CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

July, 2019

by Alan Orth in  

2019-07-01

  • Create an “AfricaRice books and book chapters” collection on CGSpace for AfricaRice
  • Last month Sisay asked why the following “most popular” statistics link for a range of months in 2018 works for the CIAT community on DSpace Test, but not on CGSpace:
  • Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
  • If I change the parameters to 2019 I see stats, so I’m really thinking it has something to do with the sharded yearly Solr statistics cores
    • I checked the Solr admin UI and I see all Solr cores loaded, so I don’t know what it could be
    • When I check the Atmire content and usage module it seems obvious that there is a problem with the old cores because I dont have anything before 2019-01

Atmire CUA 2018 stats missing

  • I don’t see anyone logged in right now so I’m going to try to restart Tomcat and see if the stats are accessible after Solr comes back up

  • I decided to run all system updates on the server (linode18) and reboot it

    • After rebooting Tomcat came back up, but the the Solr statistics cores were not all loaded

    • The error is always (with a different core):

      org.apache.solr.common.SolrException: Error CREATEing SolrCore 'statistics-2010': Unable to create core [statistics-2010] Caused by: Lock obtain timed out: NativeFSLock@/home/cgspace.cgiar.org/solr/statistics-2010/data/index/write.lock

  • I restarted Tomcat ten times and it never worked…

  • I tried to stop Tomcat and delete the write locks:

    # systemctl stop tomcat7
# find /dspace/solr/statistics* -iname "*.lock" -print -delete
/dspace/solr/statistics/data/index/write.lock
/dspace/solr/statistics-2010/data/index/write.lock
/dspace/solr/statistics-2011/data/index/write.lock
/dspace/solr/statistics-2012/data/index/write.lock
/dspace/solr/statistics-2013/data/index/write.lock
/dspace/solr/statistics-2014/data/index/write.lock
/dspace/solr/statistics-2015/data/index/write.lock
/dspace/solr/statistics-2016/data/index/write.lock
/dspace/solr/statistics-2017/data/index/write.lock
/dspace/solr/statistics-2018/data/index/write.lock
# find /dspace/solr/statistics* -iname "*.lock" -print -delete
# systemctl start tomcat7

  • But it still didn’t work!

  • I stopped Tomcat, deleted the old locks, and will try to use the “simple” lock file type in solr/statistics/conf/solrconfig.xml:

    <lockType>${solr.lock.type:simple}</lockType>

  • And after restarting Tomcat it still doesn’t work

  • Now I’ll try going back to “native” locking with unlockAtStartup:

    <unlockOnStartup>true</unlockOnStartup>

  • Now the cores seem to load, but I still see an error in the Solr Admin UI and I still can’t access any stats before 2018

  • I filed an issue with Atmire, so let’s see if they can help

  • And since I’m annoyed and it’s been a few months, I’m going to move the JVM heap settings that I’ve been testing on DSpace Test to CGSpace

  • The old ones were:

    -Djava.awt.headless=true -Xms8192m -Xmx8192m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=5400 -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false

  • And the new ones come from Solr 4.10.x’s startup scripts:

    -Djava.awt.headless=true
-Xms8192m -Xmx8192m
-Dfile.encoding=UTF-8
-XX:NewRatio=3
-XX:SurvivorRatio=4
-XX:TargetSurvivorRatio=90
-XX:MaxTenuringThreshold=8
-XX:+UseConcMarkSweepGC
-XX:+UseParNewGC
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4
-XX:+CMSScavengeBeforeRemark
-XX:PretenureSizeThreshold=64m
-XX:+UseCMSInitiatingOccupancyOnly
-XX:CMSInitiatingOccupancyFraction=50
-XX:CMSMaxAbortablePrecleanTime=6000
-XX:+CMSParallelRemarkEnabled
-XX:+ParallelRefProcEnabled
-Dcom.sun.management.jmxremote
-Dcom.sun.management.jmxremote.port=1337
-Dcom.sun.management.jmxremote.ssl=false
-Dcom.sun.management.jmxremote.authenticate=false

2019-07-02

  • Help upload twenty-seven posters from the 2019-05 Sharefair to CGSpace

    • Sisay had already done the SAFBundle so I did some minor corrections to and uploaded them to a temporary collection so I could check them in OpenRefine:

      $ sed -i 's/CC-BY 4.0/CC-BY-4.0/' item_*/dublin_core.xml
$ echo "10568/101992" >> item_*/collections
$ dspace import -a -e me@cgiar.org -m 2019-07-02-Sharefair.map -s /tmp/Sharefair_mapped

  • I noticed that all twenty-seven items had double dates like “2019-05||2019-05” so I fixed those, but the rest of the metadata looked good so I unmapped them from the temporary collection

  • Finish looking at the fifty-six AfricaRice items and upload them to CGSpace:

    $ dspace import -a -e me@cgiar.org -m 2019-07-02-AfricaRice-11to73.map -s /tmp/SimpleArchiveFormat

  • Peter pointed out that the Sharefair dates I fixed were not actually fixed

    • It seems there is a bug that causes DSpace to not detect changes if the values are the same like “2019-05||2019-05” and you try to remove one
    • To get it to work I had to change some of them to 2019-01, then remove them

2019-07-03

  • Atmire responded about the Solr issue and said they would be willing to help

2019-07-04

  • Maria Garruccio sent me some new ORCID identifiers for Bioversity authors

    • I combined them with our existing list and then used my resolve-orcids.py script to update the names from ORCID.org:

      $ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/new-bioversity-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2019-07-04-orcid-ids.txt
$ ./resolve-orcids.py -i /tmp/2019-07-04-orcid-ids.txt -o 2019-07-04-orcid-names.txt -d

  • Send and merge a pull request for the new ORCID identifiers (#428)

  • I created a CSV with some ORCID identifiers that I had seen change so I could update any existing ones in the databse:

    cg.creator.id,correct
"Marius Ekué: 0000-0002-5829-6321","Marius R.M. Ekué: 0000-0002-5829-6321"
"Mwungu: 0000-0001-6181-8445","Chris Miyinzi Mwungu: 0000-0001-6181-8445"
"Mwungu: 0000-0003-1658-287X","Chris Miyinzi Mwungu: 0000-0003-1658-287X"

  • But when I ran fix-metadata-values.py I didn’t see any changes:

    $ ./fix-metadata-values.py -i 2019-07-04-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d

2019-07-06

2019-07-08

  • Communicate with Atmire about the Solr statistics cores issue
    • I suspect we might need to get more disk space on DSpace Test so we can try to replicate the production environment more closely