CGSpace Notes

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

CGIAR Library Migration

Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.

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September, 2017

2017-09-06

  • Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours

2017-09-07

  • Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group
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August, 2017

2017-08-01

  • Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours
  • I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)
  • The good thing is that, according to dspace.log.2017-08-01, they are all using the same Tomcat session
  • This means our Tomcat Crawler Session Valve is working
  • But many of the bots are browsing dynamic URLs like:
    • /handle/10568/3353/discover
    • /handle/10568/16510/browse
  • The robots.txt only blocks the top-level /discover and /browse URLs… we will need to find a way to forbid them from accessing these!
  • Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): https://jira.duraspace.org/browse/DS-2962
  • It turns out that we’re already adding the X-Robots-Tag "none" HTTP header, but this only forbids the search engine from indexing the page, not crawling it!
  • Also, the bot has to successfully browse the page first so it can receive the HTTP header…
  • We might actually have to block these requests with HTTP 403 depending on the user agent
  • Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415
  • This was due to newline characters in the dc.description.abstract column, which caused OpenRefine to choke when exporting the CSV
  • I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
  • Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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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:
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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

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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
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