CGSpace Notes

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

CGIAR Library Migration

in  Notes  

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.

Pre-migration Technical TODOs

Things that need to happen before the migration:

  • Create top-level community on CGSpace to hold the CGIAR Library content: 10568/83389
    • Update nginx redirects in ansible templates
    • Update handle in DSpace XMLUI config
  • Set up nginx redirects for URLs like:
  • Merge #339 to 5_x-prod branch and rebuild DSpace
  • Increase max_connections in /etc/postgresql/9.5/main/postgresql.conf by ~10
    • SELECT * FROM pg_stat_activity; seems to show ~6 extra connections used by the command line tools during import
  • Temporarily disable nightly index-discovery cron job because the import process will be taking place during some of this time and I don’t want them to be competing to update the Solr index
  • Copy HTTPS certificate key pair from CGIAR Library server’s Tomcat keystore:
$ keytool -list -keystore tomcat.keystore
$ keytool -importkeystore -srckeystore tomcat.keystore -destkeystore library.cgiar.org.p12 -deststoretype PKCS12 -srcalias tomcat
$ openssl pkcs12 -in library.cgiar.org.p12 -nokeys -out library.cgiar.org.crt.pem
$ openssl pkcs12 -in library.cgiar.org.p12 -nodes -nocerts -out library.cgiar.org.key.pem
$ wget https://certs.godaddy.com/repository/gdroot-g2.crt https://certs.godaddy.com/repository/gdig2.crt.pem
$ cat library.cgiar.org.crt.pem gdig2.crt.pem > library.cgiar.org-chained.pem

Migration Process

Export all top-level communities and collections from DSpace Test:

$ export PATH=$PATH:/home/dspacetest.cgiar.org/bin
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2515 10947-2515/10947-2515.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2516 10947-2516/10947-2516.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2517 10947-2517/10947-2517.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2518 10947-2518/10947-2518.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2519 10947-2519/10947-2519.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2708 10947-2708/10947-2708.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2526 10947-2526/10947-2526.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2871 10947-2871/10947-2871.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2527 10947-2527/10947-2527.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93759 10568-93759/10568-93759.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/10568-93760.zip
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip

Import to CGSpace (also see notes from 2017-05-10):

  • Copy all exports from DSpace Test
  • Add ingestion overrides to dspace.cfg before import:
mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
mets.dspaceAIP.ingest.crosswalk.DSPACE-ROLES = NIL
  • Import communities and collections, paying attention to options to skip missing parents and ignore handles:
$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
$ export PATH=$PATH:/home/cgspace.cgiar.org/bin
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2515/10947-2515.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2516/10947-2516.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2517/10947-2517.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2518/10947-2518.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2519/10947-2519.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2708/10947-2708.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2526/10947-2526.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2871/10947-2871.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-4467/10947-4467.zip
$ dspace packager -s -u -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-2527/10947-2527.zip
$ for item in 10947-2527/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
$ dspace packager -s -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-1/10947-1.zip
$ for collection in 10947-1/COLLECTION@10947-*; do dspace packager -s -o ignoreHandle=false -t AIP -e aorth@mjanja.ch -p 10947/1 $collection; done
$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done

This submits AIP hierarchies recursively (-r) and suppresses errors when an item’s parent collection hasn’t been created yet—for example, if the item is mapped. The large historic archive (10947/1) is created in several steps because it requires a lot of memory and often crashes.

Create new subcommunities and collections for content we reorganized into new hierarchies from the original:

  • Create CGIAR System Management Board sub-community: 10568/83536
    • Content from CGIAR System Management Board documents collection (10947/4561) goes here
    • Import collection hierarchy first and then the items:
$ dspace packager -r -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83536 10568-93760/COLLECTION@10947-4651.zip
$ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
  • Create CGIAR System Management Office sub-community: 10568/83537
    • Create CGIAR System Management Office documents collection: 10568/83538
    • Import items to collection individually in replace mode (-r) while explicitly preserving handles and ignoring parents:
$ for item in 10568-93759/ITEM@10947-46*; do dspace packager -r -t AIP -o ignoreHandle=false -o ignoreParent=true -e aorth@mjanja.ch -p 10568/83538 $item; done

Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:

dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
  • Export them from the CGIAR Library:
# for handle in 10947/4658 10947/4659 10947/4660 10947/4661 10947/4665 10947/4664 10947/4666 10947/4669; do /usr/local/dspace/bin/dspace packager -d -a -t AIP -e m.marus@cgiar.org -i $handle ${handle}.zip; done
  • Import on CGSpace:
$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done

Post Migration

  • Shut down Tomcat and run update-sequences.sql as the system’s postgres user
  • Remove ingestion overrides from dspace.cfg
  • Reset PostgreSQL max_connections to 183
  • Enable nightly index-discovery cron job
  • Adjust CGSpace’s handle-server/config.dct to add the new prefix alongside our existing 10568, ie:
"server_admins" = (
"300:0.NA/10568"
"300:0.NA/10947"
)

"replication_admins" = (
"300:0.NA/10568"
"300:0.NA/10947"
)

"backup_admins" = (
"300:0.NA/10568"
"300:0.NA/10947"
)

I had been regenerated the sitebndl.zip file on the CGIAR Library server and sent it to the Handle.net admins but they said that there were mismatches between the public and private keys, which I suspect is due to make-handle-config not being very flexible. After discussing our scenario with the Handle.net admins they said we actually don’t need to send an updated sitebndl.zip for this type of change, and the above config.dct edits are all that is required. I guess they just did something on their end by setting the authoritative IP address for the 10947 prefix to be the same as ours…

  • Update DNS records:
    • CNAME: cgspace.cgiar.org
  • Re-deploy DSpace from freshly built 5_x-prod branch
  • Merge cgiar-library branch to master and re-run ansible nginx templates
  • Run system updates and reboot server
  • Switch to Let’s Encrypt HTTPS certificates (after DNS is updated and server isn’t busy):
$ sudo systemctl stop nginx
$ /opt/certbot-auto certonly --standalone -d library.cgiar.org
$ sudo systemctl start nginx

Troubleshooting

Foreign Key Error in dspace cleanup

The cleanup script is sometimes used during import processes to clean the database and assetstore after failed AIP imports. If you see the following error with dspace cleanup -v:

Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"                                                                                                                       
  Detail: Key (bitstream_id)=(119841) is still referenced from table "bundle".

The solution is to set the primary_bitstream_id to NULL in PostgreSQL:

dspace=# update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (119841);

PSQLException During AIP Ingest

After a few rounds of ingesting—possibly with failures—you might end up with inconsistent IDs in the database. In this case, during AIP ingest of a single collection in submit mode (-s):

org.dspace.content.packager.PackageValidationException: Exception while ingesting 10947-2527/10947-2527.zip, Reason: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"                                    
  Detail: Key (handle_id)=(86227) already exists.

The normal solution is to run the update-sequences.sql script (with Tomcat shut down) but it doesn’t seem to work in this case. Finding the maximum handle_id and manually updating the sequence seems to work:

dspace=# select * from handle where handle_id=(select max(handle_id) from handle);
dspace=# select setval('handle_seq',86873);