- The upgrade was mostly normal, but I had to unhold the openjdk package in order for `do-release-upgrade` to run:
```console
# apt-mark hold openjdk-8-jdk-headless:amd64 openjdk-8-jre-headless:amd64
```
- 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
- 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" >}})
- 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:
- Export CGSpace to check and update `dcterms.extent` fields
- I normalized about 1,500 to use either "p. 1-6" or "5 p." format
- 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]`
- This was over 4,000 items with a format like "p. 1-6" and "pp. 1-6" in the citation
- I used another GREL expression to extract another 5,000: `cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*?(\d+\s+?[Pp]+\.).*/)[0]`
- This was for the format like "1 p." (note we had to protect against the greedy `.*` in the beginning)
- 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
- 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:
```sql
SELECT * FROM eperson WHERE email LIKE '%cgiar.org' AND netid IS NOT NULL AND password IS NOT NULL;
```
- I am wondering if I should delete their passwords and tell them use log in using LDAP
- As an initial test I will reset a few accounts including my own that have passwords and salts:
```sql
UPDATE eperson SET password=DEFAULT,salt=DEFAULT,digest_algorithm=DEFAULT WHERE netid IN ('axxxx', 'axxxx', 'bxxxx');
```
- I also decided to reset passwords/salts for CGIAR accounts that have not been active since 2021 (1.5 years ago):
```sql
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;
```
- This was about 100 accounts...
- I will wait some more time before I decide what to do about the more current ones
- Add a few more ORCID identifiers to my list and tag them on CGSpace
## 2023-06-10
- Export CGSpace to check for missing Initiative mappings
- 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
## 2023-06-12
- Export CGSpace to do some more work extracting volume and issue from citations for items where they are missing
- I found and fixed over 7,000!
- Then I found and extracted another 7,000 items with no extents (pages)
- Then I replaced all occurences of en dashes for ranges in pages with regular hyphens
## 2023-06-13
- Last night I finally figured out how to do basic overrides to the simple item view in Angular
- Add a handful of new ORCID identifiers to my list and tag them on CGSpace
- 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)
- 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)
- Meeting with Indira, Ryan, and Abenet to discuss plans for the DSpace 7 focus group
- Did some more work on the DSpace 7 Test to improve the submission forms and the look and feel
- 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)
- I filed [an issue about the yarn merge-i18n script](https://github.com/DSpace/dspace-angular/issues/2309)
- I made [a pull request for some Finnish language i18n strings](https://github.com/DSpace/dspace-angular/pull/2306)
- I made [a pull request to lint the i18n en.json5 file](https://github.com/DSpace/dspace-angular/pull/2306)
## 2023-06-15
- A lot more work on DSpace 7
- I tested some pull requests and worked on the style of the item view and homepage
## 2023-06-16
- A lot more work on DSpace 7
- I made [a pull request to adjust font weight in item counts ](https://github.com/DSpace/dspace-angular/pull/2316)
- I made [a pull request to update the ESLint configuration for JSON5](https://github.com/DSpace/dspace-angular/pull/2317)
## 2023-06-17
- Export CGSpace to check for missing Initiative collection mappings
- I also spent some time doing sanity checks on countries, regions, DOIs, and more
- I lowercased all our AGROVOC keywords in `dcterms.subject`:
```sql
dspace=# BEGIN;
BEGIN
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:]]';
- Stefano got back to me about the MODS OAI-PMH schema test on DSpace Test
- 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
- I updated DSpace Test with the new date format and said I'd work on the custom AGRIS set
## 2023-06-25
- Export CGSpace to check for missing Initiative collection mappings
- 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
- I decided to run all updates and reboot it since it's Sunday anyway
## 2023-06-26
- Since the new DSpace 7 will respect newlines in metadata fields I am curious to see how many of our abstracts have poor newlines
- I exported CGSpace and used a custom text facet with this GREL expression in OpenRefine to count the number of newlines in each cell:
```console
value.split('\n').length()
```
- Also useful to check for general length of the text in the cell to make sure it's a reasonably long string
- 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
- I fixed a few dozen
- Do a bit of work on thumbnails on CGSpace
- I'm trying to troubleshoot the Discovery error I get on DSpace 7:
```console
java.lang.NullPointerException: Cannot invoke "org.dspace.discovery.configuration.DiscoverySearchFilterFacet.getIndexFieldName()" because the return value of "org.dspace.content.authority.DSpaceControlledVocabularyIndex.getFacetConfig()" is null
```
- I reverted to the default `submission-forms.xml` and the `getFacetConfig()` error goes away...
- Kill some long-held locks on CGSpace PostgreSQL, as some users are complaining of slowness in archiving
- I did some testing of the LDAP login issue related to groupmaps
- 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)
- 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
## 2023-06-27
- I debugged the NullPointerException and somehow it disappeared
- It seems to be related to the external controlled vocabularies in the submission form
- I removed them all, then added them all back, and now the issue is solved... hmmmm
- Oh now, now they are gone again, sigh...
## 2023-06-28
- Spent a lot of time debugging the browse indexes
- 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`
- 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
- Yes, if I remove them all from my submission form then this works: http://localhost:8080/server/api/discover/browses
- I went through each of our vocabularies and tested them one by one:
- dcterms-subject: OK
- dc-contributor-author: NO
- cg-creator-identifier: NO
- cg-contributor-affiliation: OK (and with `facetType: "affiliation"` in API response?!)
- cg-contributor-donor: OK (`facetType: "sponsorship"`)
- cg-journal: NO
- cg-coverage-subregion: NO
- cg-species-breed: NO
- Now I need to figure out what it is about those five that causes them to not work!
- 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.
- 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)
- 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
- I deployed it on CGSpace and it's working!
- I lowercased all our AGROVOC terms because I noticed a few that were not:
```console
dspace=# BEGIN;
BEGIN
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:]]';
UPDATE 53
dspace=*# COMMIT;
```
- After more discussion about the NullPointerException related to browse options, I filed [an issue](https://github.com/DSpace/DSpace/issues/8927)
## 2023-06-30
- I added another custom component to display CGIAR Impact Area icons in the DSpace 7 test
