cgspace-notes/content/posts/2020-02.md

---
title: "February, 2020"
date: 2020-02-02T11:56:30+02:00
author: "Alan Orth"
categories: ["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

<!--more-->

  - 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](https://github.com/KDE/breeze-icons) project
  - Our icons are four years old (see [my bitstream icons demo](https://alanorth.github.io/dspace-bitstream-icons/))
- Issues remaining in the DSpace 6 port of our CGSpace 5.x code:
  - [x] Community and collection pages only show one recent submission (seems that there is only one item in Solr?)
  - [x] Community and collection pages have tons of "Browse" buttons that we need to remove
  - [x] 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](https://github.com/DSpace/DSpace/pull/1791/)
  - We might want to [apply it in DSpace 6](https://github.com/DSpace/DSpace/pull/1792), as it was never merged to 6.x, but it helped with the performance of `/submissions` in XMLUI for us in [2018-03]({{< relref path="2018-03.md" >}})

## 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
```

- DSpace 5.8 was taking about 1 hour (or less on this laptop), so this is 2.5x 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
```

- Checking out the DSpace 6.x REST API query client
  - There is a [tutorial](https://terrywbrady.github.io/restReportTutorial/intro) 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](https://github.com/atmire/COUNTER-Robots/issues/30) 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

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