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Code Issues Projects Releases Wiki Activity

Update notes for 2017-09-19

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Alan Orth
2017-09-19 12:53:00 +03:00
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@ -13,7 +13,7 @@
<meta property="article:published_time" content="2017-09-18T16:38:35&#43;03:00"/>
<meta property="article:modified_time" content="2017-09-18T18:05:57&#43;03:00"/>
<meta property="article:modified_time" content="2017-09-18T21:24:27&#43;03:00"/>
@ -37,9 +37,9 @@
"@type": "BlogPosting",
"headline": "CGIAR Library Migration",
"url": "https://alanorth.github.io/cgspace-notes/cgiar-library-migration/",
"wordCount": "1169",
"wordCount": "1167",
"datePublished": "2017-09-18T16:38:35&#43;03:00",
"dateModified": "2017-09-18T18:05:57&#43;03:00",
"dateModified": "2017-09-18T21:24:27&#43;03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -108,7 +108,7 @@
</header>
<p><em>Temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in <code>config.toml</code></em></p>
<p><em>Note: I&rsquo;m temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in <code>config.toml</code></em></p>
<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>
@ -129,7 +129,7 @@
<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>
<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>
</ul></li>
<li><label><input type="checkbox" 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>
<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>
<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
<ul>
@ -138,13 +138,9 @@
<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&rsquo;t want them to be competing to update the Solr index</label></li>
</ul>
<h2 id="migration">Migration</h2>
<h2 id="migration-process">Migration Process</h2>
<p>Process for the actual migration:</p>
<ul>
<li>Export all top-level communities and collections from DSpace Test:</li>
</ul>
<p><strong>Export all top-level communities and collections from DSpace Test:</strong></p>
<pre><code>$ export PATH=$PATH:/home/dspacetest.cgiar.org/bin
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2515 10947-2515/10947-2515.zip
@ -161,51 +157,50 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/105
$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
</code></pre>
<ul class="task-list">
<li>Import to CGSpace (also see <a href="http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10">notes from 2017-05-10</a>)
<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>
<ul class="task-list">
<li><label><input type="checkbox" checked disabled class="task-list-item"> Copy all exports from DSpace Test</label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Add ingestion overrides to <code>dspace.cfg</code> before import:</label></li>
</ul></li>
</ul>
<pre><code> mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
mets.dspaceAIP.ingest.crosswalk.DSPACE-ROLES = NIL
<pre><code>mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
mets.dspaceAIP.ingest.crosswalk.DSPACE-ROLES = NIL
</code></pre>
<ul class="task-list">
<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>
</ul>
<pre><code> $ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:TieredStopAtLevel=1&quot;
$ export PATH=$PATH:/home/cgspace.cgiar.org/bin
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2515/10947-2515.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2516/10947-2516.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2517/10947-2517.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2518/10947-2518.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2519/10947-2519.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2708/10947-2708.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2526/10947-2526.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2871/10947-2871.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-4467/10947-4467.zip
$ dspace packager -s -u -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-2527/10947-2527.zip
$ for item in 10947-2527/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
$ dspace packager -s -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-1/10947-1.zip
$ 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
$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
<pre><code>$ export JAVA_OPTS=&quot;-Dfile.encoding=UTF-8 -Xmx3072m -XX:-UseGCOverheadLimit -XX:+TieredCompilation -XX:TieredStopAtLevel=1&quot;
$ export PATH=$PATH:/home/cgspace.cgiar.org/bin
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2515/10947-2515.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2516/10947-2516.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2517/10947-2517.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2518/10947-2518.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2519/10947-2519.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2708/10947-2708.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2526/10947-2526.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-2871/10947-2871.zip
$ dspace packager -r -u -a -t AIP -o skipIfParentMissing=true -e aorth@mjanja.ch -p 10568/83389 10947-4467/10947-4467.zip
$ dspace packager -s -u -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-2527/10947-2527.zip
$ for item in 10947-2527/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
$ dspace packager -s -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83389 10947-1/10947-1.zip
$ 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
$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
</code></pre>
<ul class="task-list">
<li>This submits AIP hierarchies recursively (-r) and suppresses errors when an item&rsquo;s parent collection hasn&rsquo;t been created yet—for example, if the item is mapped</li>
<li>The large historic archive (<sup>10947</sup>&frasl;<sub>1</sub>) is created in several steps because it requires a lot of memory and often crashes</li>
<p>This submits AIP hierarchies recursively (-r) and suppresses errors when an item&rsquo;s parent collection hasn&rsquo;t been created yet—for example, if the item is mapped. The large historic archive (<sup>10947</sup>&frasl;<sub>1</sub>) is created in several steps because it requires a lot of memory and often crashes.</p>
<li><p>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</p>
<p><strong>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</strong></p>
<ul class="task-list">
<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Board</em> sub-community: <sup>10568</sup>&frasl;<sub>83536</sub>
<ul class="task-list">
<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Board</em> sub-community: <sup>10568</sup>&frasl;<sub>83536</sub></label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Content from <em>CGIAR System Management Board documents</em> collection (<sup>10947</sup>&frasl;<sub>4561</sub>) goes here</label></li>
<li>Import collection hierarchy first and then the items:</li>
</ul></label></li>
</ul>
<pre><code>$ dspace packager -r -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83536 10568-93760/COLLECTION@10947-4651.zip
@ -213,45 +208,42 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
</code></pre>
<ul class="task-list">
<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office</em> sub-community: <sup>10568</sup>&frasl;<sub>83537</sub></label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office</em> sub-community: <sup>10568</sup>&frasl;<sub>83537</sub>
<ul class="task-list">
<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office documents</em> collection: <sup>10568</sup>&frasl;<sub>83538</sub></label></li>
<li>Import items to collection individually in replace mode (-r) while explicitly preserving handles and ignoring parents:</li>
</ul></label></li>
</ul>
<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
</code></pre>
<ul>
<li>Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:</li>
</ul></li>
</ul>
<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>
<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) &gt; '2017-05-01T00:00:00Z');
<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) &gt; '2017-05-01T00:00:00Z');
</code></pre>
<ul>
<li>Export them from the CGIAR Library:</li>
</ul>
<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
<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
</code></pre>
<ul>
<li>Import on CGSpace:</li>
</ul>
<pre><code> $ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
<pre><code>$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
</code></pre>
<ul class="task-list">
<li><label><input type="checkbox" disabled class="task-list-item"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system&rsquo;s <code>postgres</code> user</label></li>
</ul>
<h2 id="post-migration">Post Migration</h2>
<ul class="task-list">
<li><label><input type="checkbox" disabled class="task-list-item"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system&rsquo;s <code>postgres</code> user</label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Remove ingestion overrides from <code>dspace.cfg</code></label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Reset PostgreSQL <code>max_connections</code> to 183</label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Reset PostgreSQL <code>max_connections</code> to 183</label></li>
<li><label><input type="checkbox" checked disabled class="task-list-item"> Enable nightly <code>index-discovery</code> cron job</label></li>
<li>HTTPS certificates:
@ -260,12 +252,12 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
</ul></li>
</ul>
<pre><code> $ keytool -list -keystore tomcat.keystore
$ keytool -importkeystore -srckeystore tomcat.keystore -destkeystore library.cgiar.org.p12 -deststoretype PKCS12 -srcalias tomcat
$ openssl pkcs12 -in library.cgiar.org.p12 -nokeys -out library.cgiar.org.crt.pem
$ openssl pkcs12 -in library.cgiar.org.p12 -nodes -nocerts -out library.cgiar.org.key.pem
$ wget https://certs.godaddy.com/repository/gdroot-g2.crt https://certs.godaddy.com/repository/gdig2.crt.pem
$ cat library.cgiar.org.crt.pem gdig2.crt.pem &gt; library.cgiar.org-chained.pem
<pre><code>$ keytool -list -keystore tomcat.keystore
$ keytool -importkeystore -srckeystore tomcat.keystore -destkeystore library.cgiar.org.p12 -deststoretype PKCS12 -srcalias tomcat
$ openssl pkcs12 -in library.cgiar.org.p12 -nokeys -out library.cgiar.org.crt.pem
$ openssl pkcs12 -in library.cgiar.org.p12 -nodes -nocerts -out library.cgiar.org.key.pem
$ wget https://certs.godaddy.com/repository/gdroot-g2.crt https://certs.godaddy.com/repository/gdig2.crt.pem
$ cat library.cgiar.org.crt.pem gdig2.crt.pem &gt; library.cgiar.org-chained.pem
</code></pre>
<ul class="task-list">
@ -275,18 +267,15 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
<li>CNAME: cgspace.cgiar.org</li>
</ul></label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Re-deploy DSpace from freshly built <code>5_x-prod</code> branch</label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Run system updates and reboot server</label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Switch to Let&rsquo;s Encrypt HTTPS certificates (after DNS is updated and server isn&rsquo;t busy)</label></li>
<li><label><input type="checkbox" disabled class="task-list-item"> Switch to Let&rsquo;s Encrypt HTTPS certificates (after DNS is updated and server isn&rsquo;t busy):</label></li>
</ul>
<pre><code>$ sudo systemctl stop tomcat7
$ ./letsencrypt-auto certonly --standalone -d library.cgiar.org
</code></pre>
<ul class="task-list">
<li><label><input type="checkbox" disabled class="task-list-item"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</label></li>
</ul>
<h2 id="troubleshooting">Troubleshooting</h2>
<h3 id="foreign-key-error-in-dspace-cleanup">Foreign Key Error in <code>dspace cleanup</code></h3>