CGSpace Notes

February, 2016

Posted on
#notes

2016-02-05

  • Looking at some DAGRIS data for Abenet Yabowork
  • Lots of issues with spaces, newlines, etc causing the import to fail
  • I noticed we have a very interesting list of countries on CGSpace:

CGSpace country list

  • Not only are there 49,000 countries, we have some blanks (25)…
  • Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”

2016-02-06

  • Found a way to get items with null/empty metadata values from SQL
  • First, find the metadata_field_id for the field you want from the metadatafieldregistry table:
dspacetest=# select * from metadatafieldregistry;
  • In this case our country field is 78
  • Now find all resources with type 2 (item) that have null/empty values for that field:
dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);
  • Then you can find the handle that owns it from its resource_id:
dspacetest=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '22678';
  • It’s 25 items so editing in the web UI is annoying, let’s try SQL!
dspacetest=# delete from metadatavalue where metadata_field_id=78 and text_value='';
DELETE 25
  • After that perhaps a regular dspace index-discovery (no -b) should suffice…
  • Hmm, I indexed, cleared the Cocoon cache, and restarted Tomcat but the 25 “|||” countries are still there
  • Maybe I need to do a full re-index…
  • Yep! The full re-index seems to work.
  • Process the empty countries on CGSpace

2016-02-07

  • Working on cleaning up Abenet’s DAGRIS data with OpenRefine
  • I discovered two really nice functions in OpenRefine: value.trim() and value.escape("javascript") which shows whitespace characters like \r\n!
  • For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV
  • I re-import the resulting CSV and run a GREL on the date issued column: value.replace("\.0", "")
  • I need to start running DSpace in Mac OS X instead of a Linux VM
  • Install PostgreSQL from homebrew, then configure and import CGSpace database dump:
$ postgres -D /opt/brew/var/postgres
$ createuser --superuser postgres
$ createuser --pwprompt dspacetest
$ createdb -O dspacetest --encoding=UNICODE dspacetest
$ psql postgres
postgres=# alter user dspacetest createuser;
postgres=# \q
$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-02-07.backup 
$ psql postgres
postgres=# alter user dspacetest nocreateuser;
postgres=# \q
$ vacuumdb dspacetest
$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost
  • After building and running a fresh_install I symlinked the webapps into Tomcat’s webapps folder:
$ mv /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT.orig
$ ln -sfv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT
$ ln -sfv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/rest
$ ln -sfv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/jspui
$ ln -sfv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/oai
$ ln -sfv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/solr
$ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start
  • Add CATALINA_OPTS in /opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh, as this script is sourced by the catalina startup script
  • For example:
CATALINA_OPTS="-Djava.awt.headless=true -Xms2048m -Xmx2048m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8"
  • After verifying that the site is working, start a full index:
$ ~/dspace/bin/dspace index-discovery -b

2016-02-08

  • Finish cleaning up and importing ~400 DAGRIS items into CGSpace