cgspace-notes/content/posts/2020-04.md

title	date	author	categories
April, 2020	2020-04-02T10:53:24+03:00	Alan Orth	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:
  • The first is still missing its DOI, so I added it and tweeted its handle (after a few hours there was a donut with score 222)
  • The second item now has a donut with score 2 since I tweeted its handle last week
  • The third item now has a donut with score 1 since I tweeted it last week
• 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!