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208 lines
8.5 KiB
Markdown
208 lines
8.5 KiB
Markdown
---
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title: "March, 2024"
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date: 2024-03-01T09:55:00+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2024-03-01
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- Last week Bizu reported an issue with the "browse by issue date" drop down
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- I verified it, and suspect it could be due to missing issue dates...
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- It might be this issue: https://github.com/DSpace/dspace-angular/issues/2808
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<!--more-->
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- I spent some time trying to reproduce the bug affecting `onebox` fields that are configured to use external vocabularies and are not repeatable
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- I filed an issue: https://github.com/DSpace/dspace-angular/issues/2846
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## 2024-03-03
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- I did some cleanups on abstracts, licenses, and dates from CrossRef
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- I also did some minor cleanups to affiliations because I saw some incorrect and duplicate ones in our list
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## 2024-03-05
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- I tried a new technique to get some affiliations from Crossref using OpenRefine
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- First I split them and clustered, resolving a few hundred clusters out of 1500 (!)
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- Then I used a custom text facet with a few dozen CGIAR and other large affiliations to reduce the work
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- Then I joined them with our affiliations, paying no attention to duplicates
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- Then I deduped them using the Jython technique I learned in 2023-02
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## 2024-03-06
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- Peter sent me some more corrections for the authors that I had sent him in 2023-12
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## 2024-03-08
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- IFPRI sent me their 2023 records from CONTENTdm so I started working on those
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- I found a way to match their ORCID identifiers in our list using Jython in OpenRefine:
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```python
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import re
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with open(r"/tmp/cg-creator-identifier.txt",'r') as f :
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orcid_ids = [orcid_id.strip() for orcid_id in f]
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matched = False
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for orcid_id in orcid_ids:
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if re.search(r'.+: {}'.format(value), orcid_id):
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matched = True
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break
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if matched:
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return orcid_id
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else:
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return value
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```
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- I realized that [UNICEF was renamed to its current name in 1953](https://www.unicef.org/about-unicef/frequently-asked-questions#3) so I replaced all other variations in our vocabularies and metadata:
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```sql
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UPDATE metadatavalue SET text_value='United Nations Children''s Fund' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value IN ('United Nations International Children''s Emergency Fund', 'United Nations International Children''s Emergency Fund', 'UNICEF');
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```
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- Note the use of two single quotes to escape the one in the name
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## 2024-03-11
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- Experimenting with moving some of my Python scripts to the DSpace 7 REST API
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- I need a way to get UUIDs for Handles...
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- Seems that I can use a Discovery query like: https://dspace7test.ilri.org/server/api/discover/search/objects?dsoType=item&query=handle:10568/130864
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- Then just take the first result...?
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- I spent some time working on the script get abstracts from CGSpace, and found a bug in my logic
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- I also noticed that one item had two abstracts, but the first one was blank!
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- Looking deeper, I found 113 blank metadata values so I deleted those:
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```sql
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BEGIN;
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DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='';
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COMMIT;
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```
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- I also found a few dozen items with "N/A" for their citation, so I deleted those too:
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```sql
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BEGIN;
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DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='N/A' AND metadata_field_id=146;
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COMMIT;
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```
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- I deployed the change to disable Angular SSR's `inlineCriticalCss` on production because we had heavy load on the frontend and I've been meaning to do this permanently for some time
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- Maria asked me for a CSV with all the broken Bioversity permalinks so I exported them for her:
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```console
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$ csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],cg.link.permalink[en_US]' ~/Downloads/2024-03-05-cgspace.csv \
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| csvgrep -c 'cg.link.permalink[en_US]' -r '^.+$' > /tmp/2024-03-11-Bioversity-Permalinks.csv
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```
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## 2024-03-12
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- Run the duplicate checker for IFPRI 2023 batch upload
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## 2024-03-13
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- I found about 428 duplicates in the IFPRI 2023 batch records
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- Alarmingly, I found about 18 that are duplicated on CGSpace as well!
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- I looked closer and decided that 11 were duplicates, so I merged the metadata and withdrew the later ones
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- Alliance asked me to get him the Handles for items submitted by TIP that are not discoverable
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- I found it easiest to use the `ds6_item2itemhandle` [DSpace SQL helper function](https://wiki.lyrasis.org/display/DSPACE/Helper+SQL+functions+for+DSpace+6) with a nested query on the provenance:
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```sql
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SELECT ds6_item2itemhandle(dspace_object_id) AS handle FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item WHERE NOT discoverable) AND metadata_field_id=28 AND text_value LIKE 'Submitted by Alliance TIP Submit%';
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```
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## 2024-03-14
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- Looking in to reports of rate limiting of Altmetric's bot on CGSpace
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- I don't see any HTTP 429 responses for their user agents in any of our logs...
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- I tried myself on an item page and never hit a limit...
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```console
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$ for num in {1..60}; do echo -n "Request ${num}: "; curl -s -o /dev/null -w "%{http_code}" https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 && echo; done
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Request 1: 200
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Request 2: 200
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Request 3: 200
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Request 4: 200
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...
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Request 60: 200
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```
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- All responses were HTTP 200...
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- In any case, I whitelisted their production IPs and told them to try again
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- I imported 468 of IFPRI's 2023 records that were confirmed to not be duplicates to CGSpace
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- I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace
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- This was a bit of dirty work using csvkit, xsv, and OpenRefine
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## 2024-03-17
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- There are 17 records from IFPRI's 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
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- These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration
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- I looked closer and whittled this down to 14 actual records, and spent some time working on them
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- I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links
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- Now there only remain two confusing records about the Inkomati catchment
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## 2024-03-18
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- Checking to see how many IFPRI records we have migrated so far:
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```console
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$ csvgrep -c 'dc.description.provenance[en_US]' -m 'Original URL from IFPRI CONTENTdm' cgspace.csv \
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| csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]' \
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| tee /tmp/ifpri-records.csv \
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| csvstat --count
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898
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```
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- I finalized the remaining two on Inkomati catchment and now we are at 900!
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# 2024-03-19
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- IWMI sent me some new author ORCID identifiers so I updated our list
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- Started working on updating my data for the Ontology CoP webinar on CGIAR and AGROVOC
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- First extracting all unique subjects on CGSpace:
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```
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localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS "subject" FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119)) to /tmp/2024-03-19-cgspace-subjects.csv WITH CSV HEADER;
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COPY 28024
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```
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- Then I extracted the subjects and looked them up against AGROVOC:
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```console
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$ csvcut -c subject /tmp/2024-03-19-cgspace-subjects.csv | sed '1d' > /tmp/2024-03-19-cgspace-subjects.txt
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$ ./ilri/agrovoc_lookup.py -i /tmp/2024-03-19-cgspace-subjects.txt -o /tmp/2024-03-19-cgspace-subjects-results.csv
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```
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## 2024-03-20
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- Identify seven duplicates on CGSpace from the PRMS results and withdraw them from CGSpace
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## 2024-03-21
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- Look more closely at duplicates on CGSpace based on a fresh export
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- Using DOIs I found ~842 that occur more than once for journal articles alone, so probably around 400 duplicates
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- I did a handful of them, merging the metadata and withdrawing the duplicate, and decided to add `dcterms.replaces` with the handle in the original
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## 2024-03-22
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- Look at duplicate DOIs on CGSpace and address a dozen or so
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## 2024-03-23
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- Look at duplicate DOIs on CGSpace and address a dozen or so
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- Update Tomcat and Solr to latest versions
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- I had done some tests with these last week, and did a last minute test on DSpace 7 Test to make sure submission and searching worked
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## 2024-03-24
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- Slowly process several dozen more duplicate DOIs on CGSpace, sigh...
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## 2024-03-26
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- File an issue on dspace-angular about improving withdrawn item tombstones: https://github.com/DSpace/dspace-angular/issues/2880
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- Merge metadata and withdraw more duplicates on CGSpace
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<!-- vim: set sw=2 ts=2: -->
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