cgspace-notes/content/posts/2019-06.md

---
title: "June, 2019"
date: 2019-06-02T10:57:51+03:00
author: "Alan Orth"
categories: ["Notes"]
---

## 2019-06-02

- Merge the [Solr filterCache](https://github.com/ilri/DSpace/pull/425) and [XMLUI ISI journal](https://github.com/ilri/DSpace/pull/426) changes to the `5_x-prod` branch and deploy on CGSpace
- Run system updates on CGSpace (linode18) and reboot it

## 2019-06-03

- Skype with Marie-Angélique and Abenet about [CG Core v2](https://agriculturalsemantics.github.io/cg-core/cgcore.html)

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- Here is a list of proposed metadata migrations for CGSpace
  - dc.language.iso→DCTERMS.language (and switch to ISO 639-2 Alpha 3)
  - dc.description.abstract→DCTERMS.abstract
  - dc.identifier.citation→DCTERMS.bibliographicCitation
  - dc.contributor.author→DCTERMS.creator (for people)
  - dc.description.sponsorship→cg.contributor.donor (values from CrossRef or Grid.ac if possible)
  - dc.rights→DCTERMS.license
  - cg.identifier.status→DCTERMS.accessRights (values "open" or "restricted")
  - cg.creator.id→cg.creator.identifier?
  - dc.relation.ispartofseries→DCTERMS.isPartOf
  - cg.link.relation→DCTERMS.relation
- Marie agreed that we need to adopt some controlled lists for our values, and pointed out that the MARLO team maintains a list of CRPs and Centers at [CLARISA](https://clarisa.cgiar.org/)
  - There is an API there but it needs a password for access...

## 2019-06-04

- The MARLO team responded and said they will give us access to the CLARISA API
- Marie-Angélique [proposed](https://github.com/AgriculturalSemantics/cg-core/pull/1) to integrate `dcterms.isPartOf`, `dcterms.abstract`, and `dcterms.bibliographicCitation` into the CG Core v2 schema
  - I told her I would attempt to integrate those and the others above into DSpace Test soon and report back
  - We also need to discuss with the ILRI Data Portal, MEL/MELSpace, and users who consume the CGSpace API
- Add Arabic language to input-forms.xml ([#427](https://github.com/ilri/DSpace/pull/427)), as Bioversity is adding some Arabic items and noticed it missing

## 2019-06-05

- Send mail to CGSpace and MELSpace people to let them know about the proposed metadata field migrations after the discussion with Marie-Angélique

## 2019-06-07

- Thierry noticed that the CUA statistics were missing previous years again, and I see that the Solr admin UI has the following message:

```
statistics-2018: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher 
```

- I had to restart Tomcat a few times for all the stats cores to get loaded with no issue

## 2019-06-10

- Rename the AReS repository on GitHub to OpenRXV: https://github.com/ilri/OpenRXV
- Create a new AReS repository: https://github.com/ilri/AReS
- Start looking at the 203 IITA records on DSpace Test from last month ([IITA_May_16](https://dspacetest.cgiar.org/handle/10568/102032) aka "20194th.xls") using OpenRefine
  - Trim leading, trailing, and consecutive whitespace on all columns, but I didn't notice very many issues
  - Validate affiliations against latest list of top 1500 terms using reconcile-csv, correcting and standardizing about twenty-seven
  - Validate countries against latest list of countries using reconcile-csv, correcting three
  - Convert all DOIs to "https://dx.doi.org" format
  - Normalize all `cg.identifier.url` Google book fields to "books.google.com"
  - Correct some inconsistencies in IITA subjects
  - Correct two incorrect "Peer Review" in `dc.description.version`
  - About fifteen items have incorrect ISBNs (looks like an Excel error because the values look like scientific numbers)
  - Delete one blank item
  - I managed to get to subjects, so I'll continue from there when I start working next
- Generate a new list of countries from the database for use with reconcile-csv
  - After dumping, use csvcut to add line numbers, then change the csv header to match those you use in reconcile-csv, for example `id` and `name`:

```
dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 228 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC) to /tmp/countries.csv WITH CSV HEADER
COPY 192
$ csvcut -l -c 0 /tmp/countries.csv > 2019-06-10-countries.csv
```

- Get a list of all the unique AGROVOC subject terms in IITA's data and export it to a text file so I can validate them with my `agrovoc-lookup.py` script:

```
$ csvcut -c dc.subject ~/Downloads/2019-06-10-IITA-20194th-Round-2.csv| sed 's/||/\n/g' | grep -v dc.subject | sort -u > iita-agrovoc.txt
$ ./agrovoc-lookup.py -i iita-agrovoc.txt -om iita-agrovoc-matches.txt -or iita-agrovoc-rejects.txt
$ wc -l iita-agrovoc*
  402 iita-agrovoc-matches.txt
   29 iita-agrovoc-rejects.txt
  431 iita-agrovoc.txt
```

- Combine these IITA matches with the subjects I matched a few months ago:

```
$ csvcut -c name 2019-03-18-subjects-matched.csv | grep -v name | cat - iita-agrovoc-matches.txt | sort -u > 2019-06-10-subjects-matched.txt
```

- Then make a new list to use with reconcile-csv by adding line numbers with csvcut and changing the line number header to `id`:

```
$ csvcut -c name -l 2019-06-10-subjects-matched.txt | sed 's/line_number/id/' > 2019-06-10-subjects-matched.csv
```

## 2019-06-20

- Share some feedback about AReS v2 with the colleagues and encourage them to do the same

## 2019-06-23

- Continue work on reviewing CG Core v2 standard and its implications to CGSpace an DSpace platforms in general
  - Update my [list of fields to migrate](https://gist.github.com/alanorth/2db39e91f48d116e00a4edffd6ba6409)
  - Submit an [issue with my feedback to the CG Core project](https://github.com/AgriculturalSemantics/cg-core/issues/2)
- Update my local PostgreSQL container:

```
$ podman pull docker.io/library/postgres:9.6-alpine
$ podman rm dspacedb
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
```

## 2019-06-25

- Normalize `text_lang` values for metadata on DSpace Test and CGSpace:

```
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('ethnob', 'en', '*', 'E.', '');
UPDATE 1551
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
UPDATE 2070
dspace=# UPDATE metadatavalue SET text_lang='es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('es', 'spa');
UPDATE 2
```

- Upload 202 IITA records from earlier this month (20194th.xls) to CGSpace
- Communicate with Bioversity contractor in charge of their migration from Typo3 to CGSpace

## 2019-06-28

- Start looking at the fifty-seven AfricaRice records sent by Ibnou earlier this month
  - First, I see there are several items with type "Book" and "Book Chapter" should go in an "AfricaRice books and book chapters" collection, but none exists in the AfricaRice community
  - Trim and collapse consecutive whitespace on author, affiliation, authorship types, title, subjects, doi, issn, source, citation, country, sponsors
  - Standardize and correct affiliations like "Africa Rice Cente" and "Africa Rice Centre", including syntax errors with multi-value separators
  - Lots of variation in affiliations, for example:
    - Université Abomey-Calavi
    - Université d'Abomey
    - Université d'Abomey Calavi
    - Université d'Abomey-Calavi
    - University of Abomey-Calavi
  - Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
    - `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id`
    - I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colume and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)`
  - Replace smart quotes with standard ASCII ones
  - Fix typos in authoriship types
  - Validate and normalize subjects against our 2019-06 list using reconcile-csv and OpenRefine:
    - `$ lein run ~/src/git/DSpace/2019-06-10-subjects-matched.csv name id`
    - Also add about 30 new AGROVOC subjects to our list that I verified manually
  - There is one duplicate, both have the same DOI: https://doi.org/10.1016/j.agwat.2018.06.018
  - Fix four ISBNs that were in the ISSN field

## 2019-06-30

- Upload fifty-seven AfricaRice records to [DSpace Test](https://dspacetest.cgiar.org/handle/10568/102274)
  - I created the SAF bundler with SAFBuilder and then imported via the CLI:

```
$ dspace import -a -e me@cgiar.org -m 2019-06-30-AfricaRice-11to73.map -s /tmp/2019-06-30-AfricaRice-11to73
```

- I sent feedback about a few missing PDFs and one duplicate to Ibnou to check
- Run all system updates on DSpace Test (linode19) and reboot it

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