January, 2022
+September, 2022
2022-01-01
+2022-09-01
-
-
- Start a full harvest on AReS +
- A bit of work on the “Mapping CG Core–CGSpace–MEL–MARLO Types” spreadsheet +
- I tested an item submission on DSpace Test with the Cocoon
org.apache.cocoon.uploads.autosave=falsechange +-
+
- The submission works as expected
2022-01-06
+
+ - Start debugging some region-related issues with csv-metadata-quality
-
-
- Add ORCID identifier for Chris Jones to CGSpace
-
-
-
- Also tag eighty-eight of his items in CGSpace: +
- I created a new test file
test-geography.csvwith some different scenarios
+ - I also fixed a few bugs and improved the region-matching logic
$ 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 +
- I filed an issue for the “South-eastern Asia” case mismatch in country_converter on GitHub +
- Meeting with Moayad to discuss OpenRXV developments
-
-
- 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: +
- He demoed his new multiple dashboards feature and I helped him rebase those changes to master so we can test them more
-
+Your repository has been registered in the OAI database of conforming repositories.
-2022-09-02
-
-
- Now I’m taking a screenshot of the validation page for posterity, because the logs seem to go away after some time -
+
- Add ORCID identifier for Chris Jones to CGSpace
-
- I worked a bit more on exclusion and skipping logic in csv-metadata-quality
-
-
- 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 +
- I also pruned and updated all the Python dependencies +
- Then I released version 0.6.0 now that the excludes and region matching support is working way better
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 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.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
-
-
-
- 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.pyscript 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.pyon 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: -
-
value.contains(/:\s?\d+(-|–)\d+/) --
-
- Then I faceted by blank on
dcterms.extentand did a transform to extract the page information for over 1,000 items!
-
'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.volumeandcg.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:
-
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… -
+ + + + + + ++ +September, 2022
+ +2022-09-01
+-
+
- A bit of work on the “Mapping CG Core–CGSpace–MEL–MARLO Types” spreadsheet +
- I tested an item submission on DSpace Test with the Cocoon
org.apache.cocoon.uploads.autosave=falsechange +-
+
- The submission works as expected +
+ - Start debugging some region-related issues with csv-metadata-quality
+
-
+
- I created a new test file
test-geography.csvwith some different scenarios
+ - I also fixed a few bugs and improved the region-matching logic +
+ - I created a new test file
December, 2021
@@ -324,31 +356,6 @@ - -- - - - - -- -November, 2021
- -2021-11-02
--
-
- I experimented with manually sharding the Solr statistics on DSpace Test -
- First I exported all the 2019 stats from CGSpace: -
- Read more → -$ ./run.sh -s http://localhost:8081/solr/statistics -f 'time:2019-*' -a export -o statistics-2019.json -k uid -$ zstd statistics-2019.json -