sagecontinuum / sage-doi

Sage-DOI

Docker

Build ezid command line interface:

docker build  -t sagecontinuum/ezid -f ezid/Dockerfile .

ezid3.py is set as the ENTRYPOINT in the dockerfile so it should only need to be passing arguments to ezid3.py

Build ezid json to xml schema converter:

docker build -t sagecontinuum/ezid_schema -f ezid_schema/Dockerfile .

Convert metadata json file to xml file for Datacite

Currently, ezid only accepts the metadata as an .xml file. We will only work with json files and then convert them to valid .xml files for Datacite metadata profile.WIP for JSON support

Run ezid_schema docker container with --help:

docker run -v metadata:/workdir -it --rm sagecontinuum/ezid_schema --help

Run ezid_schema docker container to convert test-file.json to metadata.xml

docker run -v $(pwd)/metadata:/workdir/metadata --env-file=.env -it --rm sagecontinuum/ezid_schema --json_file metadata/test-file.json --xml_filename metadata.xml

ezid python cli usage

Run ezid docker container with --help:

docker run --env-file=.env -it --rm sagecontinuum/ezid --help

All the commands will prompt for a password unless password is set, EZID_USER:EZID_PASS

Create a DOI for a dataset with the converted metadata.xml file:

docker run -v $(pwd)/metadata:/workdir/metadata --env-file=.env -it --rm sagecontinuum/ezid $EZID_USER:$EZID_PASS mint doi:10.5072/FK2 datacite @metadata/metadata.xml

Succesful return:

b'success: doi:10.5072/FK2G44SJ2H | ark:/b5072/fk2g44sj2h'

View newly created DOI:

docker run --env-file=.env -it --rm sagecontinuum/ezid $EZID_USER:$EZID_PASS -dt view doi:10.5072/FK2G44SJ2H

Successful return:

b'success: doi:10.5072/FK2G44SJ2H'
b'_created: 2022-03-10T20:10:44'
b'_datacenter: CDL.CDL'
b'_export: yes'
b'_owner: apitest'
b'_ownergroup: apitest'
b'_profile: datacite'
b'_shadowedby: ark:/b5072/fk2g44sj2h'
b'_status: public'
b'_target: https://ezid.cdlib.org/id/doi:10.5072/FK2G44SJ2H'
b'_updated: 2022-03-10T20:10:44'
b'datacite: ''

Update DOI metadata: Generate the XML file from test-file-update.json:

docker run -v $(pwd)/metadata:/workdir/metadata --env-file=.env -it --rm sagecontinuum/ezid_schema --json_file metadata/test-file-update.json --xml_filename metadata-update.xml

In order to make the JSON to XML conversion, all the required fields have to be present if not it will trigger an invalid schema assert. See Datacites documentation for further details of whats required.

Now make an update based on the modified data in XML file:

docker run -v $(pwd)/metadata:/workdir/metadata --env-file=.env -it --rm sagecontinuum/ezid $EZID_USER:$EZID_PASS update doi:10.5072/FK2G44SJ2H datacite @metadata/metadata-update.xml

Successful return:

b'success: doi:10.5072/FK2G44SJ2H'