CGSpace Notes

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

July, 2017

2017-07-01

  • Run system updates and reboot DSpace Test

2017-07-04

  • Merge changes for WLE Phase II theme rename (#329)
  • Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
  • We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
Read more →

June, 2017

2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we’ll create a new sub-community for Phase II and create collections for the research themes there The current “Research Themes” community will be renamed to “WLE Phase I Research Themes” Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg. Read more →

May, 2017

2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace. Read more →

April, 2017

2017-04-02

  • Merge one change to CCAFS flagships that I had forgotten to remove last month (“MANAGING CLIMATE RISK”): https://github.com/ilri/DSpace/pull/317
  • Quick proof-of-concept hack to add dc.rights to the input form, including some inline instructions/hints:

dc.rights in the submission form

  • Remove redundant/duplicate text in the DSpace submission license
  • Testing the CMYK patch on a collection with 650 items:

    $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt
    
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March, 2017

2017-03-01

  • Run the 279 CIAT author corrections on CGSpace

2017-03-02

  • Skype with Michael and Peter, discussing moving the CGIAR Library to CGSpace
  • CGIAR people possibly open to moving content, redirecting library.cgiar.org to CGSpace and letting CGSpace resolve their handles
  • They might come in at the top level in one “CGIAR System” community, or with several communities
  • I need to spend a bit of time looking at the multiple handle support in DSpace and see if new content can be minted in both handles, or just one?
  • Need to send Peter and Michael some notes about this in a few days
  • Also, need to consider talking to Atmire about hiring them to bring ORCiD metadata to REST / OAI
  • Filed an issue on DSpace issue tracker for the filter-media bug that causes it to process JPGs even when limiting to the PDF thumbnail plugin: DS-3516
  • Discovered that the ImageMagic filter-media plugin creates JPG thumbnails with the CMYK colorspace when the source PDF is using CMYK
  • Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing regeneration using DSpace 5.x’s ImageMagick plugin creates CMYK JPGs if the source PDF was CMYK (see 1056851999):

    $ identify ~/Desktop/alc_contrastes_desafios.jpg
    /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
    
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February, 2017

2017-02-07

  • An item was mapped twice erroneously again, so I had to remove one of the mappings manually:

    dspace=# select * from collection2item where item_id = '80278';
    id   | collection_id | item_id
    -------+---------------+---------
    92551 |           313 |   80278
    92550 |           313 |   80278
    90774 |          1051 |   80278
    (3 rows)
    dspace=# delete from collection2item where id = 92551 and item_id = 80278;
    DELETE 1
    
  • Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)

  • Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name

Read more →

January, 2017

2017-01-02

  • I checked to see if the Solr sharding task that is supposed to run on January 1st had run and saw there was an error
  • I tested on DSpace Test as well and it doesn’t work there either
  • I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years
Read more →

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:

Read more →

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
    
Read more →