CGSpace Notes

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

December, 2016

2016-12-02

  • CGSpace was down for five hours in the morning while I was sleeping
  • While looking in the logs for errors, I see tons of warnings about Atmire MQM:
2016-12-02 03:00:32,352 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail="dc.title", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail="THUMBNAIL", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail="-1", transactionID="TX157907838689377964651674089851855413607")
2016-12-02 03:00:32,353 WARN  com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607")
  • I see thousands of them in the logs for the last few months, so it’s not related to the DSpace 5.5 upgrade
  • I’ve raised a ticket with Atmire to ask
  • Another worrying error from dspace.log is:
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October, 2016

2016-10-03

  • Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up
  • Need to test the following scenarios to see how author order is affected:
    • ORCIDs only
    • ORCIDs plus normal authors
  • I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry:
0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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September, 2016

2016-09-01

  • Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors
  • Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace
  • We had been using DC=ILRI to determine whether a user was ILRI or not
  • It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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August, 2016

2016-08-01

  • Add updated distribution license from Sisay (#259)
  • Play with upgrading Mirage 2 dependencies in bower.json because most are several versions of out date
  • Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more
  • bower stuff is a dead end, waste of time, too many issues
  • Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of fonts)
  • Start working on DSpace 5.1 → 5.5 port:
$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
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July, 2016

2016-07-01

  • Add dc.description.sponsorship to Discovery sidebar facets and make investors clickable in item view (#232)
  • I think this query should find and replace all authors that have “,” at the end of their names:
dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
UPDATE 95
dspacetest=# select text_value from  metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value ~ '^.+?,$';
 text_value
------------
(0 rows)
  • In this case the select query was showing 95 results before the update
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June, 2016

2016-06-01

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May, 2016

2016-05-01

  • Since yesterday there have been 10,000 REST errors and the site has been unstable again
  • I have blocked access to the API now
  • There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk '{print $1}' /var/log/nginx/rest.log  | uniq | wc -l
3168
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April, 2016

2016-04-04

  • Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit
  • We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc
  • After running DSpace for over five years I’ve never needed to look in any other log file than dspace.log, leave alone one from last year!
  • This will save us a few gigs of backup space we’re paying for on S3
  • Also, I noticed the checker log has some errors we should pay attention to:
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March, 2016

2016-03-02

  • Looking at issues with author authorities on CGSpace
  • For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
  • Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
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