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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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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-11/">November, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-11-01T09:21:00+03:00">Tue Nov 01, 2016</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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<h2 id="2016-11-01">2016-11-01</h2>
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<ul>
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<li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
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</ul>
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<p><img src="2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
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<h2 id="2016-11-02">2016-11-02</h2>
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<ul>
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<li>Migrate DSpace Test to DSpace 5.5 (<a href="https://gist.github.com/alanorth/61013895c6efe7095d7f81000953d1cf">notes</a>)</li>
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<li>Run all updates on DSpace Test and reboot the server</li>
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<li>Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (<a href="https://github.com/ilri/DSpace/issues/63">#63</a>)</li>
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<li>Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes</li>
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<li>At the end it appeared to finish correctly but there were lots of errors right after it finished:</li>
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</ul>
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<pre><code>2016-11-02 15:09:48,578 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76454 to Index
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2016-11-02 15:09:48,584 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/3202 to Index
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2016-11-02 15:09:48,589 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76455 to Index
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2016-11-02 15:09:48,590 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/51693 to Index
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2016-11-02 15:09:48,590 INFO org.dspace.discovery.IndexClient @ Done with indexing
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2016-11-02 15:09:48,600 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76456 to Index
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2016-11-02 15:09:48,613 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/55536 to Index
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2016-11-02 15:09:48,616 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76457 to Index
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2016-11-02 15:09:48,634 ERROR com.atmire.dspace.discovery.AtmireSolrService @
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java.lang.NullPointerException
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at org.dspace.discovery.SearchUtils.getDiscoveryConfiguration(SourceFile:57)
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at org.dspace.discovery.SolrServiceImpl.buildDocument(SolrServiceImpl.java:824)
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at com.atmire.dspace.discovery.AtmireSolrService.indexContent(AtmireSolrService.java:821)
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at com.atmire.dspace.discovery.AtmireSolrService.updateIndex(AtmireSolrService.java:898)
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at org.dspace.discovery.SolrServiceImpl.createIndex(SolrServiceImpl.java:370)
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at org.dspace.storage.rdbms.DatabaseUtils$ReindexerThread.run(DatabaseUtils.java:945)
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</code></pre>
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<ul>
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<li>DSpace is still up, and a few minutes later I see the default DSpace indexer is still running</li>
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<li>Sure enough, looking back before the first one finished, I see output from both indexers interleaved in the log:</li>
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</ul>
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<pre><code>2016-11-02 15:09:28,545 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/47242 to Index
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2016-11-02 15:09:28,633 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/60785 to Index
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2016-11-02 15:09:28,678 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55695 of 55722): 43557
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2016-11-02 15:09:28,688 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55703 of 55722): 34476
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</code></pre>
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<ul>
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<li>I will raise a ticket with Atmire to ask them</li>
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</ul>
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<h2 id="2016-11-06">2016-11-06</h2>
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<ul>
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<li>After re-deploying and re-indexing I didn’t see the same issue, and the indexing completed in 85 minutes, which is about how long it is supposed to take</li>
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</ul>
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<h2 id="2016-11-07">2016-11-07</h2>
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<ul>
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<li>Horrible one liner to get Linode ID from certain Ansible host vars:</li>
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</ul>
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<pre><code>$ grep -A 3 contact_info * | grep -E "(Orth|Sisay|Peter|Daniel|Tsega)" | awk -F'-' '{print $1}' | grep linode | uniq | xargs grep linode_id
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</code></pre>
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<ul>
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<li>I noticed some weird CRPs in the database, and they don’t show up in Discovery for some reason, perhaps the <code>:</code></li>
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<li>I’ll export these and fix them in batch:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=230 group by text_value order by count desc) to /tmp/crp.csv with csv;
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COPY 22
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</code></pre>
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<ul>
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<li>Test running the replacements:</li>
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</ul>
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<pre><code>$ ./fix-metadata-values.py -i /tmp/CRPs.csv -f cg.contributor.crp -t correct -m 230 -d dspace -u dspace -p 'fuuu'
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</code></pre>
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<ul>
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<li>Add <code>AMR</code> to ILRI subjects and remove one duplicate instance of IITA in author affiliations controlled vocabulary (<a href="https://github.com/ilri/DSpace/pull/288">#288</a>)</li>
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</ul>
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<h2 id="2016-11-08">2016-11-08</h2>
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<ul>
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<li>Atmire’s Listings and Reports module seems to be broken on DSpace 5.5</li>
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</ul>
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<p><img src="2016/11/listings-and-reports-55.png" alt="Listings and Reports broken in DSpace 5.5" /></p>
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<ul>
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<li>I’ve filed a ticket with Atmire</li>
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<li>Thinking about batch updates for ORCIDs and authors</li>
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<li>Playing with <a href="https://github.com/moonlitesolutions/SolrClient">SolrClient</a> in Python to query Solr</li>
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<li>All records in the authority core are either <code>authority_type:orcid</code> or <code>authority_type:person</code></li>
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<li>There is a <code>deleted</code> field and all items seem to be <code>false</code>, but might be important sanity check to remember</li>
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<li>The way to go is probably to have a CSV of author names and authority IDs, then to batch update them in PostgreSQL</li>
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<li>Dump of the top ~200 authors in CGSpace:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=3 group by text_value order by count desc limit 210) to /tmp/210-authors.csv with csv;
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</code></pre>
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<h2 id="2016-11-09">2016-11-09</h2>
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<ul>
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<li>CGSpace crashed so I quickly ran system updates, applied one or two of the waiting changes from the <code>5_x-prod</code> branch, and rebooted the server</li>
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<li>The error was <code>Timeout waiting for idle object</code> but I haven’t looked into the Tomcat logs to see what happened</li>
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<li>Also, I ran the corrections for CRPs from earlier this week</li>
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</ul>
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<h2 id="2016-11-10">2016-11-10</h2>
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<ul>
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<li>Helping Megan Zandstra and CIAT with some questions about the REST API</li>
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<li>Playing with <code>find-by-metadata-field</code>, this works:</li>
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</ul>
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<pre><code>$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS"}'
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</code></pre>
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<ul>
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<li>But the results are deceiving because metadata fields can have text languages and your query must match exactly!</li>
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</ul>
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<pre><code>dspace=# select distinct text_value, text_lang from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
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text_value | text_lang
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------------+-----------
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SEEDS |
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SEEDS |
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SEEDS | en_US
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(3 rows)
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</code></pre>
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<ul>
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<li>So basically, the text language here could be null, blank, or en_US</li>
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<li>To query metadata with these properties, you can do:</li>
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</ul>
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<pre><code>$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS"}' | jq length
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55
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$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":""}' | jq length
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34
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$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":"en_US"}' | jq length
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</code></pre>
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<ul>
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<li>The results (55+34=89) don’t seem to match those from the database:</li>
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</ul>
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<pre><code>dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang is null;
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count
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-------
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15
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dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='';
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count
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-------
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4
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dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='en_US';
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count
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-------
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66
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</code></pre>
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<ul>
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<li>So, querying from the API I get 55 + 34 = 89 results, but the database actually only has 85…</li>
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<li>And the <code>find-by-metadata-field</code> endpoint doesn’t seem to have a way to get all items with the field, or a wildcard value</li>
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<li>I’ll ask a question on the dspace-tech mailing list</li>
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<li>And speaking of <code>text_lang</code>, this is interesting:</li>
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</ul>
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<pre><code>dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2;
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text_lang
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-----------
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ethnob
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en
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spa
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EN
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es
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frn
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en_
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en_US
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EN_US
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eng
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en_U
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fr
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(14 rows)
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</code></pre>
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<ul>
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<li>Generate a list of all these so I can fix them in batch:</li>
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</ul>
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<pre><code>dspace=# \copy (select distinct text_lang, count(*) from metadatavalue where resource_type_id=2 group by text_lang order by count desc) to /tmp/text-langs.csv with csv;
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COPY 14
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</code></pre>
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<ul>
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<li>Perhaps we need to fix them all in batch, or experiment with fixing only certain metadatavalues:</li>
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</ul>
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<pre><code>dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
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UPDATE 85
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</code></pre>
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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/2016-11/">November, 2016</a></li>
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<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
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<li><a href="/cgspace-notes/2016-09/">September, 2016</a></li>
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<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
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<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
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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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