| # `intake/` — submission front-end |
|
|
| This subpackage is the HTTP submission server for the editorial pipeline. |
| See the top-level [README](../README.md) for the full architecture. |
|
|
| The intake handler lives behind [`icsacinstitute.org/submit`](https://icsacinstitute.org/submit). |
| It authenticates the upstream form, accepts a DOI / arXiv reference OR a |
| direct PDF upload, persists the submission record, and drops a queue |
| marker for the editorial worker to pick up on its next batch tick. |
|
|
| ## What lives here |
|
|
| | File | Role | |
| |------|------| |
| | `intake_server.py` | FastAPI app: `POST /api/submit`, `GET /api/submission/{id}/state`, `GET /healthz`. | |
| | `submission_worker.py` | Drains the queue, resolves deferred DOIs, calls the editorial review pipeline (`review.review_paper`), routes verdicts. | |
| | `apply_decision.py` | Finalizes a curator-driven decision on borderline submissions. | |
| | `notify_author.py` | Author-facing email. Renders panel report + RQC to PDF (WeasyPrint) and attaches. Exposes `send_published()` — imported by editorial's `publish_watcher`. | |
| | `rehydrate.py` / `rehydrate.sh` | Refetch a stubbed DOI submission's bytes from the resolver, verify SHA. | |
| | `decide.sh` | Wrapper around `apply_decision.py` for invocation from a remote curator channel. | |
| | `time_fmt.py` | UTC-on-disk / ET-on-display timestamp helpers. | |
| | `templates/` | Author-facing email templates (Markdown with `{{var}}` interpolation). | |
| | `scripts/` | Smoke tests for the test-mode pipeline. | |
|
|
| ## Required environment |
|
|
| | Variable | Required | Purpose | |
| |----------|----------|---------| |
| | `INTAKE_HMAC_SECRET` | **yes** | Shared secret with the upstream form host. Used to verify `X-ICSAC-Signature`. | |
| | `MAX_PDF_BYTES` | no | Upload size cap (default 25 MB). | |
| | `TEST_ORCIDS` | no | Comma-separated ORCIDs that short-circuit to the test pipeline. Empty default (test mode off). | |
| | `TEST_TIERS_DISABLED` | no | Force tier-1 (canned) for all test ORCIDs even if a header requests T2/T3. | |
| | `INCIDENT_SSH_HOST` | no | `user@host` for a remote incident-router (borderline-submission escalation). Empty default = skip remote handoff. | |
| | `INCIDENT_REMOTE_DIR` | no | Directory on `INCIDENT_SSH_HOST` to write incident JSON. | |
| | `ALERT_WEBHOOK_URL` | no | POST endpoint for operator-channel alerts (e.g., `ntfy`). Empty default = silent. | |
| | `INTAKE_NODE_NAME` | no | Display name prefixed on alert titles. Default `intake`. | |
| | `TELEGRAM_TEST_CHAT_ID` | no | Chat ID for test-tier Telegram drafts. Empty default = skip. | |
|
|
| Editorial-pipeline-side environment (SMTP, Zenodo token, etc.) is documented |
| in `../config.example.py`. Intake imports from the parent package directly; |
| there is no separate sibling-import path to configure. |
|
|
| ## Running locally |
|
|
| From the repo root (not from `intake/`): |
|
|
| ```bash |
| python3 -m venv .venv |
| . .venv/bin/activate |
| pip install -r requirements.txt |
| cp config.example.py config.py # edit as needed for the editorial side |
| |
| export INTAKE_HMAC_SECRET=$(openssl rand -hex 32) |
| |
| # Submission server (terminal 1): |
| uvicorn intake.intake_server:app --host 127.0.0.1 --port 8443 --log-level warning |
| |
| # Submission worker (terminal 2 — drains queue when markers appear): |
| python -m intake.submission_worker |
| ``` |
|
|
| The handler binds to localhost by default. In our deployment it sits behind a |
| reverse proxy; for a public deployment, put your own proxy in front (the |
| handler trusts the HMAC, not the network). |
|
|
| ## Import contract |
|
|
| `publish_watcher.py` at the top level imports `send_published()` from this |
| subpackage: |
|
|
| ```python |
| from intake.notify_author import send_published |
| ``` |
|
|
| The filename `notify_author.py` and the `send_published` signature are the |
| internal contract between the two halves. The other helpers in |
| `notify_author.py` are private. |
|
|
| ## A note to authors |
|
|
| Every field on the form lands here. `submission.json` records: name, email, |
| ORCID, license choice, deposit consent (upload route), and the manuscript |
| reference. No other fields are collected. The PDF (for upload submissions) |
| is kept as the archive of record. For DOI submissions, the manuscript bytes |
| are lazy-rehydratable from the resolver, and only a SHA-anchored stub is |
| kept locally after review completes. |
|
|
