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# Copy built frontend
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COPY --from=frontend-builder /app/dist /var/www/html
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# Create jobs directory
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RUN mkdir -p /app/jobs && chmod 777 /app/jobs
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# Configure Nginx
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RUN cat > /etc/nginx/sites-available/default << 'EOF'
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server {
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listen 80;
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server_name _;
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root /var/www/html;
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index index.html;
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# Gzip compression
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gzip on;
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gzip_types text/plain text/css application/json application/javascript text/xml application/xml;
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# Allow uploads up to 100M
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client_max_body_size 100M;
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# Frontend routes - serve index.html for SPA
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location / {
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try_files $uri $uri/ /index.html;
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}
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# API proxy to backend
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location /api/ {
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proxy_pass http://127.0.0.1:8000/;
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proxy_http_version 1.1;
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proxy_set_header Upgrade $http_upgrade;
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proxy_set_header Connection 'upgrade';
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proxy_set_header Host $host;
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proxy_set_header X-Real-IP $remote_addr;
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proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
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proxy_set_header X-Forwarded-Proto $scheme;
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proxy_cache_bypass $http_upgrade;
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}
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# Health check endpoint
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location /health {
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proxy_pass http://127.0.0.1:8000/api/health;
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}
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}
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EOF
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# Expose port
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EXPOSE 80
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# Health check
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HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
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CMD curl -f http://localhost/health || exit 1
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# Entrypoint
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ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
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# Command: Start Nginx and Backend
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CMD ["bash", "-c", "\
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mkdir -p /app/jobs && \
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uvicorn web.backend.main:app --host 127.0.0.1 --port 8000 & \
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nginx -g 'daemon off;' \
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"]
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@@ -1,40 +1,38 @@
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# BtToxin Pipeline - Production Dockerfile (No Nginx)
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# This version is designed to work with Traefik as the reverse proxy.
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# FastAPI serves both the API and the frontend static files.
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# BtToxin Pipeline - Production Dockerfile
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# Optimized for Traefik deployment with unified context
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# ===========================
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# Stage 1: Install dependencies using pixi
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# Stage 1: Builder (Environment & Code)
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# ===========================
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FROM ghcr.io/prefix-dev/pixi:latest AS builder
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WORKDIR /app
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# Copy project files
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COPY pixi.toml .
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COPY pyproject.toml .
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COPY scripts/ scripts/
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COPY bttoxin/ bttoxin/
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COPY backend/ backend/
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COPY Data/ Data/
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# Copy entire project context (filtered by .dockerignore)
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COPY . .
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# Install all pixi environments
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# Install dependencies
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RUN pixi install
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# Setup external database for BtToxin_Digger
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# Using the copy from tools directory included in COPY . .
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RUN DIGGER_PREFIX=$(pixi info --json | grep -A 5 '"name": "digger"' | grep '"prefix":' | cut -d '"' -f 4) && \
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mkdir -p $DIGGER_PREFIX/bin/BTTCMP_db/bt_toxin && \
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rm -rf $DIGGER_PREFIX/bin/BTTCMP_db/bt_toxin/* && \
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cp -r /app/tools/bttoxin_digger/external_dbs/bt_toxin/* $DIGGER_PREFIX/bin/BTTCMP_db/bt_toxin/ && \
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echo "Overwrote internal database with version from external_dbs"
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# Create shell hook for webbackend environment
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RUN pixi shell-hook -e webbackend > /shell-hook.sh
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RUN echo 'exec "$@"' >> /shell-hook.sh
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RUN pixi shell-hook -e webbackend > /shell-hook.sh && \
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echo 'exec "$@"' >> /shell-hook.sh
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# ===========================
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# Stage 2: Build frontend
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# Stage 2: Frontend Builder
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# ===========================
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FROM docker.m.daocloud.io/library/node:latest AS frontend-builder
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FROM docker.m.daocloud.io/library/node:20 AS frontend-builder
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WORKDIR /app
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# Set CI environment variable to prevent pnpm TTY error
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ENV CI=true
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# Copy frontend source
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# Copy only frontend source
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COPY frontend/ .
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RUN npm install -g pnpm && \
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@@ -42,49 +40,37 @@ RUN npm install -g pnpm && \
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pnpm build
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# ===========================
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# Stage 3: Production (FastAPI only)
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# Stage 3: Production (Runtime)
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# ===========================
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FROM docker.m.daocloud.io/library/ubuntu:20.04 AS production
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WORKDIR /app
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# Install runtime dependencies (only curl for healthcheck)
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# Install runtime dependencies
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RUN apt-get update && apt-get install -y --no-install-recommends \
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curl \
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&& rm -rf /var/lib/apt/lists/*
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# Copy pixi executable from builder
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# Copy pixi executable
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COPY --from=builder /usr/local/bin/pixi /usr/local/bin/pixi
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RUN chmod +x /usr/local/bin/pixi
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# Copy backend environment from builder
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COPY --from=builder /app/.pixi /app/.pixi
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# Copy entire prepared application directory (Code + Environment + Data)
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COPY --from=builder /app /app
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# Copy shell hook
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COPY --from=builder /shell-hook.sh /shell-hook.sh
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# Copy backend code
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COPY --from=builder /app/backend /app/backend
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COPY --from=builder /app/Data /app/Data
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COPY --from=builder /app/bttoxin /app/bttoxin
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COPY --from=builder /app/scripts /app/scripts
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COPY --from=builder /app/pixi.toml /app/pixi.toml
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# Copy built frontend
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# Copy built frontend assets
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COPY --from=frontend-builder /app/dist /app/frontend/dist
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# Create jobs directory
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RUN mkdir -p /app/jobs && chmod 777 /app/jobs
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# Set permissions and cleanup
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RUN chmod -R 755 /app/frontend/dist && \
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mkdir -p /app/jobs && chmod 777 /app/jobs
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# Expose port for FastAPI (will be used by Traefik)
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EXPOSE 8000
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# Health check
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HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
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CMD curl -f http://localhost:8000/health || exit 1
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# Entrypoint
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ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
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# Command: Start FastAPI backend
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# FastAPI will serve both API and frontend static files
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# Note: Using backend.app.main_spa for SPA static file support
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CMD ["uvicorn", "backend.app.main_spa:app", "--host", "0.0.0.0", "--port", "8000"]
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