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WIP: feat(zenodo): automate monthly dataset publishing to Zenodo #815

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WIP: feat(zenodo): automate monthly dataset publishing to Zenodo #815

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24af6d6
fix(exports): zip CSV archives for monthly S3 downloads
vcnainala Jun 8, 2026
1b8f8eb
feat(zenodo): publish monthly exports to Zenodo after S3 upload
vcnainala Jun 8, 2026
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10 changes: 10 additions & 0 deletions .env.example
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,16 @@ AWS_DEFAULT_REGION=us-east-1
AWS_BUCKET=
AWS_USE_PATH_STYLE_ENDPOINT=false

# Monthly export → Zenodo (https://zenodo.org/records/13897048)
ZENODO_ENABLED=false
ZENODO_ACCESS_TOKEN=
ZENODO_LATEST_DEPOSITION_ID=13897048
ZENODO_CONCEPT_DOI=10.5281/zenodo.13382750
ZENODO_API_URL=https://zenodo.org/api
ZENODO_AUTO_PUBLISH=false
ZENODO_DRY_RUN=false
ZENODO_RELEASE_NOTES=

PUSHER_APP_ID=
PUSHER_APP_KEY=
PUSHER_APP_SECRET=
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11 changes: 11 additions & 0 deletions config/services.php
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Expand Up @@ -68,4 +68,15 @@
'cas_key' => env('CAS_KEY'),
],

'zenodo' => [
'enabled' => (bool) env('ZENODO_ENABLED', false),
'access_token' => env('ZENODO_ACCESS_TOKEN'),
'latest_deposition_id' => env('ZENODO_LATEST_DEPOSITION_ID'),
'concept_doi' => env('ZENODO_CONCEPT_DOI', '10.5281/zenodo.13382750'),
'api_url' => env('ZENODO_API_URL', 'https://zenodo.org/api'),
'auto_publish' => (bool) env('ZENODO_AUTO_PUBLISH', false),
'dry_run' => (bool) env('ZENODO_DRY_RUN', false),
'release_notes' => env('ZENODO_RELEASE_NOTES'),
],

];
18 changes: 17 additions & 1 deletion resources/scripts/python/exports/generate_exports.py
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Expand Up @@ -576,7 +576,9 @@ def main():
sdf_filenames["light_sdf"] # e.g. coconut_sdf_2d_lite-03-2025.sdf
)

# Now we can safely remove the CSV files (since we've read them into SDF)
# Zip CSV exports for S3/Zenodo downloads, then remove the uncompressed files
zip_file(csv_with_collection)
zip_file(csv_without_collection)
cleanup_files(csv_with_collection, csv_without_collection)

# Zip the 2D SDF files, remove originals
Expand Down Expand Up @@ -652,5 +654,19 @@ def main():

print("All files have been successfully uploaded to S3.")

# 9. Publish to Zenodo (optional; configured via ZENODO_* env variables)
try:
from publish_zenodo import publish_monthly_release

publish_monthly_release(
env_vars=env_vars,
backup_path=backup_path,
month_year=timestamp,
full_dump_path=full_dump_path if os.path.exists(full_dump_path) else None,
db_params=db_params,
)
except ImportError as exc:
print(f"Zenodo publish skipped (publish_zenodo module unavailable): {exc}")

if __name__ == "__main__":
main()
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