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119 lines
5.9 KiB
Markdown
119 lines
5.9 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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