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Export CGSpace to cross check the DOI metadata with Crossref
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I want to try to expand my use of their data to journals, publishers, volumes, issues, etc…
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Export CGSpace to cross check the DOI metadata with Crossref
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I want to try to expand my use of their data to journals, publishers, volumes, issues, etc…
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"headline": "February, 2023",
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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/2023-02/">February, 2023</a></h2>
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<time datetime="2023-02-01T10:57:36+03:00">Wed Feb 01, 2023</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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<h2 id="2023-02-01">2023-02-01</h2>
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<ul>
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<li>Export CGSpace to cross check the DOI metadata with Crossref
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<ul>
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<li>I want to try to expand my use of their data to journals, publishers, volumes, issues, etc…</li>
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</ul>
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</li>
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</ul>
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<ul>
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<li>First, extract a list of DOIs for use with <code>crossref-doi-lookup.py</code>:</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>$ csvcut -c <span style="color:#e6db74">'cg.identifier.doi[en_US]'</span> ~/Downloads/2023-02-01-cgspace.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvgrep -c 1 -m 'doi.org' \
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</span></span><span style="display:flex;"><span> | csvgrep -c 1 -m ' ' -i \
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</span></span><span style="display:flex;"><span> | csvgrep -c 1 -r '.*cifor.*' -i \
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</span></span><span style="display:flex;"><span> | sed 1d > /tmp/2023-02-01-dois.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/crossref-doi-lookup.py -e a.orth@cgiar.org -i /tmp/2023-02-01-dois.txt -o ~/Downloads/2023-01-31-crossref-results.csv -d
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</span></span></code></pre></div><ul>
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<li>Then extract the ID, DOI, journal, volume, issue, publisher, etc from the CGSpace dump and rename the <code>cg.identifier.doi[en_US]</code> to <code>doi</code> so we can join on it with the Crossref results file:</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>$ csvcut -c <span style="color:#e6db74">'id,cg.identifier.doi[en_US],cg.journal[en_US],cg.volume[en_US],cg.issue[en_US],dcterms.publisher[en_US],cg.number[en_US],dcterms.license[en_US]'</span> ~/Downloads/2023-02-01-cgspace.csv <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvgrep -c 'cg.identifier.doi[en_US]' -r '.*cifor.*' -i \
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</span></span><span style="display:flex;"><span> | sed -e '1s/cg.identifier.doi\[en_US\]/doi/' \
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</span></span><span style="display:flex;"><span> -e 's_https://doi.org/__g' \
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</span></span><span style="display:flex;"><span> -e 's_https://dx.doi.org/__g' \
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</span></span><span style="display:flex;"><span> > /tmp/2023-02-01-cgspace-doi-metadata.csv
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</span></span><span style="display:flex;"><span>$ csvjoin -c doi /tmp/2023-02-01-cgspace-doi-metadata.csv ~/Downloads/2023-02-01-crossref-results.csv > /tmp/2023-02-01-cgspace-crossref-check.csv
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</span></span></code></pre></div><ul>
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<li>And import into OpenRefine for analysis and cleaning</li>
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<li>I just noticed that Crossref also has types, so we could use that in the future too!</li>
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<li>I got a few corrections after examining manually, but I didn’t manage to identify any patterns that I could use to do any automatic matching or cleaning</li>
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</ul>
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<h2 id="2023-02-05">2023-02-05</h2>
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<ul>
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<li>Normalize text lang attributes in PostgreSQL, run a quick Discovery index, and then export CGSpace to check Initiative mappings and countries/regions</li>
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<li>Run all system updates on CGSpace (linode18) and reboot it</li>
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</ul>
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<h2 id="2023-02-06">2023-02-06</h2>
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<ul>
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<li>Peter said that a new Initiative was approved last month so we need to add it to CGSpace: <code>Fragility, Conflict, and Migration</code></li>
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<li>There is lots of discussion about the “issue date” versus “available date” with Enrico and IFPRI, after lots of feedback from the PRMS QA
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<ul>
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<li>I filed <a href="https://github.com/AgriculturalSemantics/cg-core/issues/43">an issue on CG Core to propose using <code>dcterms.available</code> as an optional field to indicate the online date</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-02-07">2023-02-07</h2>
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<ul>
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<li>IFPRI’s web developer Tony managed to get his Drupal harvester to have a useful user agent:</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>54.x.x.x - - [06/Feb/2023:10:10:32 +0100] "POST /rest/items/find-by-metadata-field?limit=%22100&offset=0 HTTP/1.1" 200 58855 "-" "IFPRI drupal POST harvester"
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</span></span></code></pre></div><ul>
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<li>He also noticed that there is no pagination on POST requests to <code>/rest/items/find-by-metadata-field</code>, and that he needs to increase his timeout for requests that return 100+ results, ie:</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 -f -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.actionArea", "value":"Systems Transformation", "language": "en_US"}'
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</span></span></code></pre></div><ul>
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<li>I need to ask on the DSpace Slack about this POST pagination</li>
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<li>Abenet and Udana noticed that the Handle server was not running
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<ul>
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<li>Looking in the <code>error.log</code> file I see that the service is complaining about a lock file being present</li>
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<li>This is because Linode had to do emergency maintenance on the VM host this morning and the Handle server didn’t shut down properly</li>
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</ul>
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</li>
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<li>I’m having an issue with <code>poetry update</code> so I spent some time debugging and filed <a href="https://github.com/python-poetry/poetry/issues/7482">an issue</a></li>
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<li>Proof and import nine items for the Digital Innovation Inititive for IFPRI
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<ul>
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<li>There were only some minor issues in the metadata</li>
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<li>I also did a duplicate check with <code>check-duplicates.py</code> just in case</li>
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</ul>
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</li>
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<li>I did some minor updates on csv-metadata-quality
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<ul>
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<li>First, to reduce warnings on non-SPDX licenses like “Copyrighted; all rights reserved” and “Other” since they are very common for us and I’m sick of seeing the warnings</li>
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<li>Second, to skip whitespace and newline fixes on the abstract field since so many times they are intended</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-02-08">2023-02-08</h2>
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<ul>
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<li>Make some edits to IFPRI records requested by Jawoo and Leigh</li>
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<li>Help Alessandra upload a last minute report for SAPLING</li>
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<li>Proof and upload twenty-seven IFPRI records to CGSpace
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<ul>
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<li>It’s a good thing I did a duplicate check because I found three duplicates!</li>
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</ul>
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</li>
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<li>Export CGSpace to update Initiative mappings and country/region mappings
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<ul>
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<li>Then start a harvest on AReS</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-02-09">2023-02-09</h2>
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<ul>
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<li>Do some minor work on the CSS on the DSpace 7 test</li>
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</ul>
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<h2 id="2023-02-10">2023-02-10</h2>
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<ul>
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<li>I noticed a large number of PostgreSQL locks from dspaceWeb on CGSpace:</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>$ psql -c <span style="color:#e6db74">'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid;'</span> | grep -o -E <span style="color:#e6db74">'(dspaceWeb|dspaceApi|dspaceCli)'</span> | sort | uniq -c
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</span></span><span style="display:flex;"><span> 2033 dspaceWeb
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</span></span></code></pre></div><ul>
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<li>Looking at the lock age, I see some already 1 day old, including this curious query:</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>select nextval ('public.registrationdata_seq')
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</span></span></code></pre></div><ul>
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<li>I killed all locks that were more than a few hours old</li>
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<li>Export CGSpace to update Initiative collection mappings</li>
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<li>Discuss adding <code>dcterms.available</code> to the submission form
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<ul>
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<li>I also looked in the <code>dcterms.description</code> field on CGSpace and found ~1,500 items where the is an indication of an online published date</li>
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<li>Using some facets in OpenRefine I narrowed down the ones mentioning “online” and then extracted the dates to a new column:</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>cells['dcterms.description[en_US]'].value.replace(/.*?(\d+{2}) ([a-zA-Z]+) (\d+{2}).*/,"$3-$2-$1")
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</span></span></code></pre></div><ul>
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<li>Then to handle formats like “2022-April-26” and “2021-Nov-11” I used some replacement GRELs (note the order so we don’t replace short patterns in longer strings prematurely):</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>value.replace("January","01").replace("February","02").replace("March","03").replace("April","04").replace("May","05").replace("June","06").replace("July","07").replace("August","08").replace("September","09").replace("October","10").replace("November","11").replace("December","12")
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</span></span><span style="display:flex;"><span>value.replace("Jan","01").replace("Feb","02").replace("Mar","03").replace("Apr","04").replace("May","05").replace("Jun","06").replace("Jul","07").replace("Aug","08").replace("Sep","09").replace("Oct","10").replace("Nov","11").replace("Dec","12")
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</span></span></code></pre></div><ul>
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<li>This covered about 1,300 items, then I did about 100 more messier ones with some more regex wranling
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<ul>
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<li>I removed the <code>dcterms.description[en_US]</code> field from items where I updated the dates</li>
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</ul>
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</li>
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<li>Then I added <code>dcterms.available</code> to the submission form and the item view
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<ul>
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<li>We need to announce this to the editors</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-02-13">2023-02-13</h2>
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<ul>
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<li>Export CGSpace to do some metadata quality checks
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<ul>
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<li>I added CGIAR Trust Fund as a donor to some new Initiative outputs</li>
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<li>I moved some abstracts from the description field</li>
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<li>I moved some version information to the <code>cg.edition</code> field</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-02-14">2023-02-14</h2>
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<ul>
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<li>The PRMS team in Colombia sent some questions about countries on CGSpace
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<ul>
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<li>I had to fix some, that were clearly wrong, but there is also a difference between CGSpace and MEL because we use mostly iso-codes, and MEL uses the UN M.49 list</li>
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<li>Then I re-ran the country code tagger from cgspace-java-helpers, forcing the update on all items in the Initiatives community</li>
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</ul>
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</li>
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<li>Remove Alliance research levers from <code>cg.contributor.crp</code> field after discussing with Daniel and Maria
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<ul>
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<li>This was a mistake on TIP’s part, and there is no direct mapping between research levers and CRPs</li>
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</ul>
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</li>
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<li>I exported CGSpace to check Initiative collection mappings, regions, and licenses
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<ul>
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<li>Peter told me that all CGIAR blog posts for the Initiatives should be CC-BY-4.0, and I see the logo at the bottom in light gray!</li>
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<li>I had previously missed that and removed some licenses for blog posts</li>
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<li>I checked cgiar.org, ifpri.org, icarda.org, iwmi.cgiar.org, irri.org, etc and corrected a handful</li>
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</ul>
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</li>
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<li>Start a harvest on AReS</li>
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</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
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<li><a href="/cgspace-notes/2023-01/">January, 2023</a></li>
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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="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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