+++ date = "2017-05-01T16:21:52+02:00" author = "Alan Orth" title = "May, 2017" tags = ["Notes"]

+++

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.cgiar.org/handle/10568/80731

2017-05-05

• Discovered that CGSpace has ~700 items that are missing the cg.identifier.status field
• Need to perhaps try using the "required metadata" curation task to find fields missing these items:

$ [dspace]/bin/dspace curate -t requiredmetadata -i 10568/1 -r - > /tmp/curation.out

• It seems the curation task dies when it finds an item which has missing metadata

2017-05-06

• Add "Blog Post" to dc.type
• Create ticket on Atmire tracker to ask about commissioning them to develop the feature to expose ORCID via REST/OAI: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=510
• According to the DSpace curation docs the fact that the requiredmetadata curation task stops when it finds a missing metadata field is by design

2017-05-07

• Testing one replacement for CCAFS Flagships (cg.subject.ccafs), first changed in the submission forms, and then in the database:

$ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu

• Also, CCAFS wants to re-order their flagships to prioritize the Phase II ones
• Waiting for feedback from CCAFS, then I can merge #320

2017-05-08

• Start working on CGIAR Library migration
• We decided to use AIP export to preserve the hierarchies and handles of communities and collections
• When ingesting some collections I was getting java.lang.OutOfMemoryError: GC overhead limit exceeded, which can be solved by disabling the GC timeout with -XX:-UseGCOverheadLimit
• Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed
• This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using dspace cleanup -v, or else you'll run out of disk space
• In the end I realized it's better to use submission mode (-s) to ingest the community object as a single AIP without its children, followed by each of the collections:

$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done

• Note that in submission mode DSpace ignores the handle specified in mets.xml in the zip file, so you need to turn that off with -o ignoreHandle=false
• The -u option supresses prompts, to allow the process to run without user input
• Give feedback to CIFOR about their data quality:
  • Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier
  • Suggestion: use CGSpace's CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml
  • Suggestion: clean up duplicates and errors in funders, perhaps use a controlled vocabulary like ours, see: dspace/config/controlled-vocabularies/dc-description-sponsorship.xml
  • Suggestion: use dc.type "Blog Post" instead of "Blog" for your blog post items (we are also adding a "Blog Post" type to CGSpace soon)
  • Question: many of your items use dc.document.uri AND cg.identifier.url with the same text value?
• Help Marianne from WLE with an Open Search query to show the latest WLE CRP outputs: https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC
• This uses the webui's item list sort options, see webui.itemlist.sort-option in dspace.cfg
• The equivalent Discovery search would be: https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc

2017-05-09

• The CGIAR Library metadata has some blank metadata values, which leads to ||| in the Discovery facets
• Clean these up in the database using:

dspace=# delete from metadatavalue where resource_type_id=2 and text_value=''

• I ended up running into issues during data cleaning and decided to wipe out the entire community and re-sync DSpace Test assetstore and database from CGSpace rather than waiting for the cleanup task to clean up
• Hours into the re-ingestion I ran into more errors, and had to erase everything and start over again!
• Now, no matter what I do I keep getting foreign key errors...

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
  Detail: Key (handle_id)=(80928) already exists.

• I think those errors actually come from me running the update-sequences.sql script while Tomcat/DSpace are running
• Apparently you need to stop Tomcat!

2017-05-10

• Atmire says they are willing to extend the ORCID implementation, and I've asked them to provide a quote
• I clarified that the scope of the implementation should be that ORCIDs are stored in the database and exposed via REST / API like other fields
• Finally finished importing all the CGIAR Library content, final method was:

$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit"
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2517/10947-2517.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2515/10947-2515.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-2516/10947-2516.zip
$ [dspace]/bin/dspace packager -r -a -t AIP -o skipIfParentMissing=true -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ [dspace]/bin/dspace packager -s -t AIP -o ignoreHandle=false -e some@user.com -p 10568/80923 /home/aorth/10947-1/10947-1.zip
$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10947/1 $collection; done
$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e some@user.com $item; done

• Basically, import the smaller communities using recursive AIP import (with skipIfParentMissing)
• Then, for the larger collection, create the community, collections, and items separately, ingesting the items one by one
• The -XX:-UseGCOverheadLimit JVM option helps with some issues in large imports
• After this I ran the update-sequences.sql script (with Tomcat shut down), and cleaned up the 200+ blank metadata records:

dspace=# delete from metadatavalue where resource_type_id=2 and text_value='';