pathviewweb

Modern re-implementation of the (now unavailable) Pathview Web server.

Goal: Provide a web UI + REST API to run Pathview (Bioconductor R package) jobs reproducibly, securely, and at scale.

Architecture (high level)

• apps/api -- FastAPI service (job submission, status, download links)
• apps/worker -- Python RQ worker that runs Pathview via Rscript
• apps/web -- UI (Next.js) that talks to the API
• Docker-first: this project is designed to run as containers (Compose for local/prod).

Quickstart (dev)

Prereqs: Docker + Docker Compose.

docker compose up --build

Then:

• API: http://localhost:8000/docs
• Web UI: http://localhost:3000

Submit a job (upload first, then create job):

curl -X POST http://localhost:8000/v1/uploads \
  -F "file=@examples/gene_data.tsv" \
  -F "format=tsv"

curl -X POST http://localhost:8000/v1/jobs \
  -H "Content-Type: application/json" \
  -d '{
    "species": "mmu",
    "pathway_id": "04110",
    "gene_data": { "upload_id": "<upload_id>", "format": "tsv" },
    "options": { "gene_idtype": "symbol" }
  }'

Check health:

curl http://localhost:8000/healthz

Configuration

Environment variables used by containers:

• REDIS_URL (api/worker)
• STORAGE_DIR (api/worker)
• JOB_TTL_SECONDS (api/cleanup)
• CLEANUP_INTERVAL_SECONDS (cleanup)
• NEXT_PUBLIC_API_BASE (web)

Defaults are set in docker-compose.yml. To override for production, copy and edit:

cp .env.example .env

Docs

• docs/ARCHITECTURE.md - system design and runtime flow
• docs/API.md - REST API details
• docs/SECURITY.md - threat model and controls
• docs/PLAN.md - roadmap and milestones

Production-ish (Docker Compose)

Use the production compose file:

cp .env.example .env
docker compose -f docker-compose.prod.yml up -d --build

Notes

• Uploads must be TSV or CSV. The API validates delimiters before accepting files.
• Gene data files must have gene IDs in the first column and numeric values in the remaining columns.
• Results are packaged as a ZIP that includes outputs, logs, and inputs.

License

MIT (see LICENSE).