cgspace-notes/content/posts/2021-03.md

---
title: "March, 2021"
date: 2021-03-01T10:13:54+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2021-03-01

- Discuss some OpenRXV issues with Abdullah from CodeObia
  - He's trying to work on the DSpace 6+ metadata schema autoimport using the DSpace 6+ REST API
  - Also, we found some issues building and running OpenRXV currently due to ecosystem shift in the Node.js dependencies

<!--more-->

## 2021-03-02

- I fixed three build and runtime issues in OpenRXV:
  - [fix highcharts-angular and ngx-tour-core build](https://github.com/ilri/OpenRXV/pull/80)
  - [frontend/package.json: Pin @types/ramda at 0.27.34](https://github.com/ilri/OpenRXV/pull/82)
- Then I merged a few fixes that Abdullah had worked on last week

## 2021-03-03

- I [fixed another frontend build warning on OpenRXV](https://github.com/ilri/OpenRXV/issues/83)
- Then I [updated the frontend container to use Node.js 12 and Ubuntu 20.04](https://github.com/ilri/OpenRXV/pull/84)
- Also, I [added a GitHub Actions workflow to build the frontend](https://github.com/ilri/OpenRXV/pull/85)
- I did some testing of Abdullah's patch for the values mapping search on OpenRXV
  - It still doesn't work with multi-word values, so I recorded a video with wf-recorder and uploaded it to [the issue](https://github.com/ilri/OpenRXV/issues/43) for him to investigate

## 2021-03-04

- Peter is having issues with the workflow since yesterday
  - I looked at the Munin stats and see a high number of database locks since yesterday

![PostgreSQL locks week](/cgspace-notes/2021/03/postgres_locks_ALL-week.png)
![PostgreSQL connections week](/cgspace-notes/2021/03/postgres_connections_cgspace-week.png)

- I looked at the number of connections in PostgreSQL and it's definitely high again:

```console
$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;' | wc -l
1020
```

- I reported it to Atmire to take a look, on the [same issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=851) we had been tracking this before
- Abenet asked me to add a new ORCID for ILRI staff member Zoe Campbell
- I added it to the controlled vocabulary and then tagged her existing items on CGSpace using my `add-orcid-identifier.py` script:

```console
$ cat 2021-03-04-add-zoe-campbell-orcid.csv 
dc.contributor.author,cg.creator.identifier
"Campbell, Zoë","Zoe Campbell: 0000-0002-4759-9976"
"Campbell, Zoe A.","Zoe Campbell: 0000-0002-4759-9976"
$ ./ilri/add-orcid-identifiers-csv.py -i 2021-03-04-add-zoe-campbell-orcid.csv -db dspace -u dspace -p 'fuuu'
```

- I still need to do cleanup on the journal articles metadata
  - Peter sent me some cleanups but I can't use them in the search/replace format he gave
  - I think it's better to export the metadata values with IDs and import cleaned up ones as CSV

```console
localhost/dspace63= > \COPY (SELECT dspace_object_id AS id, text_value as "cg.journal" FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=251) to /tmp/2021-02-24-journals.csv WITH CSV HEADER;
COPY 32087
```

- I used OpenRefine to remove all journal values that didn't have one of these values: ; ( )
  - Then I cloned the `cg.journal` field to `cg.volume` and `cg.issue`
  - I used some GREL expressions like these to extract the journal name, volume, and issue:

```console
value.partition(';')[0].trim() # to get journal names
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^(\d+)\(\d+\)/,"$1") # to get journal volumes
value.partition(/[0-9]+\([0-9]+\)/)[1].replace(/^\d+\((\d+)\)/,"$1") # to get journal issues
```

- Then I uploaded the changes to CGSpace using `dspace metadata-import`
- Margarita from CCAFS was asking about an error deleting some items that were showing up in Google and should have been private
  - The error was "Authorization denied for action OBSOLETE (DELETE) on BITSTREAM:bd157345-448e ..."
  - I searched the DSpace issue tracker and found several issues reporting this:
    - [DS-3985 Delete item fails](https://jira.lyrasis.org/browse/DS-3985)
    - [DS-4004 Authorization denied Exception when trying to delete permanently an item, collection or community as a non-Admin user](https://jira.lyrasis.org/browse/DS-4004)
    - [DS-4297 Authorization error when trying to delete item by submitter/administrator](https://jira.lyrasis.org/browse/DS-4297)
  - The issue is apparently with non-admin users who are in the admin and submit groups of the owning collection...
  - In this case the item was uploaded to the CCAFS Reports collection, and Margarita is a non-admin user who is a member of the collection's admin and submit groups, exactly as the issue described
  - I added a comment about our issue to [DS-4297](https://jira.lyrasis.org/browse/DS-4297)
- Yesterday Abenet added me to a WLE collection approver/editer steps so we can try to figure out why Niroshini is having issues adding metadata to Udana's submissions
  - I edited Udana's submission to CGSpace:
    - corrected the title
    - added language English
    - changed the link to the external item page instead of PDF
    - added SDGs from the external item page
    - added AGROVOC subjects from the external item page
    - added pagination (extent)
    - changed the license to "other" because CC-BY-NC-ND is not printed anywhere in the PDF or external item page

## 2021-03-05

- I migrated the Docker bind mount for the AReS Elasticsearch container to a Docker volume:

```console
$ docker-compose -f docker/docker-compose.yml down
$ docker volume create docker_esData_7
$ docker container create --name dummy -v docker_esData_7:/root hello-world
$ docker container create --name es_dummy -v docker_esData_7:/usr/share/elasticsearch/data:rw elasticsearch:7.6.2
$ docker cp docker/esData_7/nodes es_dummy:/usr/share/elasticsearch/data 
$ docker rm es_dummy
# edit docker/docker-compose.yml to switch from bind mount to volume
$ docker-compose -f docker/docker-compose.yml up -d
```

- The trick is that when you create a volume like "myvolume" from a `docker-compose.yml` file, Docker will create it with the name "docker_myvolume"
  - If you create it manually on the command line with `docker volume create myvolume` then the name is literally "myvolume"
- I still need to make the changes to git master and add these notes to the pull request so Moayad and others can benefit
- Delete the `openrxv-items-temp` index to test a fresh harvesting:

```console
$ curl -XDELETE 'http://localhost:9200/openrxv-items-temp'
```

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