CGIAR Library Migration

Mon Sep 18, 2017 by Alan Orth in Notes

Note: I’m temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in config.toml

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:
- https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf
- https://library.cgiar.org/handle/10947/4258
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

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"
)

Regenerate Handle server’s sitebndl.zip on CGIAR Library server:

$ sudo su -
# cp -a /usr/local/dspace/handle-server /usr/local/dspace/handle-server-2017-09-19.bak
# /usr/local/dspace/bin/dspace make-handle-config /usr/local/dspace/handle-server

The handle setup script will ask for IP address, contact person, etc
Use CGSpace’s IP address, but give some contact person from the system organization
Copy the resulting sitebndl.zip somewhere so we can send it to Handle.net
Now I’m wondering how we’ll do this when we move servers in the future, because the make-handle-config basically assumes you only have one handle
Also, there is dspace make-handle-config and bin/make-handle-config and both behave differently (the first is interactive, the second reads your dspace.cfg and generates your handle config and sitebndl.zip accordingly)
I’m really not sure on the proper order of events actually
HTTPS certificates:
- Install current certificates from their 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

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 tomcat7
$ ./letsencrypt-auto certonly --standalone -d library.cgiar.org

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);