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334 lines
13 KiB
HTML
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta property="og:title" content="May, 2018" />
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<meta property="og:description" content="2018-05-01
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I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
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http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
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http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
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Then I reduced the JVM heap size from 6144 back to 5120m
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Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-05/" />
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<meta property="article:published_time" content="2018-05-01T16:43:54+03:00"/>
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<meta property="article:modified_time" content="2018-05-06T17:13:31+03:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="May, 2018"/>
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<meta name="twitter:description" content="2018-05-01
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I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
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http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E
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http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
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Then I reduced the JVM heap size from 6144 back to 5120m
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Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
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"/>
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<meta name="generator" content="Hugo 0.40.2" />
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<script type="application/ld+json">
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "May, 2018",
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"url": "https://alanorth.github.io/cgspace-notes/2018-05/",
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"wordCount": "841",
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"datePublished": "2018-05-01T16:43:54+03:00",
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"dateModified": "2018-05-06T17:13:31+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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},
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"keywords": "Notes"
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}
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</script>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-05/">
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<title>May, 2018 | CGSpace Notes</title>
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<link href="https://alanorth.github.io/cgspace-notes/css/style.css" rel="stylesheet" integrity="sha384-ZwlQQbzhEPf3PrXZ3h/XKT/4UHafQ/TYI72AL+7WOJ8D6JmpGC8JMMse6xX7cyeI" crossorigin="anonymous">
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<body>
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<div class="blog-masthead">
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<div class="container">
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<nav class="nav blog-nav">
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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</nav>
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</div>
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</div>
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<header class="blog-header">
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<div class="container">
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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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</div>
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</header>
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<div class="container">
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<div class="row">
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<div class="col-sm-8 blog-main">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-05/">May, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-05-01T16:43:54+03:00">Tue May 01, 2018</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="2018-05-01">2018-05-01</h2>
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<ul>
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<li>I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
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<ul>
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<li><a href="http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E">http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E</a></li>
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<li><a href="http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E">http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E</a></li>
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</ul></li>
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<li>Then I reduced the JVM heap size from 6144 back to 5120m</li>
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<li>Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure scripts</a> to support hosts choosing which distribution they want to use</li>
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</ul>
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<p></p>
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<h2 id="2018-05-02">2018-05-02</h2>
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<ul>
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<li>Advise Fabio Fidanza about integrating CGSpace content in the new CGIAR corporate website</li>
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<li>I think they can mostly rely on using the <code>cg.contributor.crp</code> field</li>
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<li>Looking over some IITA records for Sisay
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<ul>
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<li>Other than trimming and collapsing consecutive whitespace, I made some other corrections</li>
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<li>I need to check the correct formatting of COTE D’IVOIRE vs COTE D’IVOIRE</li>
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<li>I replaced all DOIs with HTTPS</li>
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<li>I checked a few DOIs and found at least one that was missing, so I Googled the title of the paper and found the correct DOI</li>
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<li>Also, I found an <a href="https://www.doi.org/factsheets/DOI_PURL.html">FAQ for DOI that says the <code>dx.doi.org</code> syntax is older</a>, so I will replace all the DOIs with <code>doi.org</code> instead</li>
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<li>I found five records with “ISI Jounal” instead of “ISI Journal”</li>
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<li>I found one item with IITA subject “.”</li>
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<li>Need to remember to check the facets for things like this in sponsorship:</li>
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<li>Deutsche Gesellschaft für Internationale Zusammenarbeit</li>
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<li>Deutsche Gesellschaft fur Internationale Zusammenarbeit</li>
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<li>Eight records with language “fn” instead of “fr”</li>
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<li>One incorrect type (lowercase “proceedings”): Conference proceedings</li>
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<li>Found some capitalized CRPs in <code>cg.contributor.crp</code></li>
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<li>Found some incorrect author affiliations, ie “Institut de Recherche pour le Developpement Agricolc” should be “Institut de Recherche pour le Developpement <em>Agricole</em>“</li>
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<li>Wow, and for sponsors there are the following:</li>
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<li>Incorrect: Flemish Agency for Development Cooperation and Technical Assistance</li>
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<li>Incorrect: Flemish Organization for Development Cooperation and Technical Assistance</li>
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<li>Correct: Flemish <em>Association</em> for Development Cooperation and Technical Assistance</li>
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<li>One item had region “WEST” (I corrected it to “WEST AFRICA”)</li>
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</ul></li>
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</ul>
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<h2 id="2018-05-03">2018-05-03</h2>
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<ul>
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<li>It turns out that the IITA records that I was helping Sisay with in March were imported in 2018-04 without a final check by Abenet or I</li>
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<li>There are lots of errors on language, CRP, and even some encoding errors on abstract fields</li>
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<li>I export them and include the hidden metadata fields like <code>dc.date.accessioned</code> so I can filter the ones from 2018-04 and correct them in Open Refine:</li>
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</ul>
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<pre><code>$ dspace metadata-export -a -f /tmp/iita.csv -i 10568/68616
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</code></pre>
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<ul>
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<li>Abenet sent a list of 46 ORCID identifiers for ILRI authors so I need to get their names using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script and merge them into our controlled vocabulary</li>
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<li>On the messed up IITA records from 2018-04 I see sixty DOIs in incorrect format (cg.identifier.doi)</li>
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</ul>
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<h2 id="2018-05-06">2018-05-06</h2>
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<ul>
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<li>Fixing the IITA records from Sisay, sixty DOIs have completely invalid format like <code>http:dx.doi.org10.1016j.cropro.2008.07.003</code></li>
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<li>I corrected all the DOIs and then checked them for validity with a quick bash loop:</li>
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</ul>
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<pre><code>$ for line in $(< /tmp/links.txt); do echo $line; http --print h $line; done
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</code></pre>
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<ul>
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<li>Most of the links are good, though one is duplicate and one seems to even be incorrect in the publisher’s site so…</li>
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<li>Also, there are some duplicates:
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<ul>
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<li><code>10568/92241</code> and <code>10568/92230</code> (same DOI)</li>
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<li><code>10568/92151</code> and <code>10568/92150</code> (same ISBN)</li>
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<li><code>10568/92291</code> and <code>10568/92286</code> (same citation, title, authors, year)</li>
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</ul></li>
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<li>Messed up abstracts:
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<ul>
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<li><code>10568/92309</code></li>
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</ul></li>
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<li>Fixed some issues in regions, countries, sponsors, ISSN, and cleaned whitespace errors from citation, abstract, author, and titles</li>
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<li>Fixed all issues with CRPs</li>
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<li>A few more interesting Unicode characters to look for in text fields like author, abstracts, and citations might be: <code>’</code> (0x2019), <code>·</code> (0x00b7), and <code>€</code> (0x20ac)</li>
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<li>A custom text facit in OpenRefine with this GREL expression could be a good for finding invalid characters or encoding errors in authors, abstracts, etc:</li>
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</ul>
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<pre><code>or(
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isNotNull(value.match(/.*[(|)].*/)),
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isNotNull(value.match(/.*\uFFFD.*/)),
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isNotNull(value.match(/.*\u00A0.*/)),
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isNotNull(value.match(/.*\u200A.*/)),
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isNotNull(value.match(/.*\u2019.*/)),
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isNotNull(value.match(/.*\u00b7.*/)),
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isNotNull(value.match(/.*\u20ac.*/))
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)
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</code></pre>
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<ul>
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<li>I found some more IITA records that Sisay imported on 2018-03-23 that have invalid CRP names, so now I kinda want to check those ones!</li>
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<li>Combine the ORCID identifiers Abenet sent with our existing list and resolve their names using the <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
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</ul>
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<pre><code>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/ilri-orcids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2018-05-06-combined.txt
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$ ./resolve-orcids.py -i /tmp/2018-05-06-combined.txt -o /tmp/2018-05-06-combined-names.txt -d
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# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
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$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
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</code></pre>
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<ul>
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<li>I made a pull request (<a href="https://github.com/ilri/DSpace/pull/373">#373</a>) for this that I’ll merge some time next week (I’m expecting Atmire to get back to us about DSpace 5.8 soon)</li>
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<li>After testing quickly I just decided to merge it, and I noticed that I don’t even need to restart Tomcat for the changes to get loaded</li>
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</ul>
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<h2 id="2018-05-07">2018-05-07</h2>
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<ul>
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<li>I spent a bit of time playing with <a href="https://github.com/codeforkjeff/conciliator">conciliator</a> and Solr, trying to figure out how to reconcile columns in OpenRefine with data in our existing Solr cores (like CRP subjects)</li>
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<li>The documentation regarding the Solr stuff is limited, and I cannot figure out what all the fields in <code>conciliator.properties</code> are supposed to be</li>
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<li>But then I found <a href="https://github.com/okfn/reconcile-csv">reconcile-csv</a>, which allows you to reconcile against values in a CSV file!</li>
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<li>That, combined with splitting our multi-value fields on “||” in OpenRefine is amaaaaazing, because after reconciliation you can just join them again</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/2018-05/">May, 2018</a></li>
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<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
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<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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<li><a href="/cgspace-notes/2018-02/">February, 2018</a></li>
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<li><a href="/cgspace-notes/2018-01/">January, 2018</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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</section>
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</aside>
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<footer class="blog-footer">
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<p>
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Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
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<p>
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<a href="#">Back to top</a>
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