CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

April, 2020

by Alan Orth in  Notes

2020-04-02

  • Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
    • I updated the fifty-eight existing items on CGSpace
  • Looking into the items Udana had asked about last week that were missing Altmetric donuts:
  • On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week
  • Altmetric responded about one item that had no donut since at least 2019-12 and said they fixed some problems with their bot’s user agent
    • I decided to tweet the item, as I can’t remember if I ever did it before

2020-04-05

  • Update PostgreSQL JDBC driver to version 42.2.12

2020-04-07

  • Yesterday Atmire sent me their pull request for DSpace 6 modules
  • Peter pointed out that some items have his ORCID identifier (cg.creator.id) twice
    • I think this is because my early add-orcid-identifiers.py script was adding identifiers to existing records without properly checking if there was already one present (at first it only checked if there was one with the exact place value)
    • As a test I dropped all his ORCID identifiers and added them back with the add-orcid-identifiers.py script:
$ psql -h localhost -U postgres dspace -c "DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value LIKE '%Ballantyne%';"
DELETE 97
$ ./add-orcid-identifiers-csv.py -i 2020-04-07-peter-orcids.csv -db dspace -u dspace -p 'fuuu' -d
  • I used this CSV with the script (all records with his name have the name standardized like this):
dc.contributor.author,cg.creator.id
"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
  • Then I tried another way, to identify all duplicate ORCID identifiers for a given resource ID and group them so I can see if count is greater than 1:
dspace=# \COPY (SELECT DISTINCT(resource_id, text_value) as distinct_orcid, COUNT(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 240 GROUP BY distinct_orcid ORDER BY count DESC) TO /tmp/2020-04-07-duplicate-orcids.csv WITH CSV HEADER;
COPY 15209
  • Of those, about nine authors had duplicate ORCID identifiers over about thirty records, so I created a CSV with all their name variations and ORCID identifiers:
dc.contributor.author,cg.creator.id
"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
"Ramirez-Villegas, Julian","Julian Ramirez-Villegas: 0000-0002-8044-583X"
"Villegas-Ramirez, J","Julian Ramirez-Villegas: 0000-0002-8044-583X"
"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
"Manabu, Ishitani","Manabu Ishitani: 0000-0002-6950-4018"
"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
"Buruchara, Robin A.","Robin Buruchara: 0000-0003-0934-1218"
"Buruchara, Robin","Robin Buruchara: 0000-0003-0934-1218"
"Jarvis, Andy","Andy Jarvis: 0000-0001-6543-0798"
"Jarvis, Andrew","Andy Jarvis: 0000-0001-6543-0798"
"Jarvis, A.","Andy Jarvis: 0000-0001-6543-0798"
"Tohme, Joseph M.","Joe Tohme: 0000-0003-2765-7101"
"Hansen, James","James Hansen: 0000-0002-8599-7895"
"Hansen, James W.","James Hansen: 0000-0002-8599-7895"
"Asseng, Senthold","Senthold Asseng: 0000-0002-7583-3811"
  • Then I deleted all their existing ORCID identifier records:
dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value SIMILAR TO '%(0000-0001-6543-0798|0000-0001-9346-2893|0000-0002-6950-4018|0000-0002-7583-3811|0000-0002-8044-583X|0000-0002-8599-7895|0000-0003-0934-1218|0000-0003-2765-7101)%';
DELETE 994
  • And then I added them again using the add-orcid-identifiers records:
$ ./add-orcid-identifiers-csv.py -i 2020-04-07-fix-duplicate-orcids.csv -db dspace -u dspace -p 'fuuu' -d
  • I ran the fixes on DSpace Test and CGSpace as well
  • I started testing the pull request sent by Atmire yesterday
    • I notice that we now need yarn to build, and I need to bump the Node.js engine version in our Mirage 2 theme in order to get it to build on Node.js 10.x
    • Font Awesome icons for GitHub etc weren’t loading, and after a bit of troubleshooting I replaced version 4.5.0 with 5.13.0 and to my surprise they now include Mendeley and ORCID so we can get rid of the Academicons dependency

2020-04-12

  • Testing the Atmire DSpace 6.3 code with a clean CGSpace DSpace 5.8 database snapshot
    • One Flyway migration failed so I had to manually remove it (and of course create the pgcrypto extension):
dspace63=# DELETE FROM schema_version WHERE version IN ('5.8.2015.12.03.3');
dspace63=# CREATE EXTENSION pgcrypto;
  • Then DSpace 6.3 started up OK and I was able to see some statistics in the Content and Usage Analysis (CUA) module, but not on community, collection, or item pages
    • I also noticed at least one of these errors in the DSpace log:
2020-04-12 16:34:33,363 ERROR com.atmire.dspace.app.xmlui.aspect.statistics.editorparts.DataTableTransformer @ java.lang.IllegalArgumentException: Invalid UUID string: 1
  • And I remembered I actually need to run the DSpace 6.4 Solr UUID migrations:
$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
  • Run system updates on DSpace Test (linode26) and reboot it
  • More work on the DSpace 6.3 stuff, improving the GDPR consent logic to use haven instead of cookieconsent
    • It works better by injecting the Google Analytics script after the user clicks agree, and it also has a preferences section that gets automatically injected on the privacy page!