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cgspace-notes/content/posts/2018-04.md

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April, 2018 2018-04-01T16:13:54+02:00 Alan Orth
Notes

2018-04-01

  • I tried to test something on DSpace Test but noticed that it's down since god knows when
  • Catalina logs at least show some memory errors yesterday:
Mar 31, 2018 10:26:42 PM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run
SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]] 
java.lang.OutOfMemoryError: Java heap space

Exception in thread "ContainerBackgroundProcessor[StandardEngine[Catalina]]" java.lang.OutOfMemoryError: Java heap space
  • So this is getting super annoying
  • I ran all system updates on DSpace Test and rebooted it
  • For some reason Listings and Reports is not giving any results for any queries now...
  • I posted a message on Yammer to ask if people are using the Duplicate Check step from the Metadata Quality Module
  • Help Lili Szilagyi with a question about statistics on some CCAFS items

2018-04-04

  • Peter noticed that there were still some old CRP names on CGSpace, because I hadn't forced the Discovery index to be updated after I fixed the others last week
  • For completeness I re-ran the CRP corrections on CGSpace:
$ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu'
Fixed 1 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH
  • Then started a full Discovery index:
$ export JAVA_OPTS='-Dfile.encoding=UTF-8 -Xmx1024m'
$ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    76m13.841s
user    8m22.960s
sys     2m2.498s
  • Elizabeth from CIAT emailed to ask if I could help her by adding ORCID identifiers to all of Joseph Tohme's items
  • I used my add-orcid-identifiers-csv.py script:
$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
  • The CSV format of jtohme-2018-04-04.csv was:
dc.contributor.author,cg.creator.id
"Tohme, Joseph M.",Joe Tohme: 0000-0003-2765-7101
  • There was a quoting error in my CRP CSV and the replacements for Forests, Trees and Agroforestry got messed up
  • So I fixed them and had to re-index again!
  • I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:
$ git checkout -b 5_x-dspace-5.8 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.8
  • I was prepared to skip some commits that I had cherry picked from the upstream dspace-5_x branch when we did the DSpace 5.5 upgrade (see notes on 2016-10-19 and 2017-12-17):
    • [DS-3246] Improve cleanup in recyclable components (upstream commit on dspace-5_x: 9f0f5940e7921765c6a22e85337331656b18a403)
    • [DS-3250] applying patch provided by Atmire (upstream commit on dspace-5_x: c6fda557f731dbc200d7d58b8b61563f86fe6d06)
    • bump up to latest minor pdfbox version (upstream commit on dspace-5_x: b5330b78153b2052ed3dc2fd65917ccdbfcc0439)
    • DS-3583 Usage of correct Collection Array (#1731) (upstream commit on dspace-5_x: c8f62e6f496fa86846bfa6bcf2d16811087d9761)
  • ... but somehow git knew, and didn't include them in my interactive rebase!
  • I need to send this branch to Atmire and also arrange payment (see ticket #560 in their tracker)