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Shaun Mahonyclaude
Shaun Mahony
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claude
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Add Next.js web platform for STAMP
Replace the legacy PHP/Perl web interface with a modern Next.js 14 app featuring anonymous job submission, real-time status via SSE, interactive D3.js phylogenetic trees, canvas sequence logos, and a password-protected admin dashboard with JASPAR database sync. Stack: Next.js 14 (App Router), MongoDB, BullMQ/Redis, Docker Compose. Supports TRANSFAC, MEME, JASPAR, and TF-MoDISco input formats. Co-Authored-By: Claude Opus 4.6 <[email protected]>
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‎.gitignore‎

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stamp
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/stamp
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outFile*

‎web/.env.example‎

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# MongoDB
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MONGODB_URI=mongodb://localhost:27017/stamp
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# Redis (for BullMQ job queue)
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REDIS_URL=redis://localhost:6379
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# Admin
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ADMIN_PASSWORD=change-me-in-production
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# STAMP binary
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STAMP_BINARY=/usr/local/bin/stamp
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SCORE_DISTS_DIR=/path/to/ScoreDists
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# Job settings
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JOB_TIMEOUT_MS=300000
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JOB_RETENTION_DAYS=7
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JOBS_DATA_DIR=/tmp/stamp-jobs
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# Rate limiting
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RATE_LIMIT_JOBS_PER_HOUR=20
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# Email notifications (optional)
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SMTP_HOST=
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SMTP_PORT=587
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SMTP_USER=
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SMTP_PASS=
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SMTP_FROM=[email protected]
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# Public URL (for email links)
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PUBLIC_URL=http://localhost:3000

‎web/.gitignore‎

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# dependencies
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/node_modules
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/.pnp
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.pnp.js
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# testing
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/coverage
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# next.js
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/.next/
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/out/
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# production
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/build
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# misc
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.DS_Store
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*.pem
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# debug
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*
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# local env files
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.env*.local
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.env
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# vercel
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.vercel
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# typescript
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*.tsbuildinfo
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next-env.d.ts

‎web/docker/Dockerfile‎

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# Stage 1: Compile STAMP binary
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FROM ubuntu:22.04 AS stamp-builder
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RUN apt-get update && \
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apt-get install -y g++ libgsl-dev && \
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rm -rf /var/lib/apt/lists/*
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WORKDIR /build
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COPY src/ ./src/
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WORKDIR /build/src
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RUN g++ -O3 -o /build/stamp \
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Motif.cpp Alignment.cpp ColumnComp.cpp \
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PlatformSupport.cpp PlatformTesting.cpp Tree.cpp \
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NeuralTree.cpp MultipleAlignment.cpp RandPSSMGen.cpp \
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ProteinDomains.cpp main.cpp \
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-lm -lgsl -lgslcblas
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# Stage 2: Build Next.js application
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FROM node:22-alpine AS app-builder
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WORKDIR /app
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COPY web/package.json web/package-lock.json* ./
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RUN npm install
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COPY web/ ./
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RUN npm run build
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# Stage 3: Production image
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FROM node:22-slim
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RUN apt-get update && \
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apt-get install -y libgsl27 && \
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rm -rf /var/lib/apt/lists/*
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WORKDIR /app
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# Copy STAMP binary and score distributions
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COPY --from=stamp-builder /build/stamp /app/stamp
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COPY ScoreDists/ /app/ScoreDists/
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# Copy Next.js standalone build
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COPY --from=app-builder /app/.next/standalone ./
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COPY --from=app-builder /app/.next/static ./.next/static
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COPY --from=app-builder /app/public ./public
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# Create data directory
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RUN mkdir -p /app/data/jobs
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ENV NODE_ENV=production
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ENV PORT=3000
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ENV HOSTNAME=0.0.0.0
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EXPOSE 3000
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CMD ["node", "server.js"]

‎web/docker/Dockerfile.worker‎

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# Stage 1: Compile STAMP binary
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FROM ubuntu:22.04 AS stamp-builder
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RUN apt-get update && \
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apt-get install -y g++ libgsl-dev && \
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rm -rf /var/lib/apt/lists/*
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WORKDIR /build
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COPY src/ ./src/
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WORKDIR /build/src
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RUN g++ -O3 -o /build/stamp \
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Motif.cpp Alignment.cpp ColumnComp.cpp \
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PlatformSupport.cpp PlatformTesting.cpp Tree.cpp \
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NeuralTree.cpp MultipleAlignment.cpp RandPSSMGen.cpp \
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ProteinDomains.cpp main.cpp \
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-lm -lgsl -lgslcblas
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# Stage 2: Build worker
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FROM node:22-slim
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RUN apt-get update && \
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apt-get install -y libgsl27 && \
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rm -rf /var/lib/apt/lists/*
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WORKDIR /app
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# Copy STAMP binary and score distributions
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COPY --from=stamp-builder /build/stamp /app/stamp
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COPY ScoreDists/ /app/ScoreDists/
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# Install dependencies
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COPY web/package.json web/package-lock.json* ./
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RUN npm install --omit=dev && npm install tsx
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# Copy worker and library source
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COPY web/worker/ ./worker/
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COPY web/src/lib/ ./src/lib/
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COPY web/src/types/ ./src/types/
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COPY web/tsconfig.json ./
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# Create data directory
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RUN mkdir -p /app/data/jobs
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ENV NODE_ENV=production
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CMD ["npx", "tsx", "worker/index.ts"]

‎web/docker/docker-compose.dev.yml‎

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# Development compose file - only runs MongoDB and Redis
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# Run the Next.js app and worker locally with `npm run dev` and `npm run worker:dev`
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services:
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mongodb:
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image: mongo:7
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ports:
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- "27017:27017"
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volumes:
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- mongo-data:/data/db
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redis:
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image: redis:7-alpine
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ports:
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- "6379:6379"
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volumes:
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- redis-data:/data
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volumes:
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mongo-data:
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redis-data:

‎web/docker/docker-compose.yml‎

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services:
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app:
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build:
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context: ../..
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dockerfile: web/docker/Dockerfile
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ports:
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- "3000:3000"
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environment:
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- MONGODB_URI=mongodb://mongodb:27017/stamp
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- REDIS_URL=redis://redis:6379
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- ADMIN_PASSWORD=${ADMIN_PASSWORD:-changeme}
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- STAMP_BINARY=/app/stamp
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- SCORE_DISTS_DIR=/app/ScoreDists
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- JOBS_DATA_DIR=/app/data/jobs
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- NODE_ENV=production
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- SMTP_HOST=${SMTP_HOST:-}
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- SMTP_PORT=${SMTP_PORT:-587}
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- SMTP_USER=${SMTP_USER:-}
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- SMTP_PASS=${SMTP_PASS:-}
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- SMTP_FROM=${SMTP_FROM:[email protected]}
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- PUBLIC_URL=${PUBLIC_URL:-http://localhost:3000}
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depends_on:
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mongodb:
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condition: service_started
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redis:
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condition: service_started
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volumes:
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- job-data:/app/data/jobs
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restart: unless-stopped
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worker:
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build:
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context: ../..
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dockerfile: web/docker/Dockerfile.worker
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environment:
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- MONGODB_URI=mongodb://mongodb:27017/stamp
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- REDIS_URL=redis://redis:6379
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- STAMP_BINARY=/app/stamp
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- SCORE_DISTS_DIR=/app/ScoreDists
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- JOBS_DATA_DIR=/app/data/jobs
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- SMTP_HOST=${SMTP_HOST:-}
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- SMTP_PORT=${SMTP_PORT:-587}
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- SMTP_USER=${SMTP_USER:-}
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- SMTP_PASS=${SMTP_PASS:-}
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- SMTP_FROM=${SMTP_FROM:[email protected]}
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- PUBLIC_URL=${PUBLIC_URL:-http://localhost:3000}
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depends_on:
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mongodb:
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condition: service_started
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redis:
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condition: service_started
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volumes:
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- job-data:/app/data/jobs
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deploy:
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replicas: 2
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restart: unless-stopped
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mongodb:
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image: mongo:7
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volumes:
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- mongo-data:/data/db
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restart: unless-stopped
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redis:
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image: redis:7-alpine
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volumes:
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- redis-data:/data
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restart: unless-stopped
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volumes:
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mongo-data:
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redis-data:
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job-data:

‎web/next.config.mjs‎

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/** @type {import('next').NextConfig} */
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const nextConfig = {
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output: "standalone",
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experimental: {
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serverComponentsExternalPackages: ["mongoose", "bullmq", "ioredis", "archiver", "nodemailer"],
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},
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};
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export default nextConfig;

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