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<meta property="og:title" content="February, 2020" />
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<meta property="og:description" content="2020-02-02
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Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
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Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database
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I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks
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Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff
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The code finally builds and runs with a fresh install
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-02/" />
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<meta property="article:published_time" content="2020-02-02T11:56:30+02:00" />
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<meta property="article:modified_time" content="2020-02-04T18:45:07+02:00" />
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<meta name="twitter:title" content="February, 2020"/>
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<meta name="twitter:description" content="2020-02-02
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Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
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Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database
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I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks
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Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff
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The code finally builds and runs with a fresh install
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<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>
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<p class="blog-post-meta"><time datetime="2020-02-02T11:56:30+02:00">Sun Feb 02, 2020</time> by Alan Orth in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2020-02-02">2020-02-02</h2>
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<ul>
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<li>Continue working on porting CGSpace’s DSpace 5 code to DSpace 6.3 that I started yesterday
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<ul>
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<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
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<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
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<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
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<li>The code finally builds and runs with a fresh install</li>
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</ul>
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</li>
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</ul>
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<ul>
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<li>Now we don’t specify the build environment because site modification are in <code>local.cfg</code>, so we just build like this:</li>
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</ul>
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<pre><code>$ schedtool -D -e ionice -c2 -n7 nice -n19 mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false clean package
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</code></pre><ul>
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<li>And it seems that we need to enabled <code>pg_crypto</code> now (used for UUIDs):</li>
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</ul>
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<pre><code>$ psql -h localhost -U postgres dspace63
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dspace63=# CREATE EXTENSION pgcrypto;
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CREATE EXTENSION pgcrypto;
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</code></pre><ul>
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<li>I tried importing a PostgreSQL snapshot from CGSpace and had errors due to missing Atmire database migrations
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<ul>
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<li>If I try to run <code>dspace database migrate</code> I get the IDs of the migrations that are missing</li>
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<li>I delete them manually in psql:</li>
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</ul>
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</li>
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</ul>
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<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');
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</code></pre><ul>
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<li>Then I ran <code>dspace database migrate</code> and got an error:</li>
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</ul>
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<pre><code>$ ~/dspace63/bin/dspace database migrate
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Database URL: jdbc:postgresql://localhost:5432/dspace63?ApplicationName=dspaceCli
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Migrating database to latest version... (Check dspace logs for details)
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Migration exception:
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java.sql.SQLException: Flyway migration error occurred
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:673)
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:576)
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at org.dspace.storage.rdbms.DatabaseUtils.main(DatabaseUtils.java:221)
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at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
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at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
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at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
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at java.lang.reflect.Method.invoke(Method.java:498)
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at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
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at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
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Caused by: org.flywaydb.core.internal.dbsupport.FlywaySqlScriptException:
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Migration V6.0_2015.03.07__DS-2701_Hibernate_migration.sql failed
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-----------------------------------------------------------------
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SQL State : 2BP01
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Error Code : 0
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Message : ERROR: cannot drop table metadatavalue column resource_id because other objects depend on it
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Detail: view eperson_metadata depends on table metadatavalue column resource_id
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Hint: Use DROP ... CASCADE to drop the dependent objects too.
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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)
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Line : 391
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Statement : ALTER TABLE metadatavalue DROP COLUMN IF EXISTS resource_id
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at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:117)
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at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:71)
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at org.flywaydb.core.internal.command.DbMigrate.doMigrate(DbMigrate.java:352)
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at org.flywaydb.core.internal.command.DbMigrate.access$1100(DbMigrate.java:47)
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at org.flywaydb.core.internal.command.DbMigrate$4.doInTransaction(DbMigrate.java:308)
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at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
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at org.flywaydb.core.internal.command.DbMigrate.applyMigration(DbMigrate.java:305)
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at org.flywaydb.core.internal.command.DbMigrate.access$1000(DbMigrate.java:47)
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at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:230)
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at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:173)
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at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
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at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:173)
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at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
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at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
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at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
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at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
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at org.dspace.storage.rdbms.DatabaseUtils.updateDatabase(DatabaseUtils.java:662)
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... 8 more
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Caused by: org.postgresql.util.PSQLException: ERROR: cannot drop table metadatavalue column resource_id because other objects depend on it
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Detail: view eperson_metadata depends on table metadatavalue column resource_id
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Hint: Use DROP ... CASCADE to drop the dependent objects too.
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at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2422)
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at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2167)
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at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:306)
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at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:441)
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at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:365)
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at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:307)
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at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:293)
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at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:270)
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at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:266)
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at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
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at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:291)
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at org.flywaydb.core.internal.dbsupport.JdbcTemplate.executeStatement(JdbcTemplate.java:238)
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at org.flywaydb.core.internal.dbsupport.SqlScript.execute(SqlScript.java:114)
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... 24 more
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</code></pre><ul>
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<li>I think I might need to update the sequences first… nope</li>
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<li>Perhaps it’s due to some missing bitstream IDs and I need to run <code>dspace cleanup</code> on CGSpace and take a new PostgreSQL dump… nope</li>
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<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>
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<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>
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</ul>
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<pre><code>dspace63=# DROP VIEW eperson_metadata;
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DROP VIEW
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</code></pre><ul>
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<li>After that the migration was successful and DSpace starts up successfully and begins indexing
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<ul>
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<li>xmlui, solr, jspui, rest, and oai are working (rest was redirecting to HTTPS, so I set the Tomcat connector to <code>secure="true"</code> and it fixed it on localhost, but caused other issues so I disabled it for now)</li>
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<li>I started diffing our themes against the Mirage 2 reference theme to capture the latest changes</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-02-03">2020-02-03</h2>
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<ul>
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<li>Update DSpace mimetype fallback images from <a href="https://github.com/KDE/breeze-icons">KDE Breeze Icons</a> project
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<ul>
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<li>Our icons are four years old (see <a href="https://alanorth.github.io/dspace-bitstream-icons/">my bitstream icons demo</a>)</li>
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</ul>
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</li>
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<li>Issues remaining in the DSpace 6 port of our CGSpace 5.x code:
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<ul>
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<li><input checked="" disabled="" type="checkbox">Community and collection pages only show one recent submission (seems that there is only one item in Solr?)</li>
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<li><input checked="" disabled="" type="checkbox">Community and collection pages have tons of “Browse” buttons that we need to remove</li>
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<li><input checked="" disabled="" type="checkbox">Order of navigation elements in right side bar (“My Account” etc, compare to DSpace Test)</li>
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<li><input disabled="" type="checkbox">Home page trail says “CGSpace Home” instead of “CGSpace Home / Community List” (see DSpace Test)</li>
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</ul>
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</li>
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<li>There are lots of errors in the DSpace log, which might explain some of the issues with recent submissions / Solr:</li>
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</ul>
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<pre><code>2020-02-03 10:27:14,485 ERROR org.dspace.browse.ItemCountDAOSolr @ caught exception:
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org.dspace.discovery.SearchServiceException: Invalid UUID string: 1
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2020-02-03 13:20:20,475 ERROR org.dspace.app.xmlui.aspect.discovery.AbstractRecentSubmissionTransformer @ Caught SearchServiceException while retrieving recent submission for: home page
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org.dspace.discovery.SearchServiceException: Invalid UUID string: 111210
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</code></pre><ul>
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<li>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…</li>
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<li>I dropped all the documents in the search core:</li>
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</ul>
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<pre><code>$ http --print b 'http://localhost:8080/solr/search/update?stream.body=<delete><query>*:*</query></delete>&commit=true'
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</code></pre><ul>
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<li>Still didn’t work, so I’m going to try a clean database import and migration:</li>
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</ul>
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<pre><code>$ createdb -h localhost -U postgres -O dspacetest --encoding=UNICODE dspace63
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$ psql -h localhost -U postgres -c 'alter user dspacetest superuser;'
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$ pg_restore -h localhost -U postgres -d dspace63 -O --role=dspacetest -h localhost dspace_2020-01-27.backup
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$ psql -h localhost -U postgres -c 'alter user dspacetest nosuperuser;'
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$ psql -h localhost -U postgres dspace63
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dspace63=# CREATE EXTENSION pgcrypto;
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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');
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dspace63=# DROP VIEW eperson_metadata;
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dspace63=# \q
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$ psql -h localhost -U postgres -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspace63
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$ ~/dspace63/bin/dspace database migrate
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</code></pre><ul>
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<li>I notice that the indexing doesn’t work correctly if I start it manually with <code>dspace index-discovery -b</code> (search.resourceid becomes an integer!)
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<ul>
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<li>If I induce an indexing by touching <code>dspace/solr/search/conf/reindex.flag</code> the search.resourceid are all UUIDs…</li>
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</ul>
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</li>
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<li>Speaking of database stuff, there was a performance-related update for the <a href="https://github.com/DSpace/DSpace/pull/1791/">indexes that we used in DSpace 5</a>
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<ul>
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<li>We might want to <a href="https://github.com/DSpace/DSpace/pull/1792">apply it in DSpace 6</a>, as it was never merged to 6.x, but it helped with the performance of <code>/submissions</code> in XMLUI for us in <a href="/cgspace-notes/2018-03/">2018-03</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-02-04">2020-02-04</h2>
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<ul>
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<li>The indexing issue I was having yesterday seems to only present itself the first time a new installation is running DSpace 6
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<ul>
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<li>Once the indexing induced by touching <code>dspace/solr/search/conf/reindex.flag</code> has finished, subsequent manual invocations of <code>dspace index-discovery -b</code> work as expected</li>
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<li>Nevertheless, I sent a message to the dspace-tech mailing list describing the issue to see if anyone has any comments</li>
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</ul>
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</li>
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<li>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
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<ul>
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<li>I did a simple test and it’s easy to rebase my current 6.3 branch on top of the upstream <code>dspace-6_x</code> branch:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ git checkout -b 6_x-dev64 6_x-dev
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$ git rebase -i upstream/dspace-6_x
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</code></pre><ul>
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<li>I finally understand why our themes show all the “Browse by” buttons on community and collection pages in DSpace 6.x
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<ul>
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<li>The code in <code>./dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/browseArtifacts/CommunityBrowse.java</code> iterates over all the browse indexes and prints them when it is called</li>
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<li>The XMLUI theme code in <code>dspace/modules/xmlui-mirage2/src/main/webapp/themes/0_CGIAR/xsl/preprocess/browse.xsl</code> calls the template because the id of the div matches “aspect.browseArtifacts.CommunityBrowse.list.community-browse”</li>
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<li>I checked the DRI of a community page on my local 6.x and DSpace Test 5.x by appending <code>?XML</code> to the URL and I see the ID is missing on DSpace 5.x</li>
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<li>The issue is the same with the ordering of the “My Account” link, but in Navigation.java</li>
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<li>I tried modifying <code>preprocess/browse.xsl</code> but it always ends up printing some default list of browse by links…</li>
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<li>I’m starting to wonder if Atmire’s modules somehow override this, as I don’t see how <code>CommunityBrowse.java</code> 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)</li>
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<li>At least the “account” link in the sidebar is overridden in our 5.x branch because Atmire copied a modified <code>Navigation.java</code> to the local xmlui modules folder… so that explains that (and it’s easy to replicate in 6.x)</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-02-05">2020-02-05</h2>
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<ul>
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<li>UptimeRobot told me that AReS Explorer crashed last night, so I logged into it, ran all updates, and rebooted it</li>
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<li>Testing Discovery indexing speed on my local DSpace 6.3:</li>
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</ul>
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<pre><code>$ time schedtool -D -e ~/dspace63/bin/dspace index-discovery -b
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schedtool -D -e ~/dspace63/bin/dspace index-discovery -b 3771.78s user 93.63s system 41% cpu 2:34:19.53 total
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schedtool -D -e ~/dspace63/bin/dspace index-discovery -b 3360.28s user 82.63s system 38% cpu 2:30:22.07 total
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</code></pre><ul>
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<li>DSpace 5.8 was taking about 1 hour (or less on this laptop), so this is 2.5x longer!</li>
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</ul>
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<pre><code>$ time schedtool -D -e ~/dspace/bin/dspace index-discovery -b
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schedtool -D -e ~/dspace/bin/dspace index-discovery -b 299.53s user 69.67s system 20% cpu 30:34.47 total
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</code></pre><!-- raw HTML omitted -->
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