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<meta property="og:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace." />
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<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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<title>May, 2017 | CGSpace Notes</title>
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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/2017-05/">May, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-05-01T16:21:52+02:00">Mon May 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-05-01">2017-05-01</h2>
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<ul>
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<li>ICARDA apparently started working on CG Core on their MEL repository</li>
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<li>They have done a few <code>cg.*</code> fields, but not very consistent and even copy some of CGSpace items:
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<ul>
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<li><a href="https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full">https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full</a></li>
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<li><a href="https://cgspace.cgiar.org/handle/10568/73683">https://cgspace.cgiar.org/handle/10568/73683</a></li>
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</ul></li>
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</ul>
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<h2 id="2017-05-02">2017-05-02</h2>
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<ul>
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<li>Atmire got back about the Workflow Statistics issue, and apparently it’s a bug in the CUA module so they will send us a pull request</li>
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</ul>
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<h2 id="2017-05-04">2017-05-04</h2>
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<ul>
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<li>Sync DSpace Test with database and assetstore from CGSpace</li>
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<li>Re-deploy DSpace Test with Atmire’s CUA patch for workflow statistics, run system updates, and restart the server</li>
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<li>Now I can see the workflow statistics and am able to select users, but everything returns 0 items</li>
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<li>Megan says there are still some mapped items are not appearing since last week, so I forced a full <code>index-discovery -b</code></li>
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<li>Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: <a href="https://cgspace.cgiar.org/handle/10568/80731">https://cgspace.cgiar.org/handle/10568/80731</a></li>
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</ul>
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<h2 id="2017-05-05">2017-05-05</h2>
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<ul>
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<li>Discovered that CGSpace has ~700 items that are missing the <code>cg.identifier.status</code> field</li>
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<li>Need to perhaps try using the “required metadata” curation task to find fields missing these items:</li>
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</ul>
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<pre><code>$ [dspace]/bin/dspace curate -t requiredmetadata -i 10568/1 -r - > /tmp/curation.out
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</code></pre>
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<ul>
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<li>It seems the curation task dies when it finds an item which has missing metadata</li>
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</ul>
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<h2 id="2017-05-06">2017-05-06</h2>
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<ul>
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<li>Add “Blog Post” to <code>dc.type</code></li>
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<li>Create ticket on Atmire tracker to ask about commissioning them to develop the feature to expose ORCID via REST/OAI: <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=510">https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=510</a></li>
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<li>According to the <a href="https://wiki.duraspace.org/display/DSDOC5x/Curation+System">DSpace curation docs</a> the fact that the <code>requiredmetadata</code> curation task stops when it finds a missing metadata field is by design</li>
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</ul>
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<h2 id="2017-05-07">2017-05-07</h2>
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<ul>
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<li>Testing one replacement for CCAFS Flagships (<code>cg.subject.ccafs</code>), first changed in the submission forms, and then in the database:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i ccafs-flagships-may7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
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</code></pre>
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<ul>
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<li>Also, CCAFS wants to re-order their flagships to prioritize the Phase II ones</li>
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<li>Waiting for feedback from CCAFS, then I can merge <a href="https://github.com/ilri/DSpace/pull/320">#320</a></li>
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</ul>
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<h2 id="2017-05-08">2017-05-08</h2>
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<ul>
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<li>Start working on CGIAR Library migration</li>
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<li>We decided to use AIP export to preserve the hierarchies and handles of communities and collections</li>
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<li>When ingesting some collections I was getting <code>java.lang.OutOfMemoryError: GC overhead limit exceeded</code>, which can be solved by disabling the GC timeout with <code>-XX:-UseGCOverheadLimit</code></li>
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<li>Other times I was getting an error about heap space, so I kept bumping the RAM allocation by 512MB each time (up to 4096m!) it crashed</li>
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<li>This leads to tens of thousands of abandoned files in the assetstore, which need to be cleaned up using <code>dspace cleanup -v</code>, or else you’ll run out of disk space</li>
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<li>In the end I realized it’s better to use submission mode (<code>-s</code>) to ingest the community object as a single AIP without its children, followed by each of the collections:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx2048m -XX:-UseGCOverheadLimit"
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$ [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e some@user.com -p 10568/87775 /home/aorth/10947-1/10947-1.zip
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$ for collection in /home/aorth/10947-1/COLLECTION@10947-*; do [dspace]/bin/dspace packager -s -o ignoreHandle=false -t AIP -e aorth@mjanja.ch -p 10947/1 $collection; done
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$ for item in /home/aorth/10947-1/ITEM@10947-*; do [dspace]/bin/dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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</code></pre>
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<ul>
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<li>Note that in submission mode DSpace ignores the handle specified in <code>mets.xml</code> in the zip file, so you need to turn that off with <code>-o ignoreHandle=false</code></li>
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<li>The <code>-u</code> option supresses prompts, to allow the process to run without user input</li>
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<li>Give feedback to CIFOR about their data quality:
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<ul>
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<li>Suggestion: uppercase dc.subject, cg.coverage.region, and cg.coverage.subregion in your crosswalk so they match CGSpace and therefore can be faceted / reported on easier</li>
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<li>Suggestion: use CGSpace’s CRP names (cg.contributor.crp), see: dspace/config/input-forms.xml</li>
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<li>Suggestion: clean up duplicates and errors in funders, perhaps use a controlled vocabulary like ours, see: dspace/config/controlled-vocabularies/dc-description-sponsorship.xml</li>
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<li>Suggestion: use dc.type “Blog Post” instead of “Blog” for your blog post items (we are also adding a “Blog Post” type to CGSpace soon)</li>
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<li>Question: many of your items use dc.document.uri AND cg.identifier.url with the same text value?</li>
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</ul></li>
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<li>Help Marianne from WLE with an Open Search query to show the latest WLE CRP outputs: <a href="https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC">https://cgspace.cgiar.org/open-search/discover?query=crpsubject:WATER%2C+LAND+AND+ECOSYSTEMS&sort_by=2&order=DESC</a></li>
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<li>This uses the webui’s item list sort options, see <code>webui.itemlist.sort-option</code> in <code>dspace.cfg</code></li>
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<li>The equivalent Discovery search would be: <a href="https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc">https://cgspace.cgiar.org/discover?filtertype_1=crpsubject&filter_relational_operator_1=equals&filter_1=WATER%2C+LAND+AND+ECOSYSTEMS&submit_apply_filter=&query=&rpp=10&sort_by=dc.date.issued_dt&order=desc</a></li>
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</ul>
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<h2 id="2017-05-09">2017-05-09</h2>
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<ul>
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<li>The CGIAR Library metadata has some blank metadata values, which leads to <code>|||</code> in the Discovery facets</li>
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<li>Clean these up in the database using:</li>
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</ul>
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<pre><code>dspace=# delete from metadatavalue where resource_type_id=2 and text_value=''
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</code></pre>
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<ul>
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<li>I ended up running into issues during data cleaning and decided to wipe out the entire community and re-sync DSpace Test assetstore and database from CGSpace rather than waiting for the cleanup task to clean up</li>
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<li>Hours into the re-ingestion I ran into more errors, and had to erase everything and start over <em>again</em>!</li>
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<li>Now, no matter what I do I keep getting foreign key errors…</li>
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</ul>
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<pre><code>Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "handle_pkey"
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Detail: Key (handle_id)=(80928) already exists.
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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 offset-sm-1 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/2017-05/">May, 2017</a></li>
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<li><a href="/cgspace-notes/2017-04/">April, 2017</a></li>
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<li><a href="/cgspace-notes/2017-03/">March, 2017</a></li>
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<li><a href="/cgspace-notes/2017-02/">February, 2017</a></li>
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<li><a href="/cgspace-notes/2017-01/">January, 2017</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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