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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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<h2 id="2020-04-17">2020-04-17</h2>
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<ul>
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<li>Atmire responded to some of the issues I raised earlier this week about the DSpace 6 pull request
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<ul>
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<li>They said they don’t think the glyphicon encoding issue is due to their changes, but I built a new clean version of the vanilla <code>6_x-dev</code> branch from before their pull request and it <em>does not</em> have the encoding issue in the Mirage 2 header trails</li>
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<li>Also, they said we need to use something called <code>AtomicStatisticsUpdateCLI</code> to do the Solr legacy integer ID to UUID conversion so I asked for more information about that workflow</li>
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</ul>
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</li>
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</ul>
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<h2 id="2020-04-20">2020-04-20</h2>
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<ul>
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<li>Looking into a high rate of outgoing bandwidth from yesterday on CGSpace (linode18):</li>
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</ul>
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<pre><code># cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "19/Apr/2020:0[6789]" | goaccess --log-format=COMBINED -
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</code></pre><ul>
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<li>One host in Russia (91.241.19.70) download 23GiB over those few hours in the morning
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<ul>
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<li>It looks like all the requests were for one single item’s bitstreams:</li>
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</ul>
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</li>
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</ul>
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<pre><code># grep -c 91.241.19.70 /var/log/nginx/access.log.1
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8900
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# grep 91.241.19.70 /var/log/nginx/access.log.1 | grep -c '10568/35187'
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8900
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</code></pre><ul>
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<li>I thought the host might have been Yandex misbehaving, but its user agent is:</li>
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</ul>
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<pre><code>Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_3; nl-nl) AppleWebKit/527 (KHTML, like Gecko) Version/3.1.1 Safari/525.20
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</code></pre><ul>
|
|
<li>I will purge that IP from the Solr statistics using my <code>check-spider-ip-hits.sh</code> script:</li>
|
|
</ul>
|
|
<pre><code>$ ./check-spider-ip-hits.sh -d -f /tmp/ip -p
|
|
(DEBUG) Using spider IPs file: /tmp/ip
|
|
(DEBUG) Checking for hits from spider IP: 91.241.19.70
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Purging 8909 hits from 91.241.19.70 in statistics
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|
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|
Total number of bot hits purged: 8909
|
|
</code></pre><ul>
|
|
<li>While investigating that I noticed ORCID identifiers missing from a few authors names, so I added them with my <code>add-orcid-identifiers.py</code> script:</li>
|
|
</ul>
|
|
<pre><code>$ ./add-orcid-identifiers-csv.py -i 2020-04-20-add-orcids.csv -db dspace -u dspace -p 'fuuu' -d
|
|
</code></pre><ul>
|
|
<li>The contents of <code>2020-04-20-add-orcids.csv</code> was:</li>
|
|
</ul>
|
|
<pre><code>dc.contributor.author,cg.creator.id
|
|
"Schut, Marc","Marc Schut: 0000-0002-3361-4581"
|
|
"Schut, M.","Marc Schut: 0000-0002-3361-4581"
|
|
"Kamau, G.","Geoffrey Kamau: 0000-0002-6995-4801"
|
|
"Kamau, G","Geoffrey Kamau: 0000-0002-6995-4801"
|
|
"Triomphe, Bernard","Bernard Triomphe: 0000-0001-6657-3002"
|
|
"Waters-Bayer, Ann","Ann Waters-Bayer: 0000-0003-1887-7903"
|
|
"Klerkx, Laurens","Laurens Klerkx: 0000-0002-1664-886X"
|
|
</code></pre><ul>
|
|
<li>I confirmed some of the authors’ names from the report itself, then by looking at their profiles on ORCID.org</li>
|
|
<li>Add new ILRI subject “COVID19” to the <code>5_x-prod</code> branch</li>
|
|
<li>Add new CCAFS Phase II project tags to the <code>5_x-prod</code> branch</li>
|
|
<li>I will deploy these to CGSpace in the next few days</li>
|
|
</ul>
|
|
<h2 id="2020-04-24">2020-04-24</h2>
|
|
<ul>
|
|
<li>Atmire responded to my ticket about the  issue with glypicons and said their test server does not show this same issue
|
|
<ul>
|
|
<li>They asked if I am using the <code>JAVA_OPTS=-Dfile.encoding=UTF-8</code> when building DSpace and running Tomcat</li>
|
|
<li>I set it explicitly for Maven and Ant just now (and cleared all XMLUI caches) but the issue is still there</li>
|
|
<li>I asked them if they are building on macOS or Linux, and which Node.js version (I’m using 10.20.1, which is the current LTS branch).</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2020-04-25">2020-04-25</h2>
|
|
<ul>
|
|
<li>I researched a bit more about the  issue with glypicons and realized it’s due to <a href="https://github.com/twbs/bootstrap-sass/issues/919">a bug in libsass</a>
|
|
<ul>
|
|
<li>I have Ruby sass version 3.4.25 installed in my local environment, but DSpace Mirage 2 is supposed to build with 3.3.14</li>
|
|
<li>Downgrading the version fixes it, though I wonder: why did I not have this issue on the <code>6.x-dev</code> branch before Atmire’s pull request, and also on <code>5_x-prod</code> where I’ve been building for a few months here…</li>
|
|
</ul>
|
|
</li>
|
|
<li>I deployed the latest <code>5_x-prod</code> branch on CGSpace (linode18), ran all updates, and rebooted the server
|
|
<ul>
|
|
<li>This includes the “COVID19” ILRI subject, the new CCAFS Phase II project tags, and the changes to an ILRI author name</li>
|
|
<li>After restarting the server I had to restart Tomcat three times before all Solr statistics cores loaded properly.</li>
|
|
<li>After that I started a full Discovery reindexing to pick up some author changes I made last week:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
|
|
$ time chrt -i 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
|
|
</code></pre><ul>
|
|
<li>I ran the <code>dspace cleanup -v</code> process on CGSpace and got an error:</li>
|
|
</ul>
|
|
<pre><code>Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
|
|
Detail: Key (bitstream_id)=(184980) is still referenced from table "bundle".
|
|
</code></pre><ul>
|
|
<li>The solution is, as always:</li>
|
|
</ul>
|
|
<pre><code>$ psql -d dspace -U dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (183996);'
|
|
UPDATE 1
|
|
</code></pre><ul>
|
|
<li>I spent some time working on the XMLUI themes in DSpace 6
|
|
<ul>
|
|
<li>Atmire’s pull request modifies <code>pom.xml</code> to <em>not</em> exclude <code>node_modules</code>, which means an extra ~260,000 files get copied to our installation folder because of all the themes</li>
|
|
<li>I worked on the <code>Gruntfile.js</code> to copy Font Awesome and Bootstrap glyphicon fonts out of <code>node_modules</code> and into <code>fonts</code> at build time, but still <code>jquery-ui.min.css</code> was being referenced as a <code>url()</code> in CSS</li>
|
|
<li>SASS can include imported CSS in your compiled CSS—instead of including an <code>@import url(..)</code> if you import it without the “.css”, but our version of Ruby SASS doesn’t support that</li>
|
|
<li>I hacked <code>Gruntfile.js</code> to use <code>dart-sass</code> instead of Ruby <code>compass</code> (including installing compass’s mixins via npm!) but then <a href="https://github.com/sass/dart-sass/issues/345">dart-sass converts all the glyphicon ASCII escape codes to Unicode literals</a> and they show up garbled in Firefox</li>
|
|
<li>I tried to use <code>node-sass</code> instead of dart-sass and it doesn’t replace the ASCII escapes with literals, but then I get the the  issue with the glyphicon in the header trail again! Back to square one!</li>
|
|
<li>So that was a waste of five hours…</li>
|
|
<li>I might just leave this <a href="https://github.com/twbs/bootstrap-sass/issues/919">tiny hack</a> in <code>0_CGIAR/styles/_style.scss</code> to override this and be done with it:</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<pre><code>.breadcrumb > li + li:before {
|
|
content: "/\00a0";
|
|
}
|
|
</code></pre><h2 id="2020-04-27">2020-04-27</h2>
|
|
<ul>
|
|
<li>File an issue on DSpace Jira about the <a href="https://jira.lyrasis.org/browse/DS-4492"><code>mvn clean</code> task not removing the Mirage 2 target directory</a></li>
|
|
<li>My changes to DSpace XMLUI Mirage 2 build process mean that we don’t need Ruby gems at all anymore! We can completely build without them!</li>
|
|
</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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|
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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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