362 lines
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Fix some incorrect regions on CGSpace
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I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions
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Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
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Replace “East Asia” with “Eastern Asia” region on CGSpace (UN M.49 region)
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<meta name="twitter:description" content="2022-12-01
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Fix some incorrect regions on CGSpace
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I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions
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Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
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Replace “East Asia” with “Eastern Asia” region on CGSpace (UN M.49 region)
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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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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2022-12/">December, 2022</a></h2>
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<time datetime="2022-12-01T08:52:36+03:00">Thu Dec 01, 2022</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</header>
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<h2 id="2022-12-01">2022-12-01</h2>
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<ul>
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<li>Fix some incorrect regions on CGSpace
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<ul>
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<li>I exported the CCAFS and IITA communities, extracted just the country and region columns, then ran them through csv-metadata-quality to fix the regions</li>
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</ul>
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</li>
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<li>Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!</li>
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<li>Replace “East Asia” with “Eastern Asia” region on CGSpace (UN M.49 region)</li>
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</ul>
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<ul>
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<li>CGSpace and PRMS information session with Enrico and a bunch of researchers</li>
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<li>I noticed some minor issues with SPDX licenses and AGROVOC terms in items submitted by TIP so I sent a message to Daniel from Alliance</li>
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<li>I startd a harvest on AReS since we’ve updated so much metadata recently</li>
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</ul>
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<h2 id="2022-12-02">2022-12-02</h2>
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<ul>
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<li>File some issues related to metadata on the MEL issue tracker
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<ul>
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<li><a href="https://github.com/CodeObia/MEL/issues/11066">Only use “Open Access” or “Limited Access” access rights when publishing items on CGSpace</a></li>
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<li><a href="https://github.com/CodeObia/MEL/issues/11067">Set the description when submitting bitstreams to CGSpace</a></li>
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<li><a href="https://github.com/CodeObia/MEL/issues/11068">Some items have a Creative Commons license, but are Limited Access and bitstreams are locked</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-12-03">2022-12-03</h2>
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<ul>
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<li>I downloaded a fresh copy of CLARISA’s institutions list as well as ROR’s latest dump from 2022-12-01 to check how many are matching:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ curl -s https://api.clarisa.cgiar.org/api/institutions | json_pp > ~/Downloads/2022-12-03-CLARISA-institutions.json
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</span></span><span style="display:flex;"><span>$ jq -r <span style="color:#e6db74">'.[] | .name'</span> ~/Downloads/2022-12-03-CLARISA-institutions.json > ~/Downloads/2022-12-03-CLARISA-institutions.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i ~/Downloads/2022-12-03-CLARISA-institutions.txt -o /tmp/clarisa-ror-matches.csv -r v1.15-2022-12-01-ror-data.json
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</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/clarisa-ror-matches.csv | wc -l
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</span></span><span style="display:flex;"><span>1864
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</span></span><span style="display:flex;"><span>$ wc -l ~/Downloads/2022-12-03-CLARISA-institutions.txt
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</span></span><span style="display:flex;"><span>7060 /home/aorth/Downloads/2022-12-03-CLARISA-institutions.txt
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</span></span></code></pre></div><ul>
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<li>Out of the box they match 26.4%, but there are many institutions with multiple languages in the text value, as well as countries in parentheses so I think it could be higher</li>
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<li>If I replace the slashes and remove the countries at the end there are slightly more matches, around 29%:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ sed -e <span style="color:#e6db74">'s_ / _\n_'</span> -e <span style="color:#e6db74">'s_/_\n_'</span> -e <span style="color:#e6db74">'s/ \?(.*)$//'</span> ~/Downloads/2022-12-03-CLARISA-institutions.txt > ~/Downloads/2022-12-03-CLARISA-institutions-alan.txt
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</span></span></code></pre></div><ul>
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<li>I checked CGSpace’s top 1,000 affiliations too, first exporting from PostgreSQL:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1000) to /tmp/2022-11-22-affiliations.csv;
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</span></span></code></pre></div><ul>
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<li>Then cutting (tab is the default delimeter):</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ cut -f <span style="color:#ae81ff">1</span> /tmp/2022-11-22-affiliations.csv > 2022-11-22-affiliations.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/ror-lookup.py -i 2022-11-22-affiliations.txt -o /tmp/cgspace-matches.csv -r v1.15-2022-12-01-ror-data.json
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</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true /tmp/cgspace-matches.csv | wc -l
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</span></span><span style="display:flex;"><span>542
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</span></span></code></pre></div><ul>
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<li>So that’s a 54% match for our top affiliations</li>
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<li>I realized we should actually check affiliations and sponsors, since those are stored in separate fields
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<ul>
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<li>When I add those the matches go down a bit to 45%</li>
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</ul>
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</li>
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<li>Oh man, I realized institutions like <code>Université d'Abomey Calavi</code> don’t match in ROR because they are like this in the JSON:</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>"name": "Universit\u00e9 d'Abomey-Calavi"
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</span></span></code></pre></div><ul>
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<li>So we likely match a bunch more than 50%…</li>
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<li>I exported a list of affiliations and donors from CGSpace for Peter to look over and send corrections</li>
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</ul>
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<h2 id="2022-12-05">2022-12-05</h2>
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<ul>
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<li>First day of PRMS technical workshop in Rome</li>
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<li>Last night I submitted a CSV import with changes to 1,500 Alliance items (adding regions) and it hadn’t completed after twenty-four hours so I canceled it
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<ul>
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<li>Not sure if there is some rollback that will happen or what state the database will be in, so I will wait a few hours to see what happens before trying to modify those items again</li>
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<li>I started it again a few hours later with a subset of the items and 4GB of RAM instead of 2</li>
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<li>It completed successfully…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-12-07">2022-12-07</h2>
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<ul>
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<li>I found a bug in my csv-metadata-quality script regarding the regions
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<ul>
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<li>I was accidentally checking <code>cg.coverage.subregion</code> due to a sloppy regex</li>
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<li>This means I’ve added a few thousand UN M.49 regions to the <code>cg.coverage.subregion</code> field in the last few days</li>
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<li>I had to extract them from CGSpace and delete them using <code>delete-metadata-values.py</code></li>
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</ul>
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</li>
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<li>My <a href="https://github.com/DSpace/DSpace/pull/8550">DSpace 7.x pull request to tell ImageMagick about the PDF CropBox</a> was merged</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2022-12-08">2022-12-08</h2>
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<ul>
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<li>While on the plane I decided to fix some ORCID identifiers, as I had seen some poorly formatted ones
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<ul>
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<li>I couldn’t remember the XPath syntax so this was kinda ghetto:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ xmllint --xpath <span style="color:#e6db74">'//node/isComposedBy/node()'</span> dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE <span style="color:#e6db74">'label=".*"'</span> | sed -e <span style="color:#e6db74">'s/label="//'</span> -e <span style="color:#e6db74">'s/"$//'</span> > /tmp/orcid-names.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/update-orcids.py -i /tmp/orcid-names.txt -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -m <span style="color:#ae81ff">247</span>
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</span></span></code></pre></div><ul>
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<li>After that there were still some poorly formatted ones that my script didn’t fix, so perhaps these are new ones not in our list
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<ul>
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<li>I dumped them and combined with the existing ones to resolve later:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>localhost/dspace= ☘ \COPY (SELECT dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=247 AND text_value LIKE '%http%') to /tmp/orcid-formatting.txt;
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</span></span><span style="display:flex;"><span>COPY 36
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</span></span></code></pre></div><ul>
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<li>I think there are really just some new ones…</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/orcid-formatting.txt| grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u > /tmp/2022-12-08-orcids.txt
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</span></span><span style="display:flex;"><span>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u | wc -l
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</span></span><span style="display:flex;"><span>1907
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/2022-12-08-orcids.txt
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</span></span><span style="display:flex;"><span>1939 /tmp/2022-12-08-orcids.txt
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</span></span></code></pre></div><ul>
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<li>Then I applied these updates on CGSpace</li>
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<li>Maria mentioned that she was getting a lot more items in her daily subscription emails
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<ul>
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<li>I had a hunch it was related to me updating the <code>last_modified</code> timestamp after updating a bunch of countries, regions, etc in items</li>
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<li>Then today I noticed this option in <code>dspace.cfg</code>: <code>eperson.subscription.onlynew</code></li>
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<li>By default DSpace sends notifications for modified items too! I’ve disabled it now…</li>
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</ul>
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</li>
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<li>I applied 498 fixes and two deletions to affiliations sent by Peter</li>
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<li>I applied 206 fixes and eighty-one deletions to donors sent by Peter</li>
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<li>I tried to figure out how to authenticate to the DSpace 7 REST API
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<ul>
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<li>First <a href="https://github.com/DSpace/RestContract/blob/main/csrf-tokens.md">you need a CSRF token</a>, before you can even try to authenticate</li>
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<li>Then you can authenticate, but I can’t get it to work:</li>
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</ul>
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</li>
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</ul>
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<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ curl -v https://dspace7test.ilri.org/server/api
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</span></span><span style="display:flex;"><span>...
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</span></span><span style="display:flex;"><span>dspace-xsrf-token: 0b7861fb-9c8a-4eea-be70-b3be3bd0a0b4
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</span></span><span style="display:flex;"><span>...
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</span></span><span style="display:flex;"><span>$ curl -v -X POST --data <span style="color:#e6db74">"user=aorth@omg.com&password=myPassword"</span> <span style="color:#e6db74">"https://dspace7test.ilri.org/server/authn/login"</span> -H <span style="color:#e6db74">"X-XSRF-TOKEN: 0b7861fb-9c8a-4eea-be70-b3be3bd0a0b4"</span>
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</span></span></code></pre></div><ul>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2022-12-09">2022-12-09</h2>
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<ul>
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<li>I found a way to check the owner of a Handle prefix
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<ul>
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<li>You query the admin Handle for the prefix, ie: <a href="https://hdl.handle.net/0.na/10568">https://hdl.handle.net/0.na/10568</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-12-11">2022-12-11</h2>
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<ul>
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<li>I got LDAP authentication working on DSpace 7</li>
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</ul>
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<h2 id="2022-12-12">2022-12-12</h2>
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<ul>
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<li>Submit some issues to MEL GitHub:
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<ul>
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<li><a href="https://github.com/CodeObia/MEL/issues/11081">Links to https://mel.cgiar.org/dspace/limited for Limited Access items on CGSpace</a></li>
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<li><a href="https://github.com/CodeObia/MEL/issues/11083">Items submitted to CGSpace without Initiative</a></li>
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</ul>
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</li>
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<li>PRMS planning meeting before tomorrow’s meeting with researchers and submitters</li>
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</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
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<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
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<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
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<li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
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<li><a href="/cgspace-notes/2022-08/">August, 2022</a></li>
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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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</div> <!-- /.row -->
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</div> <!-- /.container -->
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<footer class="blog-footer">
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<p dir="auto">
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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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<p>
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<a href="#">Back to top</a>
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</p>
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</footer>
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</body>
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</html>
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