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<meta property="og:title" content="April, 2020" />
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<meta property="og:description" content="2020-04-02
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Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
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I updated the fifty-eight existing items on CGSpace
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Looking into the items Udana had asked about last week that were missing Altmetric donuts:
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The first is still missing its DOI, so I added it and tweeted its handle (after a few hours there was a donut with score 222)
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The second item now has a donut with score 2 since I tweeted its handle last week
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The third item now has a donut with score 1 since I tweeted it last week
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On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week
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<meta name="twitter:title" content="April, 2020"/>
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<meta name="twitter:description" content="2020-04-02
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Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
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I updated the fifty-eight existing items on CGSpace
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Looking into the items Udana had asked about last week that were missing Altmetric donuts:
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The first is still missing its DOI, so I added it and tweeted its handle (after a few hours there was a donut with score 222)
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The second item now has a donut with score 2 since I tweeted its handle last week
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The third item now has a donut with score 1 since I tweeted it last week
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On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week
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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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2>
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<p class="blog-post-meta"><time datetime="2020-04-02T10:53:24+03:00">Thu Apr 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="2020-04-02">2020-04-02</h2>
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<ul>
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<li>Maria asked me to update Charles Staver’s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
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<ul>
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<li>I updated the fifty-eight existing items on CGSpace</li>
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</ul>
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</li>
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<li>Looking into the items Udana had asked about last week that were missing Altmetric donuts:
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<ul>
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<li><a href="https://hdl.handle.net/10568/103225">The first</a> is still missing its DOI, so I added it and <a href="https://twitter.com/mralanorth/status/1245632619661766657">tweeted its handle</a> (after a few hours there was a donut with score 222)</li>
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<li><a href="https://hdl.handle.net/10568/106899">The second item</a> now has a donut with score 2 since I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a> last week</li>
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<li><a href="https://hdl.handle.net/10568/107258">The third item</a> now has a donut with score 1 since I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> last week</li>
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</ul>
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</li>
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<li>On the same note, the <a href="https://hdl.handle.net/10568/106573">one item</a> Abenet pointed out last week now has a donut with score of 104 after I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> last week</li>
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</ul>
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<ul>
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<li>Altmetric responded about <a href="https://hdl.handle.net/10568/101286">one item</a> that had no donut since at least 2019-12 and said they fixed some problems with their bot’s user agent
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<ul>
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<li>I decided to <a href="https://twitter.com/mralanorth/status/1245703049445851140">tweet the item</a>, as I can’t remember if I ever did it before</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-04-05">2020-04-05</h2>
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<ul>
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<li>Update PostgreSQL JDBC driver to version 42.2.12</li>
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</ul>
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<h2 id="2020-04-07">2020-04-07</h2>
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<ul>
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<li>Yesterday Atmire sent me their <a href="https://github.com/ilri/DSpace/pull/445">pull request for DSpace 6 modules</a></li>
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<li>Peter pointed out that some items have his ORCID identifier (<code>cg.creator.id</code>) twice
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<ul>
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<li>I think this is because my early <code>add-orcid-identifiers.py</code> script was adding identifiers to existing records without properly checking if there was already one present (at first it only checked if there was one with the exact <code>place</code> value)</li>
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<li>As a test I dropped all his ORCID identifiers and added them back with the <code>add-orcid-identifiers.py</code> script:</li>
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</ul>
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</li>
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</ul>
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<pre><code>$ psql -h localhost -U postgres dspace -c "DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value LIKE '%Ballantyne%';"
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DELETE 97
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$ ./add-orcid-identifiers-csv.py -i 2020-04-07-peter-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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</code></pre><ul>
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<li>I used this CSV with the script (all records with his name have the name standardized like this):</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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</code></pre><ul>
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<li>Then I tried another way, to identify all duplicate ORCID identifiers for a given resource ID and group them so I can see if count is greater than 1:</li>
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</ul>
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<pre><code>dspace=# \COPY (SELECT DISTINCT(resource_id, text_value) as distinct_orcid, COUNT(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 240 GROUP BY distinct_orcid ORDER BY count DESC) TO /tmp/2020-04-07-duplicate-orcids.csv WITH CSV HEADER;
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COPY 15209
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</code></pre><ul>
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<li>Of those, about nine authors had duplicate ORCID identifiers over about thirty records, so I created a CSV with all their name variations and ORCID identifiers:</li>
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</ul>
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<pre><code>dc.contributor.author,cg.creator.id
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"Ballantyne, Peter G.","Peter G. Ballantyne: 0000-0001-9346-2893"
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"Ramirez-Villegas, Julian","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Villegas-Ramirez, J","Julian Ramirez-Villegas: 0000-0002-8044-583X"
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"Ishitani, Manabu","Manabu Ishitani: 0000-0002-6950-4018"
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"Manabu, Ishitani","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Ishitani, M.","Manabu Ishitani: 0000-0002-6950-4018"
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"Buruchara, Robin A.","Robin Buruchara: 0000-0003-0934-1218"
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"Buruchara, Robin","Robin Buruchara: 0000-0003-0934-1218"
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"Jarvis, Andy","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, Andrew","Andy Jarvis: 0000-0001-6543-0798"
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"Jarvis, A.","Andy Jarvis: 0000-0001-6543-0798"
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"Tohme, Joseph M.","Joe Tohme: 0000-0003-2765-7101"
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"Hansen, James","James Hansen: 0000-0002-8599-7895"
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"Hansen, James W.","James Hansen: 0000-0002-8599-7895"
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"Asseng, Senthold","Senthold Asseng: 0000-0002-7583-3811"
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</code></pre><ul>
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<li>Then I deleted <em>all</em> their existing ORCID identifier records:</li>
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</ul>
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<pre><code>dspace=# DELETE FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=240 AND text_value SIMILAR TO '%(0000-0001-6543-0798|0000-0001-9346-2893|0000-0002-6950-4018|0000-0002-7583-3811|0000-0002-8044-583X|0000-0002-8599-7895|0000-0003-0934-1218|0000-0003-2765-7101)%';
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DELETE 994
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</code></pre><ul>
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<li>And then I added them again using the <code>add-orcid-identifiers</code> records:</li>
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</ul>
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<pre><code>$ ./add-orcid-identifiers-csv.py -i 2020-04-07-fix-duplicate-orcids.csv -db dspace -u dspace -p 'fuuu' -d
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</code></pre><ul>
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<li>I ran the fixes on DSpace Test and CGSpace as well</li>
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<li>I started testing the <a href="https://github.com/ilri/DSpace/pull/445">pull request</a> sent by Atmire yesterday
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<ul>
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<li>I notice that we now need <code>yarn</code> to build, and I need to bump the Node.js <code>engine</code> version in our Mirage 2 theme in order to get it to build on Node.js 10.x</li>
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<li>Font Awesome icons for GitHub etc weren’t loading, and after a bit of troubleshooting I replaced version 4.5.0 with 5.13.0 and to my surprise they now include Mendeley and ORCID so we can get rid of the Academicons dependency</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-04-12">2020-04-12</h2>
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<ul>
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<li>Testing the Atmire DSpace 6.3 code with a clean CGSpace DSpace 5.8 database snapshot
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<ul>
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<li>One Flyway migration failed so I had to manually remove it (and of course create the pgcrypto extension):</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 ('5.8.2015.12.03.3');
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dspace63=# CREATE EXTENSION pgcrypto;
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</code></pre><ul>
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<li>Then DSpace 6.3 started up OK and I was able to see some statistics in the Content and Usage Analysis (CUA) module, but not on community, collection, or item pages
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<ul>
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<li>I also noticed at least one of these errors in the DSpace log:</li>
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</ul>
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</li>
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</ul>
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<pre><code>2020-04-12 16:34:33,363 ERROR com.atmire.dspace.app.xmlui.aspect.statistics.editorparts.DataTableTransformer @ java.lang.IllegalArgumentException: Invalid UUID string: 1
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</code></pre><ul>
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<li>And I remembered I actually need to run the DSpace 6.4 Solr UUID migrations:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
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$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x
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</code></pre><ul>
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<li>Run system updates on DSpace Test (linode26) and reboot it</li>
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<li>More work on the DSpace 6.3 stuff, improving the GDPR consent logic to use <a href="https://github.com/chiiya/haven">haven</a> instead of cookieconsent
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<ul>
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<li>It works better by injecting the Google Analytics script after the user clicks agree, and it also has a preferences section that gets automatically injected on the privacy page!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-04-13">2020-04-13</h2>
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<ul>
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<li>I realized that <code>solr-upgrade-statistics-6x</code> only processes 100,000 records by default so I think we actually need to finish running it for all legacy Solr records before asking Atmire why CUA statlets and detailed statistics aren’t working</li>
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<li>For now I am just doing 250,000 records at a time on my local environment:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Xmx2000m -Dfile.encoding=UTF-8"
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$ ~/dspace63/bin/dspace solr-upgrade-statistics-6x -n 250000
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</code></pre><ul>
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<li>Despite running the migration for all of my local 1.5 million Solr records, I still see a few hundred thousand like <code>-1</code> and <code>0-unmigrated</code>
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<ul>
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<li>I will purge them all and try to import only a subset…</li>
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<li>After importing again I see there are indeed tens of thousands of these documents with IDs “-1” and “0”</li>
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<li>They are all <code>type: 5</code>, which is “SITE” according to <code>Constants.java</code>:</li>
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</ul>
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</li>
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</ul>
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<pre><code>/** DSpace site type */
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public static final int SITE = 5;
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</code></pre><ul>
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<li>Even after deleting those documents and re-running <code>solr-upgrade-statistics-6x</code> I still get the UUID errors when using CUA and the statlets</li>
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<li>I have sent some feedback and questions to Atmire (including about the  issue with glypicons in the header trail)</li>
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<li>In other news, my local Artifactory container stopped working for some reason so I re-created it and it seems some things have changed upstream (port 8082 for web UI?):</li>
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</ul>
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<pre><code>$ podman rm artifactory
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$ podman pull docker.bintray.io/jfrog/artifactory-oss:latest
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$ podman create --ulimit nofile=32000:32000 --name artifactory -v artifactory_data:/var/opt/jfrog/artifactory -p 8081-8082:8081-8082 docker.bintray.io/jfrog/artifactory-oss
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$ podman start artifactory
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</code></pre><h2 id="2020-04-14">2020-04-14</h2>
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<ul>
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<li>A few days ago Peter asked me to update an author’s name on CGSpace and in the controlled vocabularies:</li>
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</ul>
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<pre><code>dspace=# UPDATE metadatavalue SET text_value='Knight-Jones, Theodore J.D.' WHERE resource_type_id=2 AND metadata_field_id=3 AND text_value='Knight-Jones, T.J.D.';
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</code></pre><ul>
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<li>I updated his existing records on CGSpace, changed the controlled lists, added his ORCID identifier to the controlled list, and tagged his thirty-nine items with the ORCID iD</li>
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<li>The new DSpace 6 stuff that Atmire sent modifies the Mirage 2’s <code>pom.xml</code> to copy the each theme’s resulting <code>node_modules</code> to each theme after building and installing with <code>ant update</code> because they moved some packages from bower to npm and now reference them in <code>page-structure.xsl</code>
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<ul>
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<li>This is a good idea, because bower is no longer supported, and npm has gotten a lot better, but it causes an extra 200,000 files to get copied!</li>
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<li>Most scripts are concatenated into <code>theme.js</code> during build, so we don’t need the <code>node_modules</code> after that, but there are three scripts in <code>page-structure.xsl</code> that are not included there</li>
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<li>The scripts are a very old version of modernizr which is not even available on npm, html5shiv, and respond.js</li>
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<li>For modernizr I can simply download a static copy and put it in <code>0_CGIAR/scripts</code> and concatenate it into <code>theme.js</code></li>
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<li>For the others, I can revert to using them from bower’s <code>vendor</code> directory, which is installed by the parent XMLUI Mirage 2 theme</li>
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<li>During this process I also realized that <code>mvn clean</code> doesn’t actually clean everything, and <code>dspace/modules/xmlui-mirage2/target</code> is remaining from previous builds and contains a bunch of shit from previous builds (including all the themes which I was trying to build without!)
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<ul>
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<li>This must be a DSpace bug, but I should theoretically check on vanilla DSpace and then file a bug…</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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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/2020-04/">April, 2020</a></li>
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<li><a href="/cgspace-notes/2020-03/">March, 2020</a></li>
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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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</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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