Convert Preprint DOI script to Janeway manage command

[bibliotechy]

Move the logic from a shell script to python to get better logging.

[bibliotechy]

Refers to Remind missing DOIs script

[everreau]

https://github.com/cdlib/pub-janeway-role/blob/master/bin/remint-missing-dois.sh

[everreau]

@alainna noted in a different card Hardy also had a shell script for updating dois when a new version is created. This should also be written into a janeway plugin rather than a shell script:

# !/bin/bash

# draft batch script to propagate metatdata updates to DOI metadata

# ensure the Python environment is set up correctly
set +u
source /apps/eschol/.janewayenv/bin/activate
set -u

# needs to be run from this folder: /apps/eschol/janeway
cd /apps/eschol/janeway

# get a list of preprint IDs that were updated in the past two days (casting a wide net, to avoid edge cases)
UPDATED_PREPRINTS=$(mysql --defaults-extra-file=/apps/eschol/.passwords/janeway_dba_pw.mysql -N -B -e "SELECT preprint_id FROM repository_preprintversion WHERE date_time > SUBDATE(CURDATE(),2) AND preprint_id NOT IN (SELECT id FROM repository_preprint WHERE date_accepted IS NULL);")

if [ -n "$UPDATED_PREPRINTS" ]; then
  echo "found at least one updated preprint, sending updates to Crossref..."
  # now update the metadata for those preprints
  for ID in $UPDATED_PREPRINTS
  do
    #update the metadata for this preprint
    python src/manage.py update_ezid_doi EA $ID
  done
# else
  # echo "No action required: no preprints have been updated in the past two days."
fi
****

[everreau]

If new version created events don't exist in janeway it probably wouldn't be hard to add that an respond to the event instead of using a cronjob. Changed metadata is harder to detect since there are so many places it can be changed and some many additional events would be created.

[everreau]

Here are notes from Alainna from a previous card:

Issue

Previously we had EZID update cronjob, created by Hardy:

• Preprint DOI update cronjob should ignore non-published items (PUBD-473)
• EarthArXiv: Create DOI metadata update cronjob (PUBD-432)

That cronjob has been deleted for reasons no one seems to recall, so this is a re-submission of that feature request.

Why

As an EarthArXiv/EcoEvoRxiv moderator, I expect updates made to preprint metadata to be reflected in the DOI metadata without needing to ask that CDL manually update the DOI. This can occur when:

• a new version is accepted/published
• a moderator personally updates the metadata (no version)

What

Create a cronjob that looks for any updated metadata over the previous 24hours. If there is changed metadata, perform an update via EZID.

The cronjob should ignore non-published items.

Details

Related: https://github.com/eScholarship/EarthArXiv/blob/master/plugins/ezid/management/commands/update_ezid_doi.py

Ref:

• Preprint DOI update cronjob should ignore non-published items (PUBD-473)
• EarthArXiv: Create DOI metadata update cronjob (PUBD-432)

[everreau]

Her idea to have a cronjob look for updated dates in preprints (and probably articles) in the last day or whatever would probably work but again, all this should be written in a janeway plugin not in shell scripts.