cgspace-notes/content/posts/2022-01.md

---
title: "January, 2022"
date: 2022-01-01T15:20:54+02:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2022-01-01

- Start a full harvest on AReS

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## 2022-01-06

- Add ORCID identifier for Chris Jones to CGSpace
  - Also tag eighty-eight of his items in CGSpace:

```console
$ cat 2022-01-06-add-orcids.csv 
dc.contributor.author,cg.creator.identifier
"Jones, Chris","Chris Jones: 0000-0001-9096-9728"
"Jones, Christopher S.","Chris Jones: 0000-0001-9096-9728"
$ ./ilri/add-orcid-identifiers-csv.py -i 2022-01-06-add-orcids.csv -db dspace63 -u dspacetest -p 'dom@in34sniper' 
```

## 2022-01-09

- Validate and register CGSpace on [OpenArchives](https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7)
  - Last month IWMI colleagues were asking me to look into this, and after checking the OpenArchives mailing list it seems there was a problem on the server side
  - Now it has worked and the message is "Successfully updated OAI registration database to status COMPLIANT."
  - I received an email (as the Admin contact on our OAI) that says:

> Your repository has been registered in the OAI database of conforming repositories.

- Now I'm taking a screenshot of the validation page for posterity, because the logs seem to go away after some time

![OpenArchives.org registration](/cgspace-notes/2022/01/openarchives-registration.png)

- I tried to re-build the Docker image for OpenRXV and got an error in the backend:

```console
...
> openrxv-backend@0.0.1 build
> nest build

node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself.

2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate<any> | AggregationsTermsAggregate<any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate<AggregationsBucket> | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
                 ~~~~~~~~~~~~~~~~~~~~~
node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.

3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Found 2 error(s).
```

- Ah, it seems the code on the server was slightly out of date
  - I checked out the latest master branch and it built

## 2022-01-12

- Fix some citation formatting issues in Gaia's [eighteen CAS Green Cover publications on DSpace Test](https://dspacetest.cgiar.org/handle/10568/115230)

## 2022-01-19

- Francesca was having issues with a submission on CGSpace this week
  - I checked and see a lot of locks in PostgreSQL:

```console
$ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n
      1 
      1 ------------------
      1 (3506 rows)
      1  application_name 
      9  psql
     10  
   3487  dspaceWeb
```

- As before, I see messages from PostgreSQL about processes waiting for locks since I enabled the `log_lock_waits` setting last month:

```console
$ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for'
12
```

- I set a system alert on DSpace and then restarted the server

## 2022-01-20

- Abenet gave me a thumbs up for Gaia's eighteen CAS Green Cover items from last month
  - I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:

```console
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile=./2022-01-20-green-covers.map
```

## 2022-01-21

- Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
  - I did some cleanups and standardization of author names
  - I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text
  - Otherwise all items have only a year, which is not great...
- Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
  - I did some basic tests and created a [pull request](https://github.com/ilri/OpenRXV/pull/128)

## 2022-01-22

- Spend some time adding months to the CGIAR TAC and IWC records from Gaia
  - Most of the PDFs have only YYYY, so this is annoying...

## 2022-01-23

- Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia
- Rebuild AReS and start a fresh harvest

## 2022-01-25

- Help Udana from IWMI answer some questions about licenses on their journal articles
  - I was surprised to see they have 921 total, but only about 200 have a `dcterms.license` field
  - I updated about thirty manually, but really Udana should do more...
- Normalize the metadata `text_lang` attributes on CGSpace database:

```console
dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
 text_lang |  count  
-----------+---------
 en_US     | 2803350
 en        |    6232
           |    3200
 fr        |       2
 vn        |       2
 92        |       1
 sp        |       1
           |       0
(8 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en', '92', '');
UPDATE 9433
```

- Then export the WLE Journal Articles collection again so there are fewer columns to mess with

## 2022-01-26

- Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks

## 2022-01-27

- Work on WLE's Journal Articles a bit more
  - I realized that ~130 items have DOIs in their citation, but no `cg.identifier.doi` field
  - I used this OpenRefine GREL to copy them:

```
cells['dcterms.bibliographicCitation[en_US]'].value.split("doi: ")[1]
```

- I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don't put DOIs in the citation so it's not possible to fix items that are missing DOIs that way
  - And I cleaned up and normalized some licenses
- Francesca from Bioversity was having issues with a submission on CGSpace again
  - I looked at PostgreSQL and see an increasing number of locks:

```console
$ psql -c "SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid" | sort | uniq -c | sort -n
      1 
      1 ------------------
      1 (537 rows)
      1  application_name 
      9  psql
     51  dspaceApi
    477  dspaceWeb
$ grep -E '^2022-01*' /var/log/postgresql/postgresql-10-main.log | grep -c 'still waiting for'
3
```

- I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
  - The issue in Francesca's case was actually that someone had taken the task, not that PostgreSQL transactions were locked!

## 2022-01-28

- Finalize the last ~100 WLE Journal Article items without licensese and DOIs
  - I did as many as I could, also updating http links to https for many journal links
- Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid)
  - She created an account on CGSpace and now we need to see which workflows she should belong to
- Start a fresh harvesting on AReS
- I adjusted the `check-duplicates.py` script to write the output to a CSV file including the id, both titles, both dates, and the handle link
  - I included the id because I will need a unique field to join the resulting list of non-duplicates with the original CSV where the rest of the metadata and filenames are
  - Since these items are not in DSpace yet, I generated simple numeric IDs in OpenRefine using this GREL transform: `row.index + 1`
  - Then I ran `check-duplicates.py` on items 1–200 and sent the resulting CSV to Gaia
- Delete one duplicate item I saw in IITA's Journal Articles that was uploaded earlier in WLE
  - Also do some general cleanup on IITA's Journal Articles collection in OpenRefine
- Delete one duplicate item I saw in ILRI's Journal Articles collection
  - Also do some general cleanup on ILRI's Journal Articles collection in OpenRefine and csv-metadata-quality

## 2022-01-29

- I did some more cleanup on the ILRI Journal Articles
  - I added missing journal titles for items that had ISSNs
  - Then I added pages for items that had them in the citation
  - First, I faceted the citation field based on whether or not the item had something like ": 232-234" present:

```console
value.contains(/:\s?\d+(-|–)\d+/)
```

- Then I faceted by blank on `dcterms.extent` and did a transform to extract the page information for over 1,000 items!

```console
'p. ' +
cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[0] +
'-' +
cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[2]
```

- Then I did similar for `cg.volume` and `cg.issue`, also based on the citation, for example to extract the "16" from "Journal of Blah 16(1)", where "16" is the second capture group in a zero-based match:

```console
cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*( |;)(\d+)\((\d+)\).*/)[1]
```

- This was 3,000 items so I imported the changes on CGSpace 1,000 at a time...

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