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Continue working on porting CGSpace&rsquo;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
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Continue working on porting CGSpace&rsquo;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
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-02-02T11:56:30&#43;02:00">Sun Feb 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2020-02-02">2020-02-02</h2>
<ul>
<li>Continue working on porting CGSpace&rsquo;s DSpace 5 code to DSpace 6.3 that I started yesterday
<ul>
<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
<li>The code finally builds and runs with a fresh install</li>
</ul>
</li>
</ul>
<ul>
<li>Now we don&rsquo;t specify the build environment because site modification are in <code>local.cfg</code>, so we just build like this:</li>
</ul>
<pre><code>$ schedtool -D -e ionice -c2 -n7 nice -n19 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false clean package
</code></pre><ul>
<li>And it seems that we need to enabled <code>pg_crypto</code> now (used for UUIDs):</li>
</ul>
<pre><code>$ psql -h localhost -U postgres dspace63
dspace63=# CREATE EXTENSION pgcrypto;
CREATE EXTENSION pgcrypto;
</code></pre><ul>
<li>I tried importing a PostgreSQL snapshot from CGSpace and had errors due to missing Atmire database migrations
<ul>
<li>If I try to run <code>dspace database migrate</code> I get the IDs of the migrations that are missing</li>
<li>I delete them manually in psql:</li>
</ul>
</li>
</ul>
<pre><code>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');
</code></pre><ul>
<li>Then I ran <code>dspace database migrate</code> and got an error:</li>
</ul>
<pre><code>$ ~/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
</code></pre><ul>
<li>I think I might need to update the sequences first&hellip; nope</li>
<li>Perhaps it&rsquo;s due to some missing bitstream IDs and I need to run <code>dspace cleanup</code> on CGSpace and take a new PostgreSQL dump&hellip; nope</li>
<li>A thread on the dspace-tech mailing list regarding this migration noticed that his database had some views created that were using the <code>resource_id</code> column</li>
<li>Our database had the same issue, where the <code>eperson_metadata</code> 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:</li>
</ul>
<pre><code>dspace63=# DROP VIEW eperson_metadata;
DROP VIEW
</code></pre><ul>
<li>After that the migration was successful and DSpace starts up successfully and begins indexing
<ul>
<li>XMLUI, Solr, JSPUI, and OAI are working, but rest is not starting up</li>
<li>I started diffing our themes against the Mirage 2 reference theme to capture the latest changes</li>
</ul>
</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
<li><a href="/cgspace-notes/2019-12/">December, 2019</a></li>
<li><a href="/cgspace-notes/2019-11/">November, 2019</a></li>
<li><a href="/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></li>
</ol>
</section>
<section class="sidebar-module">
<h4>Links</h4>
<ol class="list-unstyled">
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
</ol>
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