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cgspace-notes/content/posts/2018-06.md

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June, 2018 2018-06-04T19:49:54-07:00 Alan Orth
Notes

2018-06-04

  • Test the DSpace 5.8 module upgrades from Atmire (#378)
    • There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn't build
  • I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
  • I proofed and tested the ILRI author corrections that Peter sent back to me this week:
$ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
  • I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in [March, 2018]({{< relref "2018-03.md" >}})
  • Time to index ~70,000 items on CGSpace:
$ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b                                  

real    74m42.646s
user    8m5.056s
sys     2m7.289s

2018-06-06

  • It turns out that I needed to add a server block for atmire.com-snapshots to my Maven settings, so now the Atmire code builds
  • Now Maven and Ant run properly, but I'm getting SQL migration errors in dspace.log after starting Tomcat
  • I've updated my ticket on Atmire's bug tracker: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560

2018-06-07

  • Proofing 200 IITA records on DSpace Test for Sisay: IITA_Junel_06 (10568/95391)
    • Mispelled authorship type: CGAIR single center should be: CGIAR single centre
    • I see some encoding errors in author affiliations, for example:
      • Universidade de SÆo Paulo
      • Institut National des Recherches Agricoles du B nin
      • Centre de Coop ration Internationale en Recherche Agronomique pour le D veloppement
      • Institut des Recherches Agricoles du B nin
      • Institut des Savannes, C te d' Ivoire
      • Institut f r Pflanzenpathologie und Pflanzenschutz der Universit t, Germany
      • Projet de Gestion des Ressources Naturelles, B nin
      • Universit t Hannover
      • Universit F lix Houphouet-Boigny
  • I uploaded fixes for all those now, but I will continue with the rest of the data later
  • Regarding the SQL migration errors, Atmire told me I need to run some migrations manually in PostgreSQL:
delete from schema_version where version = '5.6.2015.12.03.2';
update schema_version set version = '5.6.2015.12.03.2' where version = '5.5.2015.12.03.2';
update schema_version set version = '5.8.2015.12.03.3' where version = '5.5.2015.12.03.3';
  • And then I need to ignore the ignored ones:
$ ~/dspace/bin/dspace database migrate ignored
  • Now DSpace starts up properly!
  • Gabriela from CIP got back to me about the author names we were correcting on CGSpace
  • I did a quick sanity check on them and then did a test import with my fix-metadata-value.py script:
$ ./fix-metadata-values.py -i /tmp/2018-06-08-CIP-Authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3
  • I will apply them on CGSpace tomorrow I think...

2018-06-09

  • It's pretty annoying, but the JVM monitoring for Munin was never set up when I migrated DSpace Test to its new server a few months ago
  • I ran the tomcat and munin-node tags in Ansible again and now the stuff is all wired up and recording stats properly
  • I applied the CIP author corrections on CGSpace and DSpace Test and re-ran the Discovery indexing