March, 2021
2021-03-01
- Discuss some OpenRXV issues with Abdullah from CodeObia
- He’s trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
- Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
2021-03-02
- I fixed three build and runtime issues in OpenRXV:
- Then I merged a few fixes that Abdullah had worked on last week
2021-03-03
- I fixed another frontend build warning on OpenRXV
- Then I updated the frontend container to use Node.js 12 and Ubuntu 20.04
- Also, I added a GitHub Actions workflow to build the frontend
- I did some testing of Abdullah’s patch for the values mapping search on OpenRXV
- It still doesn’t work with multi-word values, so I recorded a video with wf-recorder and uploaded it to the issue for him to investigate
2021-03-04
- Peter is having issues with the workflow since yesterday
- I looked at the Munin stats and see a high number of database locks since yesterday
- I looked at the number of connections in PostgreSQL and it’s definitely high again:
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1020
- I reported it to Atmire to take a look, on the same issue we had been tracking this before
- Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell
- I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my
add-orcid-identifier.pyscript:
$ cat 2021-03-04-add-zoe-campbell-orcid.csv
dc.contributor.author,cg.creator.identifier
"Campbell, Zoë","Zoe Campbell: 0000-0002-4759-9976"
"Campbell, Zoe A.","Zoe Campbell: 0000-0002-4759-9976"
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
- I still need to do cleanup on the journal articles metadata
- Peter sent me some cleanups but I can’t use them in the search/replace format he gave
- I think it’s better to export the metadata values with IDs and import cleaned up ones as CSV
localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
COPY 32087
- I used OpenRefine to remove all journal values that didn’t have one of these values: ; ( )
- Then I cloned the
cg.journalfield tocg.volumeandcg.issue - I used some GREL expressions like these to extract the journal name, volume, and issue:
- Then I cloned the
value.partition(';')[0].trim() # to get journal names
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
- Then I uploaded the changes to CGSpace using
dspace metadata-import - Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
- The error was “Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e …”
- I searched the DSpace issue tracker and found several issues reporting this:
- The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection…
- In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection’s admin and submit groups, exactly as the issue described
- I added a comment about our issue to DS-4297
- Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana’s submissions
- I edited Udana’s submission to CGSpace:
- corrected the title
- added language English
- changed the link to the external item page instead of PDF
- added SDGs from the external item page
- added AGROVOC subjects from the external item page
- added pagination (extent)
- changed the license to “other” because CC-BY-NC-ND is not printed anywhere in the PDF or external item page
- I edited Udana’s submission to CGSpace: