cgspace-notes/content/posts/2018-05.md

---
title: "May, 2018"
date: 2018-05-01T16:43:54+03:00
author: "Alan Orth"
tags: ["Notes"]
---

## 2018-05-01

- I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
  - http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
  - http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
- Then I reduced the JVM heap size from 6144 back to 5120m
- Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public) to support hosts choosing which distribution they want to use

<!--more-->

## 2018-05-02

- Advise Fabio Fidanza about integrating CGSpace content in the new CGIAR corporate website
- I think they can mostly rely on using the `cg.contributor.crp` field
- Looking over some IITA records for Sisay
  - Other than trimming and collapsing consecutive whitespace, I made some other corrections
  - I need to check the correct formatting of COTE D'IVOIRE vs COTE D’IVOIRE
  - I replaced all DOIs with HTTPS
  - I checked a few DOIs and found at least one that was missing, so I Googled the title of the paper and found the correct DOI
  - Also, I found an [FAQ for DOI that says the `dx.doi.org` syntax is older](https://www.doi.org/factsheets/DOI_PURL.html), so I will replace all the DOIs with `doi.org` instead
  - I found five records with "ISI Jounal" instead of "ISI Journal"
  - I found one item with IITA subject "."
  - Need to remember to check the facets for things like this in sponsorship:
    - Deutsche Gesellschaft für Internationale Zusammenarbeit
    - Deutsche Gesellschaft fur Internationale Zusammenarbeit
  - Eight records with language "fn" instead of "fr"
  - One incorrect type (lowercase "proceedings"): Conference proceedings
  - Found some capitalized CRPs in `cg.contributor.crp`
  - Found some incorrect author affiliations, ie "Institut de Recherche pour le Developpement Agricolc" should be "Institut de Recherche pour le Developpement *Agricole*"
  - Wow, and for sponsors there are the following:
    - Incorrect: Flemish Agency for Development Cooperation and Technical Assistance
    - Incorrect: Flemish Organization for Development Cooperation and Technical Assistance
    - Correct: Flemish *Association* for Development Cooperation and Technical Assistance
  - One item had region "WEST" (I corrected it to "WEST AFRICA")

## 2018-05-03

- It turns out that the IITA records that I was helping Sisay with in March were imported in 2018-04 without a final check by Abenet or I
- There are lots of errors on language, CRP, and even some encoding errors on abstract fields
- I export them and include the hidden metadata fields like `dc.date.accessioned` so I can filter the ones from 2018-04 and correct them in Open Refine:

```
$ dspace metadata-export -a -f /tmp/iita.csv -i 10568/68616
```

- Abenet sent a list of 46 ORCID identifiers for ILRI authors so I need to get their names using my [resolve-orcids.py](https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b) script and merge them into our controlled vocabulary
- On the messed up IITA records from 2018-04 I see sixty DOIs in incorrect format (cg.identifier.doi)

## 2018-05-06

- Fixing the IITA records from Sisay, sixty DOIs have completely invalid format like `http:dx.doi.org10.1016j.cropro.2008.07.003`
- I corrected all the DOIs and then checked them for validity with a quick bash loop:

```
$ for line in $(< /tmp/links.txt); do echo $line; http --print h $line; done
```

- Most of the links are good, though one is duplicate and one seems to even be incorrect in the publisher's site so...
- Also, there are some duplicates:
  - `10568/92241` and `10568/92230` (same DOI)
  - `10568/92151` and `10568/92150` (same ISBN)
  - `10568/92291` and `10568/92286` (same citation, title, authors, year)
- Messed up abstracts:
  - `10568/92309`
- Fixed some issues in regions, countries, sponsors, ISSN, and cleaned whitespace errors from citation, abstract, author, and titles
- Fixed all issues with CRPs
- A few more interesting Unicode characters to look for in text fields like author, abstracts, and citations  might be: `’` (0x2019), `·` (0x00b7), and `€` (0x20ac)
- A custom text facit in OpenRefine with this GREL expression could be a good for finding invalid characters or encoding errors in authors, abstracts, etc:

```
or(
  isNotNull(value.match(/.*[(|)].*/)),
  isNotNull(value.match(/.*\uFFFD.*/)),
  isNotNull(value.match(/.*\u00A0.*/)),
  isNotNull(value.match(/.*\u200A.*/)),
  isNotNull(value.match(/.*\u2019.*/)),
  isNotNull(value.match(/.*\u00b7.*/)),
  isNotNull(value.match(/.*\u20ac.*/))
)
```

- I found some more IITA records that Sisay imported on 2018-03-23 that have invalid CRP names, so now I kinda want to check those ones!
- Combine the ORCID identifiers Abenet sent with our existing list and resolve their names using the [resolve-orcids.py](https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b) script:

```
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/ilri-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2018-05-06-combined.txt
$ ./resolve-orcids.py -i /tmp/2018-05-06-combined.txt -o /tmp/2018-05-06-combined-names.txt -d
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
```

- I made a pull request ([#373](https://github.com/ilri/DSpace/pull/373)) for this that I'll merge some time next week (I'm expecting Atmire to get back to us about DSpace 5.8 soon)
- After testing quickly I just decided to merge it, and I noticed that I don't even need to restart Tomcat for the changes to get loaded

## 2018-05-07

- I spent a bit of time playing with [conciliator](https://github.com/codeforkjeff/conciliator) and Solr, trying to figure out how to reconcile columns in OpenRefine with data in our existing Solr cores (like CRP subjects)
- The documentation regarding the Solr stuff is limited, and I cannot figure out what all the fields in `conciliator.properties` are supposed to be
- But then I found [reconcile-csv](https://github.com/okfn/reconcile-csv), which allows you to reconcile against values in a CSV file!
- That, combined with splitting our multi-value fields on "||" in OpenRefine is amaaaaazing, because after reconciliation you can just join them again
- Oh wow, you can also facet on the individual values once you've split them! That's going to be amazing for proofing CRPs, subjects, etc.

## 2018-05-09

- Udana asked about the Book Chapters we had been proofing on DSpace Test in 2018-04
- I told him that there were still some TODO items for him on that data, for example to update the `dc.language.iso` field for the Spanish items