February, 2020

Sun Feb 02, 2020 by Alan Orth in Notes

2020-02-02

Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
- Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database
- I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks
- Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff
- The code finally builds and runs with a fresh install

Now we don’t specify the build environment because site modification are in local.cfg, so we just build like this:

$ schedtool -D -e ionice -c2 -n7 nice -n19 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false clean package

And it seems that we need to enabled pg_crypto now (used for UUIDs):

$ psql -h localhost -U postgres dspace63
dspace63=# CREATE EXTENSION pgcrypto;
CREATE EXTENSION pgcrypto;

I tried importing a PostgreSQL snapshot from CGSpace and had errors due to missing Atmire database migrations
- If I try to run dspace database migrate I get the IDs of the migrations that are missing
- I delete them manually in psql:

dspace63=# DELETE FROM schema_version WHERE version IN ('5.0.2015.01.27', '5.6.2015.12.03.2', '5.6.2016.08.08', '5.0.2017.04.28', '5.0.2017.09.25', '5.8.2015.12.03.3');

Then I ran dspace database migrate and got an error:

$ ~/dspace63/bin/dspace database migrate

Database URL: jdbc:postgresql://localhost:5432/dspace63?ApplicationName=dspaceCli
Migrating database to latest version... (Check dspace logs for details)
Migration exception:
java.sql.SQLException: Flyway migration error occurred
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:673)
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:576)
        at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:221)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
Caused by: org.flywaydb.core.internal.dbsupport.FlywaySqlScriptException:
Migration V6.0_2015.03.07__DS-2701_Hibernate_migration.sql failed
-----------------------------------------------------------------
SQL State  : 2BP01
Error Code : 0
Message    : ERROR: cannot drop table metadatavalue column resource_id because other objects depend on it
  Detail: view eperson_metadata depends on table metadatavalue column resource_id
  Hint: Use DROP ... CASCADE to drop the dependent objects too.
Location   : org/dspace/storage/rdbms/sqlmigration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql (/home/aorth/src/git/DSpace-6.3/file:/home/aorth/dspace63/lib/dspace-api-6.3.jar!/org/dspace/storage/rdbms/sqlmigration/postgres/V6.0_2015.03.07__DS-2701_Hibernate_migration.sql)
Line       : 391
Statement  : ALTER TABLE metadatavalue DROP COLUMN IF EXISTS resource_id

        at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:117)
        at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:71)
        at org.flywaydb.core.internal.command.DbMigrate.doMigrate(DbMigrate.java:352)
        at org.flywaydb.core.internal.command.DbMigrate.access$1100(DbMigrate.java:47)
        at org.flywaydb.core.internal.command.DbMigrate$4.doInTransaction(DbMigrate.java:308)
        at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
        at org.flywaydb.core.internal.command.DbMigrate.applyMigration(DbMigrate.java:305)
        at org.flywaydb.core.internal.command.DbMigrate.access$1000(DbMigrate.java:47)
        at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:230)
        at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:173)
        at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
        at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:173)
        at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
        at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
        at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
        at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
        at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:662)
        ... 8 more
Caused by: org.postgresql.util.PSQLException: ERROR: cannot drop table metadatavalue column resource_id because other objects depend on it
  Detail: view eperson_metadata depends on table metadatavalue column resource_id
  Hint: Use DROP ... CASCADE to drop the dependent objects too.
        at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2422)
        at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2167)
        at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
        at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:307)
        at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:293)
        at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:270)
        at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:266)
        at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
        at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
        at org.flywaydb.core.internal.dbsupport.JdbcTemplate.executeStatement(JdbcTemplate.java:238)
        at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:114)
        ... 24 more

I think I might need to update the sequences first… nope
Perhaps it’s due to some missing bitstream IDs and I need to run dspace cleanup on CGSpace and take a new PostgreSQL dump… nope
A thread on the dspace-tech mailing list regarding this migration noticed that his database had some views created that were using the resource_id column
Our database had the same issue, where the eperson_metadata view was created by something (Atmire module?) but has no references in the vanilla DSpace code, so I dropped it and tried the migration again:

dspace63=# DROP VIEW eperson_metadata;
DROP VIEW

After that the migration was successful and DSpace starts up successfully and begins indexing
- xmlui, solr, jspui, rest, and oai are working (rest was redirecting to HTTPS, so I set the Tomcat connector to secure="true" and it fixed it on localhost, but caused other issues so I disabled it for now)
- I started diffing our themes against the Mirage 2 reference theme to capture the latest changes

2020-02-03

Update DSpace mimetype fallback images from KDE Breeze Icons project
- Our icons are four years old (see my bitstream icons demo)
Issues remaining in the DSpace 6 port of our CGSpace 5.x code:
- Community and collection pages only show one recent submission (seems that there is only one item in Solr?)
- Community and collection pages have tons of “Browse” buttons that we need to remove
- Order of navigation elements in right side bar (“My Account” etc, compare to DSpace Test)
- Home page trail says “CGSpace Home” instead of “CGSpace Home / Community List” (see DSpace Test)
There are lots of errors in the DSpace log, which might explain some of the issues with recent submissions / Solr:

2020-02-03 10:27:14,485 ERROR org.dspace.browse.ItemCountDAOSolr @ caught exception: 
org.dspace.discovery.SearchServiceException: Invalid UUID string: 1
2020-02-03 13:20:20,475 ERROR org.dspace.app.xmlui.aspect.discovery.AbstractRecentSubmissionTransformer @ Caught SearchServiceException while retrieving recent submission for: home page
org.dspace.discovery.SearchServiceException: Invalid UUID string: 111210

If I look in Solr’s search core I do actually see items with integers for their resource ID, which I think are all supposed to be UUIDs now…
I dropped all the documents in the search core:

$ http --print b 'http://localhost:8080/solr/search/update?stream.body=<delete><query>*:*</query></delete>&commit=true'

Still didn’t work, so I’m going to try a clean database import and migration:

$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspace63
$ psql -h localhost -U postgres -c 'alter user dspacetest superuser;'
$ pg_restore -h localhost -U postgres -d dspace63 -O --role=dspacetest -h localhost dspace_2020-01-27.backup
$ psql -h localhost -U postgres -c 'alter user dspacetest nosuperuser;'
$ psql -h localhost -U postgres dspace63                               
dspace63=# CREATE EXTENSION pgcrypto;
dspace63=# DELETE FROM schema_version WHERE version IN ('5.0.2015.01.27', '5.6.2015.12.03.2', '5.6.2016.08.08', '5.0.2017.04.28', '5.0.2017.09.25', '5.8.2015.12.03.3');
dspace63=# DROP VIEW eperson_metadata;
dspace63=# \q
$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspace63
$ ~/dspace63/bin/dspace database migrate

I notice that the indexing doesn’t work correctly if I start it manually with dspace index-discovery -b (search.resourceid becomes an integer!)
- If I induce an indexing by touching dspace/solr/search/conf/reindex.flag the search.resourceid are all UUIDs…
Speaking of database stuff, there was a performance-related update for the indexes that we used in DSpace 5
- We might want to apply it in DSpace 6, as it was never merged to 6.x, but it helped with the performance of /submissions in XMLUI for us in 2018-03

2020-02-04

The indexing issue I was having yesterday seems to only present itself the first time a new installation is running DSpace 6
- Once the indexing induced by touching dspace/solr/search/conf/reindex.flag has finished, subsequent manual invocations of dspace index-discovery -b work as expected
- Nevertheless, I sent a message to the dspace-tech mailing list describing the issue to see if anyone has any comments
I am seeing that the number of important commits on the unreleased DSpace 6.4 are really numerous and it might be better for us to target that version
- I did a simple test and it’s easy to rebase my current 6.3 branch on top of the upstream dspace-6_x branch:

$ git checkout -b 6_x-dev64 6_x-dev
$ git rebase -i upstream/dspace-6_x

I finally understand why our themes show all the “Browse by” buttons on community and collection pages in DSpace 6.x
- The code in ./dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/browseArtifacts/CommunityBrowse.java iterates over all the browse indexes and prints them when it is called
- The XMLUI theme code in dspace/modules/xmlui-mirage2/src/main/webapp/themes/0_CGIAR/xsl/preprocess/browse.xsl calls the template because the id of the div matches “aspect.browseArtifacts.CommunityBrowse.list.community-browse”
- I checked the DRI of a community page on my local 6.x and DSpace Test 5.x by appending ?XML to the URL and I see the ID is missing on DSpace 5.x
- The issue is the same with the ordering of the “My Account” link, but in Navigation.java
- I tried modifying preprocess/browse.xsl but it always ends up printing some default list of browse by links…
- I’m starting to wonder if Atmire’s modules somehow override this, as I don’t see how CommunityBrowse.java can behave like ours on DSpace 5.x unless they have overridden it (as the open source code is the same in 5.x and 6.x)
- At least the “account” link in the sidebar is overridden in our 5.x branch because Atmire copied a modified Navigation.java to the local xmlui modules folder… so that explains that (and it’s easy to replicate in 6.x)

2020-02-05

UptimeRobot told me that AReS Explorer crashed last night, so I logged into it, ran all updates, and rebooted it
Testing Discovery indexing speed on my local DSpace 6.3:

$ time schedtool -D -e ~/dspace63/bin/dspace index-discovery -b
schedtool -D -e ~/dspace63/bin/dspace index-discovery -b  3771.78s user 93.63s system 41% cpu 2:34:19.53 total
schedtool -D -e ~/dspace63/bin/dspace index-discovery -b  3360.28s user 82.63s system 38% cpu 2:30:22.07 total
schedtool -D -e ~/dspace63/bin/dspace index-discovery -b  4678.72s user 138.87s system 42% cpu 3:08:35.72 total
schedtool -D -e ~/dspace63/bin/dspace index-discovery -b  3334.19s user 86.54s system 35% cpu 2:41:56.73 total

DSpace 5.8 was taking about 1 hour (or less on this laptop), so this is 2-3 times longer!

$ time schedtool -D -e ~/dspace/bin/dspace index-discovery -b
schedtool -D -e ~/dspace/bin/dspace index-discovery -b  299.53s user 69.67s system 20% cpu 30:34.47 total
schedtool -D -e ~/dspace/bin/dspace index-discovery -b  270.31s user 69.88s system 19% cpu 29:01.38 total

Checking out the DSpace 6.x REST API query client
- There is a tutorial that explains how it works and I see it is very powerful because you can export a CSV of results in order to fix and re-upload them with batch import!
- Custom queries can be added in dspace-rest/src/main/webapp/static/reports/restQueryReport.js
I noticed two new bots in the logs with the following user agents:
- Jersey/2.6 (HttpUrlConnection 1.8.0_152)
- magpie-crawler/1.1 (U; Linux amd64; en-GB; +http://www.brandwatch.net)
I filed an issue to add Jersey to the COUNTER-Robots list
Peter noticed that the statlets on community, collection, and item pages aren’t working on CGSpace
- I thought it might be related to the fact that the yearly sharding didn’t complete successfully this year so the statistics-2019 core is empty
- I removed the statistics-2019 core and had to restart Tomcat like six times before all cores would load properly (ugh!!!!)
- After that the statlets were working properly…
Run all system updates on DSpace Test (linode19) and restart it

2020-02-06

I sent a mail to the dspace-tech mailing list asking about slow Discovery indexing speed in DSpace 6
I destroyed my PostgreSQL 9.6 containers and re-created them using PostgreSQL 10 to see if there are any speedups with DSpace 6.x:

$ podman pull postgres:10-alpine
$ podman run --name dspacedb10 -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:10-alpine
$ createuser -h localhost -U postgres --pwprompt dspacetest
$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspacetest
$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspace63
$ psql -h localhost -U postgres -c 'alter user dspacetest superuser;'
$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/cgspace_2020-02-06.backup
$ pg_restore -h localhost -U postgres -d dspace63 -O --role=dspacetest -h localhost ~/Downloads/cgspace_2020-02-06.backup
$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest
$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspace63
$ psql -h localhost -U postgres -c 'alter user dspacetest nosuperuser;'
$ psql -h localhost -U postgres dspace63                               
dspace63=# CREATE EXTENSION pgcrypto;
dspace63=# DELETE FROM schema_version WHERE version IN ('5.0.2015.01.27', '5.6.2015.12.03.2', '5.6.2016.08.08', '5.0.2017.04.28', '5.0.2017.09.25', '5.8.2015.12.03.3');
dspace63=# DROP VIEW eperson_metadata;
dspace63=# \q

I purged ~33,000 hits from the “Jersey/2.6” bot in CGSpace’s statistics using my check-spider-hits.sh script:

$ ./check-spider-hits.sh -d -p -f /tmp/jersey -s statistics -u http://localhost:8081/solr
$ for year in 2018 2017 2016 2015; do ./check-spider-hits.sh -d -p -f /tmp/jersey -s "statistics-${year}" -u http://localhost:8081/solr; done

I noticed another user agen in the logs that we should add to the list:

ReactorNetty/0.9.2.RELEASE

I made an issue on the COUNTER-Robots repository
I found a nice tool for exporting and importing Solr records and it seems to workfor exporting our 2019 stats from the large statistics core!

$ ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2019-01.json -f 'dateYearMonth:2019-01' -k uid
$ ls -lh /tmp/statistics-2019-01.json
-rw-rw-r-- 1 aorth aorth 3.7G Feb  6 09:26 /tmp/statistics-2019-01.json

Then I tested importing this by creating a new core in my development environment:

$ curl 'http://localhost:8080/solr/admin/cores?action=CREATE&name=statistics-2019&instanceDir=/home/aorth/dspace63/solr/statistics&dataDir=/home/aorth/dspace63/solr/statistics-2019/data'
$ ./run.sh -s http://localhost:8080/solr/statistics-2019 -a import -o ~/Downloads/statistics-2019-01.json -k uid

This imports the records into the core, but DSpace can’t see them, and when I restart Tomcat the core is not seen by Solr…