Add notes for 2020-04-07

content/posts/2020-04.md

@@ -20,4 +20,72 @@ categories: ["Notes"]
 - Altmetric responded about [one item](https://hdl.handle.net/10568/101286) 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](https://twitter.com/mralanorth/status/1245703049445851140), 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](https://github.com/ilri/DSpace/pull/445)
+- 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
+
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