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

title	date	author	tags
May, 2018	2018-05-01T16:43:54+03:00	Alan Orth	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 to support hosts choosing which distribution they want to use

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, 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 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 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) 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 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, 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