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253 lines
13 KiB
Markdown
253 lines
13 KiB
Markdown
---
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title: "June, 2023"
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date: 2023-06-02T10:29:36+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2023-06-02
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- Spend some time testing my `post_bitstreams.py` script to update thumbnails for items on CGSpace
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- Interestingly I found an item with a JFIF thumbnail and another with a WebP thumbnail...
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- Meeting with Valentina, Stefano, and Sara about MODS metadata in CGSpace
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- They have experience with improving the MODS interface in MELSpace's OAI-PMH for use with AGRIS and were curious if we could do the same in CGSpace
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- From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then just add a bunch of our fields to the crosswalk
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<!--more-->
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## 2023-06-04
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- Upgrade CGSpace to Ubuntu 22.04
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- The upgrade was mostly normal, but I had to unhold the openjdk package in order for `do-release-upgrade` to run:
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```console
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# apt-mark hold openjdk-8-jdk-headless:amd64 openjdk-8-jre-headless:amd64
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```
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- In [2022-11]({{< relref "2022-11.md" >}}) an upstream Java update broke the DSpace 6 Handle server so we will have to pin this again after the upgrade to Ubuntu 22.04
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- After the upgrade I made sure CGSpace was working, then proceeded to upgrade PostgreSQL from 12 to 14, like I did on [DSpace Test in 2023-03]({{< relref "2023-03.md" >}})
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- Then I had to downgrade OpenJDK to fix the Handle server using the ones I had previously downloaded for Ubuntu 20.04 because they no longer exist on Launchpad:
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```console
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# dpkg -i openjdk-8-j*8u342-b07*.deb
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```
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- Export CGSpace to fix missing Initiative collection mappings
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- Start a harvest on AReS
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- Work on the DSpace 7 migration a bit more
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- I decided to rebase and drop all the submission form edits because they conflict every time upstream changes!
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## 2023-06-06
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- Fix some incorrect ORCID identifiers for an Alliance author on CGSpace
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- Export our list of ORCID identifiers, resolve them, and update the records in CGSpace:
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```console
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$ cat dspace/config/controlled-vocabularies/cg-creator-identifier.xml 2022-09-22-add-orcids.csv| grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2023-06-06-orcids.txt
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$ ./ilri/resolve_orcids.py -i /tmp/2023-06-06-orcids.txt -o /tmp/2023-06-06-orcids-names.txt -d
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$ ./ilri/update_orcids.py -i /tmp/2023-06-06-orcids-names.txt -db dspacetest -u dspace -p 'ffff' -m 247
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```
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- Start working on updating the MODS schema in CGSpace from 3.1 to 3.8 based on Stefano and Salem's work last year
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## 2023-06-08
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- Continue working on the MODS schema mapping
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- Export CGSpace to check and update `dcterms.extent` fields
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- I normalized about 1,500 to use either "p. 1-6" or "5 p." format
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- Also, I used this GREL expression to extract missing pages from the citation field: `cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*(pp?\.\s?\d+[-–]\d+).*/)[0]`
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- This was over 4,000 items with a format like "p. 1-6" and "pp. 1-6" in the citation
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- I used another GREL expression to extract another 5,000: `cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*?(\d+\s+?[Pp]+\.).*/)[0]`
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- This was for the format like "1 p." (note we had to protect against the greedy `.*` in the beginning)
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- I also did some work to capture a handful of missing DOIs and ISSNs, but it was only about 100 items and I will have to wait until the 10,000+ above finish importing
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## 2023-06-09
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- I see there are ~200 users in CGSpace that have registered with their CGIAR email address using a password as opposed to using Active Directory:
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```sql
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SELECT * FROM eperson WHERE email LIKE '%cgiar.org' AND netid IS NOT NULL AND password IS NOT NULL;
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```
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- I am wondering if I should delete their passwords and tell them use log in using LDAP
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- As an initial test I will reset a few accounts including my own that have passwords and salts:
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```sql
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UPDATE eperson SET password=DEFAULT,salt=DEFAULT,digest_algorithm=DEFAULT WHERE netid IN ('axxxx', 'axxxx', 'bxxxx');
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```
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- I also decided to reset passwords/salts for CGIAR accounts that have not been active since 2021 (1.5 years ago):
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```sql
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UPDATE eperson SET password=DEFAULT,salt=DEFAULT,digest_algorithm=DEFAULT WHERE email LIKE '%cgiar.org' AND netid IS NOT NULL AND password IS NOT NULL AND salt IS NOT NULL AND last_active < '2022-01-01'::date;
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```
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- This was about 100 accounts...
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- I will wait some more time before I decide what to do about the more current ones
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- Add a few more ORCID identifiers to my list and tag them on CGSpace
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## 2023-06-10
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- Export CGSpace to check for missing Initiative mappings
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- Start a harvest on AReS
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## 2023-06-11
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- File [an issue](https://github.com/DSpace/DSpace/issues/8900) on DSpace for the `Content-Disposition` bug causing images to get downloaded instead of opened inline
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## 2023-06-12
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- Export CGSpace to do some more work extracting volume and issue from citations for items where they are missing
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- I found and fixed over 7,000!
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- Then I found and extracted another 7,000 items with no extents (pages)
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- Then I replaced all occurences of en dashes for ranges in pages with regular hyphens
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## 2023-06-13
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- Last night I finally figured out how to do basic overrides to the simple item view in Angular
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- Add a handful of new ORCID identifiers to my list and tag them on CGSpace
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- Extract a list of all the proposed actions for CG Core output types and create a [new issue for them on CG Core's GitHub repository](https://github.com/AgriculturalSemantics/cg-core/issues/45)
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- Extract a list of all the proposed actions for CG Core output types for MARLO and create [a new issue for them on MARLO's GitHub repository](https://github.com/CCAFS/MARLO/issues/2479)
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- Meeting with Indira, Ryan, and Abenet to discuss plans for the DSpace 7 focus group
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## 2023-06-14
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- Did some more work on the DSpace 7 Test to improve the submission forms and the look and feel
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- Extract a list of all the proposed actions for CG Core output types for MEL and create [a new issue for them on MEL's GitHub repository](https://github.com/CodeObia/MEL/issues/11216)
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- I filed [an issue about the yarn merge-i18n script](https://github.com/DSpace/dspace-angular/issues/2309)
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- I made [a pull request for some Finnish language i18n strings](https://github.com/DSpace/dspace-angular/pull/2306)
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- I made [a pull request to lint the i18n en.json5 file](https://github.com/DSpace/dspace-angular/pull/2306)
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## 2023-06-15
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- A lot more work on DSpace 7
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- I tested some pull requests and worked on the style of the item view and homepage
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## 2023-06-16
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- A lot more work on DSpace 7
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- I made [a pull request to adjust font weight in item counts ](https://github.com/DSpace/dspace-angular/pull/2316)
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- I made [a pull request to update the ESLint configuration for JSON5](https://github.com/DSpace/dspace-angular/pull/2317)
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## 2023-06-17
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- Export CGSpace to check for missing Initiative collection mappings
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- I also spent some time doing sanity checks on countries, regions, DOIs, and more
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- I lowercased all our AGROVOC keywords in `dcterms.subject`:
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```sql
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dspace=# BEGIN;
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BEGIN
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dspace=*# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value ~ '[[:upper:]]';
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UPDATE 2392
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dspace=*# COMMIT;
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COMMIT
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```
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- Start a harvest on AReS
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## 2023-06-19
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- Today I started getting an error on DSpace 7 Test
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- The page loads, and then when it is almost done it goes blank to white with this in the console:
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```console
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ERROR DOMException: CSSStyleSheet.cssRules getter: Not allowed to access cross-origin stylesheet
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```
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- I restarted Angular, but it didn't fix it
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- The `yarn test:rest` script shows everything OK, and I haven't changed anything recently...
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- I re-compiled the Angular UI using the default theme and it was the same...
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- I tried in Firefox Nightly and it works...
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- So it must be something related to the browser
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- I tried clearing all the session storage / cookies and refreshing and it worked
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- I switched back to the CGSpace theme and it happened again
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- I had a hunch it might be due to the GDPR cookie plugin in my browser, so I disabled that and then refreshed and it worked... hmmm
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- Upload thumbnails for about 42 IITA Journal Articles after resolving their DOIs and making sure they were not CC ND
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- I fixed a few bugs in `get_scihub_pdfs.py` in the process
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## 2023-06-21
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- Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
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- He said that it's fine if we use iso8601 encoding for dates instead of w3cdtf and asked if we can create a custom end point for AGRIS that only includes types like Journal Articles similar to how Salem did it: https://melspace.loc.codeobia.com/oai/agris?verb=ListRecords&metadataPrefix=mods
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- I updated DSpace Test with the new date format and said I'd work on the custom AGRIS set
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## 2023-06-25
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- Export CGSpace to check for missing Initiative collection mappings
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- I wanted to start a harvest on AReS but I've seen the load on the server high for a few days and I'm not sure what it is
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- I decided to run all updates and reboot it since it's Sunday anyway
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## 2023-06-26
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- Since the new DSpace 7 will respect newlines in metadata fields I am curious to see how many of our abstracts have poor newlines
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- I exported CGSpace and used a custom text facet with this GREL expression in OpenRefine to count the number of newlines in each cell:
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```console
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value.split('\n').length()
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```
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- Also useful to check for general length of the text in the cell to make sure it's a reasonably long string
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- I spent some time trying to find a pattern that I could use to identify "easy" targets, but there are so many exceptions that it will have to be done manually
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- I fixed a few dozen
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- Do a bit of work on thumbnails on CGSpace
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- I'm trying to troubleshoot the Discovery error I get on DSpace 7:
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```console
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java.lang.NullPointerException: Cannot invoke "org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()" because the return value of "org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()" is null
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```
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- I reverted to the default `submission-forms.xml` and the `getFacetConfig()` error goes away...
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- Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving
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- I did some testing of the LDAP login issue related to groupmaps
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- It does seem to be a regression from the [LDAP auth patch](https://github.com/DSpace/DSpace/pull/8814) from last month, so I [filed an issue](https://github.com/DSpace/DSpace/issues/8920)
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- I spent some time on working on Angular and I figured out how to add a custom Angular component to show the UN SDG Goal icons on DSpace 7
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## 2023-06-27
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- I debugged the NullPointerException and somehow it disappeared
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- It seems to be related to the external controlled vocabularies in the submission form
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- I removed them all, then added them all back, and now the issue is solved... hmmmm
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- Oh now, now they are gone again, sigh...
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## 2023-06-28
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- Spent a lot of time debugging the browse indexes
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- Looking at the [DSpace 7 demo API](https://api7.dspace.org/server/api/discover/browses) I see the four default browse indexes from `dspace.cfg` and the one default `srsc` one that gets automatically enabled from the `<vocabulary>srsc</vocabulary>` in the `submission-forms.xml`
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- The same API call on my test DSpace 7 configuration results in the HTTP 500 I've been seeing for some time, and I am pretty sure it's due to the automagic configuration of hierarchical browses based on the submission form
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- Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses
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- I went through each of our vocabularies and tested them one by one:
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- dcterms-subject: OK
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- dc-contributor-author: NO
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- cg-creator-identifier: NO
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- cg-contributor-affiliation: OK (and with `facetType: "affiliation"` in API response?!)
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- cg-contributor-donor: OK (`facetType: "sponsorship"`)
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- cg-journal: NO
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- cg-coverage-subregion: NO
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- cg-species-breed: NO
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- Now I need to figure out what it is about those five that causes them to not work!
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- Ah, after debugging with someone on the DSpace Slack, I realized that DSpace expects these vocabularies to have corresponding indexes configured in `discovery.xml`, and they must be added as search filters AND sidebar facets.
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## 2023-06-29
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- I noticed there is now a [patched version of the Handle JAR for DSpace 6.x](https://github.com/DSpace/DSpace/issues/8557#issuecomment-1595340249)
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- This fixes the [issue in OpenJDK 1.8.0_352](https://groups.google.com/g/dspace-tech/c/PqjfA5mqG4w/m/FhxI5oXhFwAJ?pli=1), so we can remove the apt pin on JDK now
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- I deployed it on CGSpace and it's working!
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- I lowercased all our AGROVOC terms because I noticed a few that were not:
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```console
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dspace=# BEGIN;
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BEGIN
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dspace=*# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value ~ '[[:upper:]]';
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UPDATE 53
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dspace=*# COMMIT;
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```
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- After more discussion about the NullPointerException related to browse options, I filed [an issue](https://github.com/DSpace/DSpace/issues/8927)
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## 2023-06-30
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- I added another custom component to display CGIAR Impact Area icons in the DSpace 7 test
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<!-- vim: set sw=2 ts=2: -->
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