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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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" />
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<meta property="og:type" content="article" />
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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 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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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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"@type": "BlogPosting",
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"headline": "February, 2020",
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"author": {
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2020-02/">
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<title>February, 2020 | CGSpace Notes</title>
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<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.90e14c13cee52929ac33e1c21694a3cc95063a194eb22aad9f7976434e1a9125.js" integrity="sha256-kOFME87lKSmsM+HCFpSjzJUGOhlOsiqtn3l2Q04akSU=" crossorigin="anonymous"></script>
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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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<article class="blog-post">
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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, and OAI are working, but rest is not starting up</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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<!-- raw HTML omitted -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2020-02/">February, 2020</a></li>
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<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
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<li><a href="/cgspace-notes/2019-12/">December, 2019</a></li>
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<li><a href="/cgspace-notes/2019-11/">November, 2019</a></li>
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<li><a href="/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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</aside>
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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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</p>
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<p>
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<a href="#">Back to top</a>
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