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GBIF Registry CLI

This module provides a CLI service that listens for updates to DOIs and updates the registry database accordingly.

Usage

The project is built as a single JAR, and run using a configuration file. Examples are in the example-confs directory.

doi-updater

Listen to DoiUpdate messages, take DOI updates and send them to DataCite. Updates the status of the DOI in the Registry database.

java -jar registry-cli.jar doi-updater --log-config logback-doi-updater.xml --conf registry-doi-updater.yaml

directory-update

Used to update the participant/node information of the Registry from the Directory API.

java -jar registry-cli.jar directory-update --log-config logback-directory-update.xml --conf directory-update.yaml

doi-synchronizer

CLI to display and possibly fix DOI status between GBIF database and Datacite. This CLI is an administrative tool designed to be used manually.

java -jar registry-cli.jar doi-synchronizer --log-config logback-doi-synchronizer.xml --conf doi-synchronizer.yaml --doi 10.15468/dl.4d4nny

Options:

  • --doi: specify a single DOI
  • --doi-list <DOI file>: specify a list of DOIs stored in a file, one DOI per line
  • --fix-doi: try to rebuild the DataCite metadata document and to resend it to the doi-updater cli. Used with --doi of --doi-list
  • --list-failed-doi: list all DOIs from the database (dataset and download) with the status FAILED
  • --doi <doi> --export: export the DataCite metadata document from the database into the file
  • --skip-dia: skip the diagnostic, used with --doi-list <DOI file> --fix-doi to not print the diagnostic of each DOIs
  • --display-metadata-diff: display metadata difference between GBIF and DataCite if they do not match

dataset-updater

Temporary tool to force the update of a dataset in the database by re-interpreting its metadata document (EML).

java -jar registry-cli.jar dataset-updater --log-config logback-util.xml --conf dataset-updater.yaml --dataset-key e95d0010-b3f1-11de-82f8-b8a03c50a862