CGSpace Notes

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:

2016-11-01

• Add dc.type to the output options for Atmire’s Listings and Reports module (#286)

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

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)"

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

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

2016-06-01

• Experimenting with IFPRI OAI (we want to harvest their publications)
• After reading the ContentDM documentation I found IFPRI’s OAI endpoint: http://ebrary.ifpri.org/oai/oai.php
• After reading the OAI documentation and testing with an OAI validator I found out how to get their publications
• This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc
• You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
• Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship

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

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: