January, 2022
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:
$ 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
- 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
- I tried to re-build the Docker image for OpenRXV and got an error in the backend:
...
> 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<any> | AggregationsTermsAggregate<any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate<AggregationsBucket> | 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- Ah, it seems the code on the server was slightly out of date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
2022-01-19
- Francesca was having issues with a submission on CGSpace this week
- I checked and see a lot of locks in PostgreSQL:
$ 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_waitssetting last month:
$ 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:
$ 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
2022-01-22
- Spend some time adding months to the CGIAR TAC and IWC records from Gaia
- Most of the PDFs have months 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.licensefield - I updated about thirty manually, but really Udana should do more…
- I was surprised to see they have 921 total, but only about 200 have a
- Normalize the metadata
text_langattributes on CGSpace database:
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.doifield - I used this OpenRefine GREL to copy them:
- I realized that ~130 items have DOIs in their citation, but no
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:
$ 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