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<h1 class="blog-title"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">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"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
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<p class="blog-post-meta"><time datetime="2017-09-18T16:38:35+03:00">Mon Sep 18, 2017</time> by Alan Orth in
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<i class="fa fa-folder" aria-hidden="true"></i> <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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<p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p>
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<p></p>
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<h2 id="pre-migration-technical-todos">Pre-migration Technical TODOs</h2>
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<p>Things that need to happen before the migration:</p>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create top-level community on CGSpace to hold the CGIAR Library content: <code>10568/83389</code>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Update nginx redirects in ansible templates</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Update handle in DSpace XMLUI config</label></li>
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</ul></label></li>
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<li>Set up nginx redirects for URLs like:
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> <a href="https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf">https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf</a></label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> <a href="https://library.cgiar.org/handle/10947/4258">https://library.cgiar.org/handle/10947/4258</a></label></li>
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</ul></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Merge <a href="https://github.com/ilri/DSpace/pull/339">#339</a> to <code>5_x-prod</code> branch and rebuild DSpace</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Increase <code>max_connections</code> in <code>/etc/postgresql/9.5/main/postgresql.conf</code> by ~10
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<ul>
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<li><code>SELECT * FROM pg_stat_activity;</code> seems to show ~6 extra connections used by the command line tools during import</li>
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</ul></label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Temporarily disable nightly <code>index-discovery</code> cron job because the import process will be taking place during some of this time and I don’t want them to be competing to update the Solr index</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Copy HTTPS certificate key pair from CGIAR Library server’s Tomcat keystore:</label></li>
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</ul>
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<pre><code>$ keytool -list -keystore tomcat.keystore
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$ keytool -importkeystore -srckeystore tomcat.keystore -destkeystore library.cgiar.org.p12 -deststoretype PKCS12 -srcalias tomcat
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$ openssl pkcs12 -in library.cgiar.org.p12 -nokeys -out library.cgiar.org.crt.pem
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$ openssl pkcs12 -in library.cgiar.org.p12 -nodes -nocerts -out library.cgiar.org.key.pem
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$ wget https://certs.godaddy.com/repository/gdroot-g2.crt https://certs.godaddy.com/repository/gdig2.crt.pem
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$ cat library.cgiar.org.crt.pem gdig2.crt.pem > library.cgiar.org-chained.pem
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</code></pre>
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<h2 id="migration-process">Migration Process</h2>
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<p><strong>Export all top-level communities and collections from DSpace Test:</strong></p>
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<pre><code>$ export PATH=$PATH:/home/dspacetest.cgiar.org/bin
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2515 10947-2515/10947-2515.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2516 10947-2516/10947-2516.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2517 10947-2517/10947-2517.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2518 10947-2518/10947-2518.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2519 10947-2519/10947-2519.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2708 10947-2708/10947-2708.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2526 10947-2526/10947-2526.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2871 10947-2871/10947-2871.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2527 10947-2527/10947-2527.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93759 10568-93759/10568-93759.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/10568-93760.zip
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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</code></pre>
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<p><strong>Import to CGSpace (also see <a href="http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10">notes from 2017-05-10</a>):</strong></p>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Copy all exports from DSpace Test</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Add ingestion overrides to <code>dspace.cfg</code> before import:</label></li>
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</ul>
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<pre><code>mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
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mets.dspaceAIP.ingest.crosswalk.DSPACE-ROLES = NIL
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</code></pre>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Import communities and collections, paying attention to options to skip missing parents and ignore handles:</label></li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
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$ export PATH=$PATH:/home/cgspace.cgiar.org/bin
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2515/10947-2515.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2516/10947-2516.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2517/10947-2517.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2518/10947-2518.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2519/10947-2519.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2708/10947-2708.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2526/10947-2526.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2871/10947-2871.zip
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$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-4467/10947-4467.zip
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$ dspace packager -s -u -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-2527/10947-2527.zip
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$ for item in 10947-2527/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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$ dspace packager -s -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-1/10947-1.zip
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$ for collection in 10947-1/COLLECTION@10947-*; do dspace packager -s -o ignoreHandle=false -t AIP -e aorth@mjanja.ch -p 10947/1 $collection; done
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$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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</code></pre>
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<p>This submits AIP hierarchies recursively (-r) and suppresses errors when an item’s parent collection hasn’t been created yet—for example, if the item is mapped. The large historic archive (<sup>10947</sup>⁄<sub>1</sub>) is created in several steps because it requires a lot of memory and often crashes.</p>
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<p><strong>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</strong></p>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Board</em> sub-community: <code>10568/83536</code>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Content from <em>CGIAR System Management Board documents</em> collection (<code>10947/4561</code>) goes here</label></li>
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<li>Import collection hierarchy first and then the items:</li>
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</ul></label></li>
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</ul>
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<pre><code>$ dspace packager -r -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83536 10568-93760/COLLECTION@10947-4651.zip
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$ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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</code></pre>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office</em> sub-community: <code>10568/83537</code>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office documents</em> collection: <code>10568/83538</code></label></li>
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<li>Import items to collection individually in replace mode (-r) while explicitly preserving handles and ignoring parents:</li>
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</ul></label></li>
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</ul>
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<pre><code>$ for item in 10568-93759/ITEM@10947-46*; do dspace packager -r -t AIP -o ignoreHandle=false -o ignoreParent=true -e aorth@mjanja.ch -p 10568/83538 $item; done
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</code></pre>
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<p><strong>Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:</strong></p>
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<pre><code>dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
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</code></pre>
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<ul>
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<li>Export them from the CGIAR Library:</li>
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</ul>
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<pre><code># for handle in 10947/4658 10947/4659 10947/4660 10947/4661 10947/4665 10947/4664 10947/4666 10947/4669; do /usr/local/dspace/bin/dspace packager -d -a -t AIP -e m.marus@cgiar.org -i $handle ${handle}.zip; done
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</code></pre>
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<ul>
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<li>Import on CGSpace:</li>
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</ul>
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<pre><code>$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
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</code></pre>
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<h2 id="post-migration">Post Migration</h2>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system’s <code>postgres</code> user</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Remove ingestion overrides from <code>dspace.cfg</code></label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Reset PostgreSQL <code>max_connections</code> to 183</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Enable nightly <code>index-discovery</code> cron job</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Adjust CGSpace’s <code>handle-server/config.dct</code> to add the new prefix alongside our existing 10568, ie:</label></li>
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</ul>
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<pre><code>"server_admins" = (
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"300:0.NA/10568"
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"300:0.NA/10947"
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)
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"replication_admins" = (
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"300:0.NA/10568"
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"300:0.NA/10947"
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)
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"backup_admins" = (
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"300:0.NA/10568"
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"300:0.NA/10947"
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)
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</code></pre>
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<p>I had been regenerated the <code>sitebndl.zip</code> file on the CGIAR Library server and sent it to the Handle.net admins but they said that there were mismatches between the public and private keys, which I suspect is due to <code>make-handle-config</code> not being very flexible. After discussing our scenario with the Handle.net admins they said we actually don’t need to send an updated <code>sitebndl.zip</code> for this type of change, and the above <code>config.dct</code> edits are all that is required. I guess they just did something on their end by setting the authoritative IP address for the 10947 prefix to be the same as ours…</p>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Update DNS records:
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<ul>
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<li>CNAME: cgspace.cgiar.org</li>
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</ul></label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Re-deploy DSpace from freshly built <code>5_x-prod</code> branch</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Run system updates and reboot server</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Switch to Let’s Encrypt HTTPS certificates (after DNS is updated and server isn’t busy):</label></li>
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</ul>
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<pre><code>$ sudo systemctl stop nginx
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$ /opt/certbot-auto certonly --standalone -d library.cgiar.org
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$ sudo systemctl start nginx
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</code></pre>
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<h2 id="troubleshooting">Troubleshooting</h2>
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<h3 id="foreign-key-error-in-dspace-cleanup">Foreign Key Error in <code>dspace cleanup</code></h3>
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<p>The cleanup script is sometimes used during import processes to clean the database and assetstore after failed AIP imports. If you see the following error with <code>dspace cleanup -v</code>:</p>
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<pre><code>Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
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Detail: Key (bitstream_id)=(119841) is still referenced from table "bundle".
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</code></pre>
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<p>The solution is to set the <code>primary_bitstream_id</code> to NULL in PostgreSQL:</p>
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<pre><code>dspace=# update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (119841);
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</code></pre>
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<h3 id="psqlexception-during-aip-ingest">PSQLException During AIP Ingest</h3>
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<p>After a few rounds of ingesting—possibly with failures—you might end up with inconsistent IDs in the database. In this case, during AIP ingest of a single collection in submit mode (-s):</p>
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<pre><code>org.dspace.content.packager.PackageValidationException: Exception while ingesting 10947-2527/10947-2527.zip, Reason: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
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Detail: Key (handle_id)=(86227) already exists.
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</code></pre>
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<p>The normal solution is to run the <code>update-sequences.sql</code> script (with Tomcat shut down) but it doesn’t seem to work in this case. Finding the maximum <code>handle_id</code> and manually updating the sequence seems to work:</p>
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<pre><code>dspace=# select * from handle where handle_id=(select max(handle_id) from handle);
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dspace=# select setval('handle_seq',86873);
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</code></pre>
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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/2018-01/">January, 2018</a></li>
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<li><a href="/cgspace-notes/2017-12/">December, 2017</a></li>
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<li><a href="/cgspace-notes/2017-11/">November, 2017</a></li>
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<li><a href="/cgspace-notes/2017-10/">October, 2017</a></li>
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<li><a href="/cgspace-notes/cgiar-library-migration/">CGIAR Library 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> <!-- /.container -->
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<footer class="blog-footer">
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<p>
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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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