--- title: "January, 2022" date: 2022-01-01T15:20:54+02:00 author: "Alan Orth" categories: ["Notes"] --- ## 2022-01-01 - Start a full harvest on AReS ## 2022-01-06 - Add ORCID identifier for Chris Jones to CGSpace - Also tag eighty-eight of his items in CGSpace: ```console $ cat 2022-01-06-add-orcids.csv dc.contributor.author,cg.creator.identifier "Jones, Chris","Chris Jones: 0000-0001-9096-9728" "Jones, Christopher S.","Chris Jones: 0000-0001-9096-9728" $ ./ilri/add-orcid-identifiers-csv.py -i 2022-01-06-add-orcids.csv -db dspace63 -u dspacetest -p 'dom@in34sniper' ``` ## 2022-01-09 - Validate and register CGSpace on [OpenArchives](https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7) - Last month IWMI colleagues were asking me to look into this, and after checking the OpenArchives mailing list it seems there was a problem on the server side - Now it has worked and the message is "Successfully updated OAI registration database to status COMPLIANT." - I received an email (as the Admin contact on our OAI) that says: > Your repository has been registered in the OAI database of conforming repositories. - Now I'm taking a screenshot of the validation page for posterity, because the logs seem to go away after some time ![OpenArchives.org registration](/cgspace-notes/2022/01/openarchives-registration.png) - I tried to re-build the Docker image for OpenRXV and got an error in the backend: ```console ... > openrxv-backend@0.0.1 build > nest build node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself. 2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate | AggregationsTermsAggregate | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate ~~~~~~~~~~~~~~~~~~~~~ node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself. 3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Found 2 error(s). ``` - Ah, it seems the code on the server was slightly out of date - I checked out the latest master branch and it built ## 2022-01-12 - Fix some citation formatting issues in Gaia's [eighteen CAS Green Cover publications on DSpace Test](https://dspacetest.cgiar.org/handle/10568/115230) ## 2022-01-19 - Francesca was having issues with a submission on CGSpace this week - I checked and see a lot of locks in PostgreSQL: ```console $ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n 1 1 ------------------ 1 (3506 rows) 1 application_name 9 psql 10 3487 dspaceWeb ``` - As before, I see messages from PostgreSQL about processes waiting for locks since I enabled the `log_lock_waits` setting last month: ```console $ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for' 12 ``` - I set a system alert on DSpace and then restarted the server ## 2022-01-20 - Abenet gave me a thumbs up for Gaia's eighteen CAS Green Cover items from last month - I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace: ```console $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-01-20-green-covers.map ``` ## 2022-01-21 - Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia - I did some cleanups and standardization of author names - I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text - Otherwise all items have only a year, which is not great... - Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10 - I did some basic tests and created a [pull request](https://github.com/ilri/OpenRXV/pull/128) ## 2022-01-22 - Spend some time adding months to the CGIAR TAC and IWC records from Gaia - Most of the PDFs have only YYYY, so this is annoying... ## 2022-01-23 - Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia - Rebuild AReS and start a fresh harvest ## 2022-01-25 - Help Udana from IWMI answer some questions about licenses on their journal articles - I was surprised to see they have 921 total, but only about 200 have a `dcterms.license` field - I updated about thirty manually, but really Udana should do more... - Normalize the metadata `text_lang` attributes on CGSpace database: ```console dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC; text_lang | count -----------+--------- en_US | 2803350 en | 6232 | 3200 fr | 2 vn | 2 92 | 1 sp | 1 | 0 (8 rows) dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en', '92', ''); UPDATE 9433 ``` - Then export the WLE Journal Articles collection again so there are fewer columns to mess with ## 2022-01-26 - Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks ## 2022-01-27 - Work on WLE's Journal Articles a bit more - I realized that ~130 items have DOIs in their citation, but no `cg.identifier.doi` field - I used this OpenRefine GREL to copy them: ``` cells['dcterms.bibliographicCitation[en_US]'].value.split("doi: ")[1] ``` - I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don't put DOIs in the citation so it's not possible to fix items that are missing DOIs that way - And I cleaned up and normalized some licenses - Francesca from Bioversity was having issues with a submission on CGSpace again - I looked at PostgreSQL and see an increasing number of locks: ```console $ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n 1 1 ------------------ 1 (537 rows) 1 application_name 9 psql 51 dspaceApi 477 dspaceWeb $ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for' 3 ``` - I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL - The issue in Francesca's case was actually that someone had taken the task, not that PostgreSQL transactions were locked! ## 2022-01-28 - Finalize the last ~100 WLE Journal Article items without licensese and DOIs - I did as many as I could, also updating http links to https for many journal links - Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid) - She created an account on CGSpace and now we need to see which workflows she should belong to - Start a fresh harvesting on AReS - I adjusted the `check-duplicates.py` script to write the output to a CSV file including the id, both titles, both dates, and the handle link - I included the id because I will need a unique field to join the resulting list of non-duplicates with the original CSV where the rest of the metadata and filenames are - Since these items are not in DSpace yet, I generated simple numeric IDs in OpenRefine using this GREL transform: `row.index + 1` - Then I ran `check-duplicates.py` on items 1–200 and sent the resulting CSV to Gaia - Delete one duplicate item I saw in IITA's Journal Articles that was uploaded earlier in WLE - Also do some general cleanup on IITA's Journal Articles collection in OpenRefine - Delete one duplicate item I saw in ILRI's Journal Articles collection - Also do some general cleanup on ILRI's Journal Articles collection in OpenRefine and csv-metadata-quality ## 2022-01-29 - I did some more cleanup on the ILRI Journal Articles - I added missing journal titles for items that had ISSNs - Then I added pages for items that had them in the citation - First, I faceted the citation field based on whether or not the item had something like ": 232-234" present: ```console value.contains(/:\s?\d+(-|–)\d+/) ``` - Then I faceted by blank on `dcterms.extent` and did a transform to extract the page information for over 1,000 items! ```console 'p. ' + cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[0] + '-' + cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[2] ``` - Then I did similar for `cg.volume` and `cg.issue`, also based on the citation, for example to extract the "16" from "Journal of Blah 16(1)", where "16" is the second capture group in a zero-based match: ```console cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*( |;)(\d+)\((\d+)\).*/)[1] ``` - This was 3,000 items so I imported the changes on CGSpace 1,000 at a time...