cgspace-notes/content/posts/2023-02.md

---
title: "February, 2023"
date: 2023-02-01T10:57:36+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2023-02-01

- Export CGSpace to cross check the DOI metadata with Crossref
  - I want to try to expand my use of their data to journals, publishers, volumes, issues, etc...

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- First, extract a list of DOIs for use with `crossref-doi-lookup.py`:

```console
$ csvcut -c 'cg.identifier.doi[en_US]' ~/Downloads/2023-02-01-cgspace.csv \
  | csvgrep -c 1 -m 'doi.org' \
  | csvgrep -c 1 -m ' ' -i \
  | csvgrep -c 1 -r '.*cifor.*' -i \
  | sed 1d > /tmp/2023-02-01-dois.txt
$ ./ilri/crossref-doi-lookup.py -e a.orth@cgiar.org -i /tmp/2023-02-01-dois.txt -o ~/Downloads/2023-01-31-crossref-results.csv -d
```

- Then extract the ID, DOI, journal, volume, issue, publisher, etc from the CGSpace dump and rename the `cg.identifier.doi[en_US]` to `doi` so we can join on it with the Crossref results file:

```console
$ csvcut -c 'id,cg.identifier.doi[en_US],cg.journal[en_US],cg.volume[en_US],cg.issue[en_US],dcterms.publisher[en_US],cg.number[en_US],dcterms.license[en_US]' ~/Downloads/2023-02-01-cgspace.csv \
  | csvgrep -c 'cg.identifier.doi[en_US]' -r '.*cifor.*' -i \
  | sed -e '1s/cg.identifier.doi\[en_US\]/doi/' \
    -e 's_https://doi.org/__g' \
    -e 's_https://dx.doi.org/__g' \
  > /tmp/2023-02-01-cgspace-doi-metadata.csv
$ csvjoin -c doi /tmp/2023-02-01-cgspace-doi-metadata.csv ~/Downloads/2023-02-01-crossref-results.csv > /tmp/2023-02-01-cgspace-crossref-check.csv
```

- And import into OpenRefine for analysis and cleaning
- I just noticed that Crossref also has types, so we could use that in the future too!
- I got a few corrections after examining manually, but I didn't manage to identify any patterns that I could use to do any automatic matching or cleaning

## 2023-02-05

- Normalize text lang attributes in PostgreSQL, run a quick Discovery index, and then export CGSpace to check Initiative mappings and countries/regions
- Run all system updates on CGSpace (linode18) and reboot it

## 2023-02-06

- Peter said that a new Initiative was approved last month so we need to add it to CGSpace: `Fragility, Conflict, and Migration`
- There is lots of discussion about the "issue date" versus "available date" with Enrico and IFPRI, after lots of feedback from the PRMS QA
  - I filed [an issue on CG Core to propose using `dcterms.available` as an optional field to indicate the online date](https://github.com/AgriculturalSemantics/cg-core/issues/43)


## 2023-02-07

- IFPRI's web developer Tony managed to get his Drupal harvester to have a useful user agent:

```console
54.x.x.x - - [06/Feb/2023:10:10:32 +0100] "POST /rest/items/find-by-metadata-field?limit=%22100&offset=0 HTTP/1.1" 200 58855 "-" "IFPRI drupal POST harvester"
```

- He also noticed that there is no pagination on POST requests to `/rest/items/find-by-metadata-field`, and that he needs to increase his timeout for requests that return 100+ results, ie:


```console
curl -f -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.actionArea", "value":"Systems Transformation", "language": "en_US"}'
```

- I need to ask on the DSpace Slack about this POST pagination
- Abenet and Udana noticed that the Handle server was not running
  - Looking in the `error.log` file I see that the service is complaining about a lock file being present
  - This is because Linode had to do emergency maintenance on the VM host this morning and the Handle server didn't shut down properly
- I'm having an issue with `poetry update` so I spent some time debugging and filed [an issue](https://github.com/python-poetry/poetry/issues/7482)
- Proof and import nine items for the Digital Innovation Inititive for IFPRI
  - There were only some minor issues in the metadata
  - I also did a duplicate check with `check-duplicates.py` just in case
- I did some minor updates on csv-metadata-quality
  - First, to reduce warnings on non-SPDX licenses like "Copyrighted; all rights reserved" and "Other" since they are very common for us and I'm sick of seeing the warnings
  - Second, to skip whitespace and newline fixes on the abstract field since so many times they are intended

## 2023-02-08

- Make some edits to IFPRI records requested by Jawoo and Leigh
- Help Alessandra upload a last minute report for SAPLING
- Proof and upload twenty-seven IFPRI records to CGSpace
  - It's a good thing I did a duplicate check because I found three duplicates!
- Export CGSpace to update Initiative mappings and country/region mappings
  - Then start a harvest on AReS

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