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