CGSpace Notes

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

May, 2017

in  

2017-05-01

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

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

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 -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='';

2017-05-13

  • After quite a bit of troubleshooting with importing cleaned up data as CSV, it seems that there are actually NUL characters in the dc.description.abstract field (at least) on the lines where CSV importing was failing
  • I tried to find a way to remove the characters in vim or Open Refine, but decided it was quicker to just remove the column temporarily and import it
  • The import was successful and detected 2022 changes, which should likely be the rest that were failing to import before

2017-05-15

  • To delete the blank lines that cause isses during import we need to use a regex in vim g/^$/d
  • After that I started looking in the dc.subject field to try to pull countries and regions out, but there are too many values in there
  • Bump the Academicons dependency of the Mirage 2 themes from 1.6.0 to 1.8.0 because the upstream deleted the old tag and now the build is failing: #321
  • Merge changes to CCAFS project identifiers and flagships: #320
  • Run updates for CCAFS flagships on CGSpace:
$ ./fix-metadata-values.py -i /tmp/ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p 'fuuu'

  • These include:

    • GENDER AND SOCIAL DIFFERENTIATION→GENDER AND SOCIAL INCLUSION
    • MANAGING CLIMATE RISK→CLIMATE SERVICES AND SAFETY NETS

  • Re-deploy CGSpace and DSpace Test and run system updates

  • Reboot DSpace Test

  • Fix cron jobs for log management on DSpace Test, as they weren’t catching dspace.log.* files correctly and we had over six months of them and they were taking up many gigs of disk space

2017-05-16

  • Discuss updates to WLE themes for their Phase II
  • Make an issue to track the changes to cg.subject.wle: #322

2017-05-17

  • Looking into the error I get when trying to create a new collection on DSpace Test:
ERROR: duplicate key value violates unique constraint "handle_pkey" Detail: Key (handle_id)=(84834) already exists.
  • I tried updating the sequences a few times, with Tomcat running and stopped, but it hasn’t helped
  • It appears item with handle_id 84834 is one of the imported CGIAR Library items:
dspace=# select * from handle where handle_id=84834;
 handle_id |   handle   | resource_type_id | resource_id
-----------+------------+------------------+-------------
     84834 | 10947/1332 |                2 |       87113
  • Looks like the max handle_id is actually much higher:
dspace=# select * from handle where handle_id=(select max(handle_id) from handle);
 handle_id |  handle  | resource_type_id | resource_id
-----------+----------+------------------+-------------
     86873 | 10947/99 |                2 |       89153
(1 row)
  • I’ve posted on the dspace-test mailing list to see if I can just manually set the handle_seq to that value
  • Actually, it seems I can manually set the handle sequence using:
dspace=# select setval('handle_seq',86873);
  • After that I can create collections just fine, though I’m not sure if it has other side effects

2017-05-21

  • Start creating a basic theme for the CGIAR System Organization’s community on CGSpace
  • Using colors from the CGIAR Branding guidelines (2014)
  • Make a GitHub issue to track this work: #324

2017-05-22

  • Do some cleanups of community and collection names in CGIAR System Management Office community on DSpace Test, as well as move some items as Peter requested
  • Peter wanted a list of authors in here, so I generated a list of collections using the “View Source” on each community and this hacky awk:
$ grep 10947/ /tmp/collections | grep -v cocoon | awk -F/ '{print $3"/"$4}' | awk -F\" '{print $1}' | vim -
  • Then I joined them together and ran this old SQL query from the dspace-tech mailing list which gives you authors for items in those collections:
dspace=# select distinct text_value
from metadatavalue
where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
AND resource_type_id = 2
AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/1
0', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '109
47/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947
/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947
/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521',
'10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '109
47/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2
531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535'
, '10947/2537', '10568/93761')));
  • To get a CSV (with counts) from that:
dspace=# \copy (select distinct text_value, count(*)
from metadatavalue
where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author')
AND resource_type_id = 2
AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10947/2', '10947/3', '10947/10', '10947/4', '10947/5', '10947/6', '10947/7', '10947/8', '10947/9', '10947/11', '10947/25', '10947/12', '10947/26', '10947/27', '10947/28', '10947/29', '10947/30', '10947/13', '10947/14', '10947/15', '10947/16', '10947/31', '10947/32', '10947/33', '10947/34', '10947/35', '10947/36', '10947/37', '10947/17', '10947/18', '10947/38', '10947/19', '10947/39', '10947/40', '10947/41', '10947/42', '10947/43', '10947/2512', '10947/44', '10947/20', '10947/21', '10947/45', '10947/46', '10947/47', '10947/48', '10947/49', '10947/22', '10947/23', '10947/24', '10947/50', '10947/51', '10947/2518', '10947/2776', '10947/2790', '10947/2521', '10947/2522', '10947/2782', '10947/2525', '10947/2836', '10947/2524', '10947/2878', '10947/2520', '10947/2523', '10947/2786', '10947/2631', '10947/2589', '10947/2519', '10947/2708', '10947/2526', '10947/2871', '10947/2527', '10947/4467', '10947/3457', '10947/2528', '10947/2529', '10947/2533', '10947/2530', '10947/2531', '10947/2532', '10947/2538', '10947/2534', '10947/2540', '10947/2900', '10947/2539', '10947/2784', '10947/2536', '10947/2805', '10947/2541', '10947/2535', '10947/2537', '10568/93761'))) group by text_value order by count desc) to /tmp/cgiar-librar-authors.csv with csv;

2017-05-23

  • Add Affiliation to filters on Listing and Reports module (#325)
  • Start looking at WLE’s Phase II metadata updates but it seems they are not tagging their items properly, as their website importer infers which theme to use based on the name of the CGSpace collection!
  • For now I’ve suggested that they just change the collection names and that we fix their metadata manually afterwards
  • Also, they have a lot of messed up values in their cg.subject.wle field so I will clean up some of those first:
dspace=# \copy (select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id=119) to /tmp/wle.csv with csv;
COPY 111
  • Respond to Atmire message about ORCIDs, saying that right now we’d prefer to just have them available via REST API like any other metadata field, and that I’m available for a Skype

2017-05-26

  • Increase max file size in nginx so that CIP can upload some larger PDFs
  • Agree to talk with Atmire after the June DSpace developers meeting where they will be discussing exposing ORCIDs via REST/OAI

2017-05-28

  • File an issue on GitHub to explore/track migration to proper country/region codes (ISO 2/3 and UN M.49): #326
  • Ask Peter how the Landportal.info people should acknowledge us as the source of data on their website
  • Communicate with MARLO people about progress on exposing ORCIDs via the REST API, as it is set to be discussed in the June, 2017 DCAT meeting
  • Find all of Amos Omore’s author name variations so I can link them to his authority entry that has an ORCID:
dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Omore, A%';
  • Set the authority for all variations to one containing an ORCID:
dspace=# update metadatavalue set authority='4428ee88-90ef-4107-b837-3c0ec988520b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Omore, A%';
UPDATE 187
  • Next I need to do Edgar Twine:
dspace=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like 'Twine, E%';
  • But it doesn’t look like any of his existing entries are linked to an authority which has an ORCID, so I edited the metadata via “Edit this Item” and looked up his ORCID and linked it there
  • Now I should be able to set his name variations to the new authority:
dspace=# update metadatavalue set authority='f70d0a01-d562-45b8-bca3-9cf7f249bc8b', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Twine, E%';
  • Run the corrections on CGSpace and then update discovery / authority
  • I notice that there are a handful of java.lang.OutOfMemoryError: Java heap space errors in the Catalina logs on CGSpace, I should go look into that…

2017-05-29

  • Discuss WLE themes and subjects with Mia and Macaroni Bros
  • We decided we need to create metadata fields for Phase I and II themes
  • I’ve updated the existing GitHub issue for Phase II (#322) and created a new one to track the changes for Phase I themes (#327)
  • After Macaroni Bros update the WLE website importer we will rename the WLE collections to reflect Phase II
  • Also, we need to have Mia and Udana look through the existing metadata in cg.subject.wle as it is quite a mess