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98 lines
5.2 KiB
Markdown
98 lines
5.2 KiB
Markdown
---
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title: "March, 2021"
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date: 2021-03-01T10:13:54+02:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2021-03-01
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- Discuss some OpenRXV issues with Abdullah from CodeObia
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- He's trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
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- Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies
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<!--more-->
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## 2021-03-02
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- I fixed three build and runtime issues in OpenRXV:
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- [fix highcharts-angular and ngx-tour-core build](https://github.com/ilri/OpenRXV/pull/80)
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- [frontend/package.json: Pin @types/ramda at 0.27.34](https://github.com/ilri/OpenRXV/pull/82)
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- Then I merged a few fixes that Abdullah had worked on last week
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## 2021-03-03
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- I [fixed another frontend build warning on OpenRXV](https://github.com/ilri/OpenRXV/issues/83)
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- Then I [updated the frontend container to use Node.js 12 and Ubuntu 20.04](https://github.com/ilri/OpenRXV/pull/84)
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- Also, I [added a GitHub Actions workflow to build the frontend](https://github.com/ilri/OpenRXV/pull/85)
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- I did some testing of Abdullah's patch for the values mapping search on OpenRXV
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- It still doesn't work with multi-word values, so I recorded a video with wf-recorder and uploaded it to [the issue](https://github.com/ilri/OpenRXV/issues/43) for him to investigate
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## 2021-03-04
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- Peter is having issues with the workflow since yesterday
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- I looked at the Munin stats and see a high number of database locks since yesterday
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- I looked at the number of connections in PostgreSQL and it's definitely high again:
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```console
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$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
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1020
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```
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- I reported it to Atmire to take a look, on the [same issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=851) we had been tracking this before
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- Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell
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- I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my `add-orcid-identifier.py` script:
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```console
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$ cat 2021-03-04-add-zoe-campbell-orcid.csv
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dc.contributor.author,cg.creator.identifier
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"Campbell, Zoë","Zoe Campbell: 0000-0002-4759-9976"
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"Campbell, Zoe A.","Zoe Campbell: 0000-0002-4759-9976"
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$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
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```
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- I still need to do cleanup on the journal articles metadata
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- Peter sent me some cleanups but I can't use them in the search/replace format he gave
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- I think it's better to export the metadata values with IDs and import cleaned up ones as CSV
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```console
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localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
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COPY 32087
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```
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- I used OpenRefine to remove all journal values that didn't have one of these values: ; ( )
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- Then I cloned the `cg.journal` field to `cg.volume` and `cg.issue`
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- I used some GREL expressions like these to extract the journal name, volume, and issue:
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```console
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value.partition(';')[0].trim() # to get journal names
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value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
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value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
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```
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- Then I uploaded the changes to CGSpace using `dspace metadata-import`
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- Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
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- The error was "Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e ..."
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- I searched the DSpace issue tracker and found several issues reporting this:
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- [DS-3985 Delete item fails](https://jira.lyrasis.org/browse/DS-3985)
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- [DS-4004 Authorization denied Exception when trying to delete permanently an item, collection or community as a non-Admin user](https://jira.lyrasis.org/browse/DS-4004)
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- [DS-4297 Authorization error when trying to delete item by submitter/administrator](https://jira.lyrasis.org/browse/DS-4297)
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- The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection...
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- In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection's admin and submit groups, exactly as the issue described
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- I added a comment about our issue to [DS-4297](https://jira.lyrasis.org/browse/DS-4297)
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- Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana's submissions
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- I edited Udana's submission to CGSpace:
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- corrected the title
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- added language English
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- changed the link to the external item page instead of PDF
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- added SDGs from the external item page
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- added AGROVOC subjects from the external item page
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- added pagination (extent)
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- changed the license to "other" because CC-BY-NC-ND is not printed anywhere in the PDF or external item page
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<!-- vim: set sw=2 ts=2: -->
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