mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-10 17:15:46 +01:00
225 lines
9.2 KiB
Markdown
225 lines
9.2 KiB
Markdown
---
|
||
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
|
||
|
||
<!--more-->
|
||
|
||
## 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
|
||
|
||
|
||
|
||
- 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...
|
||
|
||
<!-- vim: set sw=2 ts=2: -->
|