cgspace-notes/content/posts/2023-07.md

---
title: "July, 2023"
date: 2023-07-01T17:14:36+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2023-07-01

- Export CGSpace to check for missing Initiative collection mappings
- Start harvesting on AReS

## 2023-07-02

- Minor edits to the `crossref_doi_lookup.py` script while running some checks from 22,000 CGSpace DOIs

## 2023-07-03

- I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect
  - I took the more accurate ones from Crossref and updated the items on CGSpace
  - I took a few hundred ISBNs as well for where we were missing them
  - I also tagged ~4,700 items with missing licenses as "Copyrighted; all rights reserved" based on their Crossref license status being TDM, mostly from Elsevier, Wiley, and Springer
  - Checking a dozen or so manually, I confirmed that if Crossref only has a TDM license then it's usually copyrighted (could still be open access, but we can't tell via Crossref)
  - I would be curious to write a script to check the Unpaywall API for open access status...
  - In the past I found that their *license* status was not very accurate, but the open access status might be more reliable
- More minor work on the DSpace 7 item views
  - I learned some new Angular template syntax
  - I created a custom component to show Creative Commons licenses on the simple item page
  - I also decided that I don't like the Impact Area icons as a component because they don't have any visual meaning

## 2023-07-04

- Focus group meeting with CGSpace partners about DSpace 7
- I added a themed file selection component to the CGSpace theme
  - It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI
- I added a custom component to show share icons

## 2023-07-05

- I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13
  - Most things work but there are some minor bugs it seems
- Mishell from CIP emailed me to say she was having problems approving an item on CGSpace
  - Looking at PostgreSQL I saw there were a dozen or so locks that were several hours and even over one day old so I killed those processes and told her to try again

## 2023-07-06

- Types meeting
- I wrote a Python script to check Unpaywall for some information about DOIs

## 2023-07-7

- Continue exploring Unpaywall data for some of our DOIs
  - In the past I've found their _licensing_ information to not be very reliable (preferring Crossref), but I think their _open access status_ is more reliable, especially when the provider is listed as being the publisher
  - Even so, sometimes the version can be "acceptedVersion", which is presumably the author's version, as opposed to the "publishedVersion", which means it's available as open access on the publisher's website
  - I did some quality assurance and found ~100 that were marked as Limited Access, but should have been Open Access, and fixed a handful of licenses
- Delete duplicate metadata as describe in my DSpace issue from last year: https://github.com/DSpace/DSpace/issues/8253
- Start working on some statistics on AGROVOC usage for my presenation next week
  - I used the following SQL query to dump values from all subject fields and lower case them:

```console
localhost/dspacetest= ☘ \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/2023-07-07-cgspace-subjects.csv WITH CSV HEADER;
COPY 26443
Time: 2564.851 ms (00:02.565)
```

- Then I extracted the subjects and looked them up against AGROVOC:

```console
$ csvcut -c subject /tmp/2023-07-07-cgspace-subjects.csv | sed '1d' > /tmp/2023-07-07-cgspace-subjects.txt
$ ./ilri/agrovoc_lookup.py -i /tmp/2023-07-07-cgspace-subjects.txt -o /tmp/2023-07-07-cgspace-subjects-results.csv
```

- I did some more tests with Angular 13 on OpenRXV and found out why the repository type dropdown wasn't working
  - It was because of a missing 1-line JSON file in the data directory, which is runtime data, not code
  - I copied the data directory from the production serve and rebuild and the site is working well now
  - I did a full harvest with plugins and it worked!
  - So it seems Angular 13.4.0 will work, yay

## 2023-07-08

- Export CGSpace to check for missing Initiative collection mappings
  - Start a harvest on AReS
- The AGROVOC lookup finished, so I checked the number of matches:

```console
$ csvgrep -c 'match type' -r '^.+$' ~/Downloads/2023-07-07-cgspace-subjects-resolved.csv | sed 1d | wc -l
12528
```

- So that's 12,528 out of 26,443 unique terms (47.3%)
- I did a LOT of work on the OpenRXV frontend build dependencies to bring more in line with Angular 13

## 2023-07-10

- I did a lot more work on OpenRXV to test and update dependencies
- I deployed the latest version on the production server

## 2023-07-12

- CGSpace upgrade meeting with Americas and Africa group

## 2023-07-13

- Michael Victor asked me to help Aditi extract some information from CGSpace
  - She was interested in journal articles published between 2018 and 2023 with a range of subjects related to drought, flooding, resilience, etc
  - I used an advanced query with some AGROVOC terms:

```console
dcterms.issued:[2018 TO 2023] AND dcterms.type:"Journal Article" AND (dcterms.subject:flooding OR dcterms.subject:flood OR dcterms.subject:"extreme weather events" OR dcterms.subject:drought OR dcterms.subject:"drought resistance" OR dcterms.subject:"drought tolerance" OR dcterms.subject:"soil salinity" OR dcterms.subject:"pests of plants" OR dcterms.subject:pests OR dcterms.subject:heat OR dcterms.subject:fertilizers OR dcterms.subject:"fertilizer technology" OR dcterms.subject:"rice fields" OR dcterms.subject:"landscape conservation" OR dcterms.subject:"landscape restoration" OR dcterms.subject:livestock)
```

- Interestingly, some variations of this same exact query produce no search results, and I see this error in the DSpace log:

```console
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dcterms.issued:[2018 TO 2023] AND dcterms.type:"Journal Article" AND (dcterms.subject:flooding OR dcterms.subject:flood OR dcterms.subject:"extreme weather events" OR dcterms.subject:drought OR dcterms.subject:"drought resistance" OR dcterms.subject:"drought tolerance" OR dcterms.subject:"soil salinity" OR dcterms.subject:"pests of plants" OR dcterms.subject:pests OR dcterms.subject:heat OR dcterms.subject:fertilizers OR dcterms.subject:"fertilizer technology" OR dcterms.subject:"rice fields" OR dcterms.subject:livestock OR dcterms.subject:"landscape conservation" OR dcterms.subject:"landscape restoration\"\)': Lexical error at line 1, column 617.  Encountered: <EOF> after : "\"landscape restoration\\\"\\)"
```

- It seems to be when there is a quoted search term at the end of the parenthesized group
  - For what it's worth this same query worked fine on DSpace 7.6

## 2023-07-15

- Export CGSpace to fix missing Initiative collection mappings
- Start a harvest on AReS

## 2023-07-17

- Rasika had sent me a list of new ORCID identifiers for new IWMI staff so I combined them with our existing list and ran `resolve_orcids.py` to refresh the names in our database
  - I updated the list, updated names in the database, and tagged new authors with missing identifiers in existing items

## 2023-07-18

- Meeting with IWMI, IRRI, and IITA colleagues about CGSpace upgrade plans
- Maria from the Alliance mentioned having some submissions stuck on CGSpace
  - I looked and found a number of locks stuck for many nineteen, eighteen, and more hours...
  - I killed them and told her to try again

```console
$ psql < locks-age.sql | less -S
$ psql < locks-age.sql | grep -E " (19|18|17|16|12):" | awk -F"|" '{print $10}' | sort -u | xargs kill
```

## 2023-07-19

- I had to kill a bunch more locked processes in PostgreSQL, I'm not sure what's going on
- After some discussion about an advanced search bug with Tim on Slack, I filed [an issue on GitHub](https://github.com/DSpace/DSpace/issues/8962)

## 2023-07-20

- I added a new metadata field for CGIAR Impact Platforms (`cg.subject.impactPlatform`) to CGSpace

## 2023-07-22

- Export CGSpace tp fix missing Initiative collections
- Start a harvest on AReS

## 2023-07-24

- Test Salem's new JavaScript-based DSpace Statistics API and send him some feedback
- I noticed a few times that the Solr service on my DSpace 7 instance is getting OOM killed
  - I had been using a 4g Solr heap, but maybe we don't need that much
  - Tomcat is also using 4.6GB, and then there's PostgreSQL... so perhaps it's all a bit much on this system now

## 2023-07-25

- Start testing exporting DSpace 6 Solr cores to import on DSpace 7:

```console
$ chrt -b 0 dspace solr-export-statistics -i statistics
```

- I'm curious how long it takes and how much data there will be
  - The size of the Solr data directory is currently 82GB
  - The export took about 2.5 hours and created 6,000 individual CSVs, one for each day of Solr stats
  - The size of the exported CSVs is about 88GB 
  - I will copy just a few years to import on the DSpace 7 test server
  - So importing these is going to require removing the Atmire custom fields:

```console
$ dspace solr-import-statistics -i statistics
Exception: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field 'containerCommunity'
org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field 'containerCommunity'
        at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:681)
        at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:266)
        at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:248)
        at org.apache.solr.client.solrj.SolrClient.request(SolrClient.java:1290)
        at org.dspace.util.SolrImportExport.importIndex(SolrImportExport.java:465)
        at org.dspace.util.SolrImportExport.main(SolrImportExport.java:148)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:277)
        at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:133)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:98)
```

- I will try using solr-import-export-json, which I've used in the past to skip Atmire custom fields in Solr:

```console
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2022.json -f 'time:[2022-01-01T00\:00\:00Z TO 2022-12-31T23\:59\:59Z]' -k uid -S author_mtdt,author_mtdt_search,iso_mtdt_search,iso_mtdt,subject_mtdt,subject_mtdt_search,containerCollection,containerCommunity,containerItem,countryCode_ngram,countryCode_search,cua_version,dateYear,dateYearMonth,geoipcountrycode,geoIpCountryCode,ip_ngram,ip_search,isArchived,isInternal,isWithdrawn,containerBitstream,file_id,referrer_ngram,referrer_search,userAgent_ngram,userAgent_search,version_id,complete_query,complete_query_search,filterquery,ngram_query_search,ngram_simplequery_search,simple_query,simple_query_search,range,rangeDescription,rangeDescription_ngram,rangeDescription_search,range_ngram,range_search,actingGroupId,actorMemberGroupId,bitstreamCount,solr_update_time_stamp,bitstreamId,core_update_run_nb
```

- Some users complained that CGSpace was slow and I found a handful of locks that were hours and days old...
  - I killed those and told them to try again
- After importing the Solr statistics into DSpace 7 I realized that my DSpace Statistics API will work fine
  - I made some minor modifications to the Ansible infrastructure scripts to make sure it is enabled and then activated it on DSpace 7 Test

<!-- vim: set sw=2 ts=2: -->