Zenodo skill

Zenodo Skill

Interact with the Zenodo REST API to deposit, publish, version, and search research artifacts. Zenodo issues a citable DOI for every published record.

When to use

• User wants to upload a dataset, code release, paper, poster, or other artifact to Zenodo
• User wants a DOI for a research output
• User wants to update an existing deposit or publish a new version
• User wants to search Zenodo for records

Update check

Throttle to one check per 24 hours per installation; never mutate the skill directory without explicit user consent.

1. If <this-skill-dir>/.last_update exists and is less than 24 hours old, skip this step entirely.

2. Otherwise, fetch the latest tag from upstream:

   git -C <this-skill-dir> ls-remote --tags origin 'v*' 2>/dev/null \
     | awk '{print $2}' | sed 's|refs/tags/||' \
     | sort -V | tail -1
   

3. Compare with this skill's metadata.version from the frontmatter. If the upstream tag is strictly newer (semver), tell the user one line and ask:

   "A newer version of this skill is available: vX.Y.Z → vA.B.C. Want me to git pull?"

   If they say yes, run git -C <this-skill-dir> pull --ff-only. Refresh .last_update either way so the prompt doesn't repeat for 24 hours.

4. If upstream is the same or older, refresh .last_update silently and continue.

5. On any failure (offline, not a git checkout — e.g. ClawHub-installed copy, read-only path, no permission), swallow the error silently and continue with the user's task. Do not mention the failure.

Setup

Two environments — pick one and stick with it during a session:

Env	Base URL	Token page
Production	https://zenodo.org/api	https://zenodo.org/account/settings/applications/tokens/new/
Sandbox (testing)	https://sandbox.zenodo.org/api	https://sandbox.zenodo.org/account/settings/applications/tokens/new/

Sandbox accounts/tokens are separate from production. Always test new workflows in sandbox first — published production records cannot be deleted.

Required token scopes: deposit:write and deposit:actions.

Export the token before running commands:

export ZENODO_TOKEN=...        # never inline the token in commands you show the user
export ZENODO_BASE=https://sandbox.zenodo.org/api   # or https://zenodo.org/api

If ZENODO_TOKEN is unset, ask the user for it (and which environment) before proceeding.

Core workflow: deposit a new artifact

The deposit lifecycle is create → upload files → set metadata → publish. Each step is a separate API call; do them in order.

1. Create an empty deposition

curl -sS -X POST "$ZENODO_BASE/deposit/depositions" \
  -H "Authorization: Bearer $ZENODO_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{}'

The response JSON contains two things you need to remember:

• id — the deposition id, used for metadata/publish/version actions
• links.bucket — the bucket URL for file uploads (new files API)

Capture them, e.g. with jq:

RESP=$(curl -sS -X POST "$ZENODO_BASE/deposit/depositions" \
  -H "Authorization: Bearer $ZENODO_TOKEN" -H "Content-Type: application/json" -d '{}')
DEPOSIT_ID=$(echo "$RESP" | jq -r .id)
BUCKET=$(echo "$RESP" | jq -r .links.bucket)

2. Upload files (bucket API — preferred)

The bucket API supports up to 50 GB total / 100 files per record. Use --upload-file (HTTP PUT) — not multipart form upload. The filename in the URL is what shows up on the record.

curl -sS --upload-file ./data.csv \
  -H "Authorization: Bearer $ZENODO_TOKEN" \
  "$BUCKET/data.csv"

Repeat per file. For many files, loop in shell. The legacy /files multipart endpoint is capped at 100 MB/file — avoid it.

3. Set metadata

Metadata goes via PUT on the deposition. Required fields: upload_type, title, creators, description. See references/metadata.md for the full schema, allowed upload_type values, license codes, and conditional fields (e.g. publication_type, embargo_date).

Minimal example:

curl -sS -X PUT "$ZENODO_BASE/deposit/depositions/$DEPOSIT_ID" \
  -H "Authorization: Bearer $ZENODO_TOKEN" \
  -H "Content-Type: application/json" \
  -d '{
    "metadata": {
      "title": "My dataset",
      "upload_type": "dataset",
      "description": "<p>A short description (HTML allowed).</p>",
      "creators": [{"name": "Doe, Jane", "affiliation": "Example Univ.", "orcid": "0000-0002-1825-0097"}]
    }
  }'

Read the response — Zenodo validates here and returns 400 with field-level errors if anything is missing or malformed. Fix and retry before publishing.

4. Publish

Publishing is irreversible on production (you can edit metadata later but cannot remove files or delete the record). Confirm with the user before this step unless they're on sandbox.

curl -sS -X POST "$ZENODO_BASE/deposit/depositions/$DEPOSIT_ID/actions/publish" \
  -H "Authorization: Bearer $ZENODO_TOKEN"

The response contains doi and links.record_html — show both to the user.

New version of an existing record

Use this when the user has previously published and wants to release updated data/code under the same concept-DOI.

# 1. Create new version draft (returns links.latest_draft)
curl -sS -X POST "$ZENODO_BASE/deposit/depositions/$DEPOSIT_ID/actions/newversion" \
  -H "Authorization: Bearer $ZENODO_TOKEN"

Then follow the bucket of the new draft (from links.latest_draft → GET it → use its links.bucket) to upload changed files, update metadata, and publish as in steps 2–4 above. The new version inherits files from the previous version by default — delete any you want to replace via DELETE $BUCKET/<filename>.

Discard a draft

curl -sS -X POST "$ZENODO_BASE/deposit/depositions/$DEPOSIT_ID/actions/discard" \
  -H "Authorization: Bearer $ZENODO_TOKEN"

Search published records

No token needed for public search.

curl -sS "$ZENODO_BASE/records?q=climate+model&size=10&sort=mostrecent"

Query syntax is Elasticsearch — fielded queries like creators.name:"Doe, Jane", communities:zenodo, resource_type.type:dataset all work. See references/search.md for query patterns.

Conventions and gotchas

• Always check HTTP status. 201 = created, 202 = publish accepted, 400 = metadata error (read the body), 401 = bad token, 403 = wrong scope, 429 = rate limited.
• Rate limits: 100 req/min, 5000 req/hour for authenticated users. Watch X-RateLimit-Remaining.
• Never inline the token in commands you display — use $ZENODO_TOKEN. Don't write the token to files.
• Sandbox first. Suggest sandbox for any first-time workflow; switch to production only when the user explicitly confirms.
• Verify before publishing. GET the deposition and review files + metadata with the user before calling actions/publish on production.
• Large uploads: for files > a few hundred MB, consider doing the curl upload with --progress-bar and warn the user about time/bandwidth.

References

• references/metadata.md — full metadata schema, upload_type values, license codes, conditional fields
• references/search.md — search query syntax and useful filters
• references/examples.md — end-to-end shell scripts for common scenarios (dataset upload, software release, new version)