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98 lines
5.5 KiB
Markdown
98 lines
5.5 KiB
Markdown
---
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title: "May, 2018"
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date: 2018-05-01T16:43:54+03:00
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author: "Alan Orth"
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tags: ["Notes"]
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---
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## 2018-05-01
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- I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
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- http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
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- http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
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- Then I reduced the JVM heap size from 6144 back to 5120m
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- 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
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<!--more-->
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## 2018-05-02
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- Advise Fabio Fidanza about integrating CGSpace content in the new CGIAR corporate website
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- I think they can mostly rely on using the `cg.contributor.crp` field
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- Looking over some IITA records for Sisay
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- Other than trimming and collapsing consecutive whitespace, I made some other corrections
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- I need to check the correct formatting of COTE D'IVOIRE vs COTE D’IVOIRE
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- I replaced all DOIs with HTTPS
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- 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
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- 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
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- I found five records with "ISI Jounal" instead of "ISI Journal"
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- I found one item with IITA subject "."
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- Need to remember to check the facets for things like this in sponsorship:
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- Deutsche Gesellschaft für Internationale Zusammenarbeit
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- Deutsche Gesellschaft fur Internationale Zusammenarbeit
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- Eight records with language "fn" instead of "fr"
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- One incorrect type (lowercase "proceedings"): Conference proceedings
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- Found some capitalized CRPs in `cg.contributor.crp`
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- Found some incorrect author affiliations, ie "Institut de Recherche pour le Developpement Agricolc" should be "Institut de Recherche pour le Developpement *Agricole*"
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- Wow, and for sponsors there are the following:
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- Incorrect: Flemish Agency for Development Cooperation and Technical Assistance
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- Incorrect: Flemish Organization for Development Cooperation and Technical Assistance
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- Correct: Flemish *Association* for Development Cooperation and Technical Assistance
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- One item had region "WEST" (I corrected it to "WEST AFRICA")
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## 2018-05-03
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- 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
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- There are lots of errors on language, CRP, and even some encoding errors on abstract fields
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- 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:
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```
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$ dspace metadata-export -a -f /tmp/iita.csv -i 10568/68616
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```
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- 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
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- On the messed up IITA records from 2018-04 I see sixty DOIs in incorrect format (cg.identifier.doi)
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## 2018-05-06
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- Fixing the IITA records from Sisay, sixty DOIs have completely invalid format like `http:dx.doi.org10.1016j.cropro.2008.07.003`
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- I corrected all the DOIs and then checked them for validity with a quick bash loop:
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```
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$ for line in $(< /tmp/links.txt); do echo $line; http --print h $line; done
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```
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- Most of the links are good, though one is duplicate and one seems to even be incorrect in the publisher's site so...
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- Also, there are some duplicates:
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- `10568/92241` and `10568/92230` (same DOI)
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- `10568/92151` and `10568/92150` (same ISBN)
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- `10568/92291` and `10568/92286` (same citation, title, authors, year)
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- Messed up abstracts:
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- `10568/92309`
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- Fixed some issues in regions, countries, sponsors, ISSN, and cleaned whitespace errors from citation, abstract, author, and titles
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- Fixed all issues with CRPs
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- A few more interesting Unicode characters to look for in text fields like author, abstracts, and citations might be: `’` (0x2019), `·` (0x00b7), and `€` (0x20ac)
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- 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:
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```
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or(
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isNotNull(value.match(/.*[(|)].*/)),
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isNotNull(value.match(/.*\uFFFD.*/)),
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isNotNull(value.match(/.*\u00A0.*/)),
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isNotNull(value.match(/.*\u200A.*/)),
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isNotNull(value.match(/.*\u2019.*/)),
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isNotNull(value.match(/.*\u00b7.*/)),
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isNotNull(value.match(/.*\u20ac.*/))
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)
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```
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- 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!
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- 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:
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```
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$ 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
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$ ./resolve-orcids.py -i /tmp/2018-05-06-combined.txt -o /tmp/2018-05-06-combined-names.txt -d
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# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
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$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
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```
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