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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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<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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<h2 id="2023-02-15">2023-02-15</h2>
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<ul>
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<li>Work on rebasing my local DSpace 7 dev branches on top of the latest 7.5-SNAPSHOT
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<ul>
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<li>It seems the issues I had with the <code>dspace submission-forms-migrate</code> tool in <a href="/cgspace-notes/2022-08/">August, 2022</a> were fixed</li>
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</ul>
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</li>
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<li>I imported a fresh PostgreSQL snapshot from CGSpace and then removed the Atmire migrations and ran the new migrations as I originally noted in <a href="/cgspace-notes/2022-03/">March, 2022</a>, and is pointed out in the <a href="https://wiki.lyrasis.org/display/DSDOC7x/Upgrading+DSpace">DSpace 7 upgrade notes</a>
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<ul>
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<li>Now I get a new error:</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/dspace7= ☘ DELETE FROM schema_version WHERE version IN ('5.0.2017.09.25', '6.0.2017.01.30', '6.0.2017.09.25');
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</span></span><span style="display:flex;"><span>localhost/dspace7= ☘ DELETE FROM schema_version WHERE description LIKE '%Atmire%' OR description LIKE '%CUA%' OR description LIKE '%cua%';
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</span></span><span style="display:flex;"><span>localhost/dspace7= \q
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</span></span><span style="display:flex;"><span>$ ./bin/dspace database migrate ignored
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</span></span><span style="display:flex;"><span>...
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>CREATE INDEX resourcepolicy_action_idx ON resourcepolicy(action_id)
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span> at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.handleException(DefaultSqlScriptExecutor.java:275)
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</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:222)
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</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.execute(DefaultSqlScriptExecutor.java:126)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.executeOnce(SqlMigrationExecutor.java:69)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.lambda$execute$0(SqlMigrationExecutor.java:58)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.database.DefaultExecutionStrategy.execute(DefaultExecutionStrategy.java:27)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.resolver.sql.SqlMigrationExecutor.execute(SqlMigrationExecutor.java:57)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.command.DbMigrate.doMigrateGroup(DbMigrate.java:377)
|
||
</span></span><span style="display:flex;"><span> ... 24 more
|
||
</span></span><span style="display:flex;"><span>Caused by: org.postgresql.util.PSQLException: ERROR: relation "resourcepolicy_action_idx" already exists
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2676)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2366)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:356)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:496)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:413)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:333)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:319)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:295)
|
||
</span></span><span style="display:flex;"><span> at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:290)
|
||
</span></span><span style="display:flex;"><span> at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193)
|
||
</span></span><span style="display:flex;"><span> at org.apache.commons.dbcp2.DelegatingStatement.execute(DelegatingStatement.java:193)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.jdbc.JdbcTemplate.executeStatement(JdbcTemplate.java:201)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.sqlscript.ParsedSqlStatement.execute(ParsedSqlStatement.java:95)
|
||
</span></span><span style="display:flex;"><span> at org.flywaydb.core.internal.sqlscript.DefaultSqlScriptExecutor.executeStatement(DefaultSqlScriptExecutor.java:210)
|
||
</span></span><span style="display:flex;"><span> ... 30 more
|
||
</span></span></code></pre></div><ul>
|
||
<li>I dropped that index and then the migration succeeded:</li>
|
||
</ul>
|
||
<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/dspace7= ☘ DROP INDEX resourcepolicy_action_idx;
|
||
</span></span><span style="display:flex;"><span>localhost/dspace7= ☘ \q
|
||
</span></span><span style="display:flex;"><span>$ ./bin/dspace database migrate ignored
|
||
</span></span><span style="display:flex;"><span>Done.
|
||
</span></span></code></pre></div><ul>
|
||
<li>I think that particular error is because I applied the <a href="https://github.com/DSpace/DSpace/pull/1792">indexes in this unmerged DSpace 6 patch</a>, so I don’t need to report this as an error in DSpace 7</li>
|
||
</ul>
|
||
<h2 id="2023-02-16">2023-02-16</h2>
|
||
<ul>
|
||
<li>I found a suspicious number of PostgreSQL locks on CGSpace and decided to investigate:</li>
|
||
</ul>
|
||
<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
|
||
</span></span><span style="display:flex;"><span> 44 dspaceApi
|
||
</span></span><span style="display:flex;"><span> 372 dspaceCli
|
||
</span></span><span style="display:flex;"><span> 446 dspaceWeb
|
||
</span></span></code></pre></div><ul>
|
||
<li>This started happening yesterday and I killed a few locks that were several hours old after inspecting the <code>locks-age.sql</code> output</li>
|
||
<li>I also checked the <code>locks.sql</code> output, which helpfully lists the blocked PID and the blocking PID, to find one blocking PID that was idle in transaction
|
||
<ul>
|
||
<li>I killed that process and then all other locks were instantly processed</li>
|
||
</ul>
|
||
</li>
|
||
<li>I filed <a href="https://github.com/DSpace/dspace-angular/issues/2103">a GitHub issue</a> on dspace-angular requesting the item view to use the bitstream description instead of the file name if present</li>
|
||
<li>Weekly CG Core types meeting
|
||
<ul>
|
||
<li>I need to go through the actions and remove those items that are only for CGSpace internal use, ie:
|
||
<ul>
|
||
<li>CD-ROM</li>
|
||
<li>Manuscript-unpublished</li>
|
||
<li>Photo Report</li>
|
||
<li>Questionnaire</li>
|
||
<li>Wiki</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>Weekly CGIAR Repository Working Group meeting</li>
|
||
<li>I did some experiments with Crossref dates for about 20,000 DOIs in CGSpace using my <code>crossref-doi-lookup.py</code> script</li>
|
||
<li>Some things I noted from reading the <a href="https://github.com/CrossRef/rest-api-doc/blob/master/api_format.md">Crossref API docs</a> and inspecting the records for a few dozen DOIs manually:
|
||
<ul>
|
||
<li><code>["created"]["date-parts"]</code> → Date on which the DOI was first registered (not useful for us)</li>
|
||
<li><code>["published-print"]["date-parts"]</code> → Date on which the work was published in print</li>
|
||
<li><code>["journal-issue"]["published-print"]["date-parts"]</code> → When present, is 99% the same as the above</li>
|
||
<li><code>["published-online"]["date-parts"]</code> → Date on which the work was published online</li>
|
||
<li><code>["journal-issue"]["published-online"]["date-parts"]</code> → Much more rare, and only 50% the same as the above, so unreliable</li>
|
||
<li><code>["issued"]["date-parts"]</code> → Earliest of published-print and published-online (not useful to us)</li>
|
||
</ul>
|
||
</li>
|
||
<li>After checking the DOIs manully I decided that when the <code>published-print</code> date exists, it is usually more accurate than our issued dates
|
||
<ul>
|
||
<li>I set 12,300 issue dates to those from Crossref</li>
|
||
</ul>
|
||
</li>
|
||
<li>I also decided that, when <code>published-online</code> exists, it is usually accurate when I check the publisher page (we don’t have many online dates to compare)
|
||
<ul>
|
||
<li>I set the available date for ~7,000 items to the published-online date as long as:
|
||
<ul>
|
||
<li>There was no <code>dcterms.available</code> date already</li>
|
||
<li>It was different than the issued date, because for now I only want online dates that are different, in case this is an online only journal in which case that can be the issue date… maybe I’ll re-visit that later</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-17">2023-02-17</h2>
|
||
<ul>
|
||
<li>It seems some (all?) of the changes I applied to dates last night didn’t get saved…
|
||
<ul>
|
||
<li>I don’t know what happened, so I will run them again after some investigation</li>
|
||
<li>I submitted the first batch of ~7,600 changes and it took twelve hours!</li>
|
||
<li>I almost cancelled it because after applying the changes there was a lock blocking everything for two hours, and it seemed to be stuck, but I kept checking it and saw that the <code>query_start</code> and <code>state_change</code> were being updated despite it being state “idle in transaction”:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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_stat_activity WHERE pid=1025176'</span> | less -S
|
||
</span></span></code></pre></div><ul>
|
||
<li>I will apply the other changes in smaller batches…</li>
|
||
<li>Lately I’ve noticed a lot of activity from the country code tagger curation task
|
||
<ul>
|
||
<li>Looking in the logs I see items being tagged that are very old and should have already been tagged years ago</li>
|
||
<li>Also, I see a ton of these errors whenever the task is updating an item:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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>2023-02-17 08:01:00,252 INFO org.dspace.curate.Curator @ Curation task: countrycodetagger performed on: 10568/89020 with status: 0. Result: '10568/89020: added 1 alpha2 country code(s)'
|
||
</span></span><span style="display:flex;"><span>2023-02-17 08:01:00,467 ERROR com.atmire.versioning.ModificationLogger @ Error while writing item to versioning index: a0fe9d9a-6ac1-4b6a-8fcb-dae07a6bbf58 message:missing required field: epersonID
|
||
</span></span><span style="display:flex;"><span>org.apache.solr.client.solrj.impl.HttpSolrServer$RemoteSolrException: missing required field: epersonID
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrServer.executeMethod(HttpSolrServer.java:552)
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:210)
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:116)
|
||
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:102)
|
||
</span></span><span style="display:flex;"><span> at com.atmire.versioning.ModificationLogger.indexItem(ModificationLogger.java:263)
|
||
</span></span><span style="display:flex;"><span> at com.atmire.versioning.ModificationConsumer.end(ModificationConsumer.java:134)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:157)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.core.Context.dispatchEvents(Context.java:455)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.visit(Curator.java:541)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator$TaskRunner.run(Curator.java:568)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.doCollection(Curator.java:515)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.doCommunity(Curator.java:487)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.doSite(Curator.java:451)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.curate(Curator.java:269)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.Curator.curate(Curator.java:203)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.curate.CurationCli.main(CurationCli.java:220)
|
||
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
|
||
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
|
||
</span></span><span style="display:flex;"><span> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||
</span></span><span style="display:flex;"><span> at java.lang.reflect.Method.invoke(Method.java:498)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
|
||
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
|
||
</span></span></code></pre></div><ul>
|
||
<li>This must be related…</li>
|
||
</ul>
|
||
<h2 id="2023-02-18">2023-02-18</h2>
|
||
<ul>
|
||
<li>I realized why the country-code-tagger was tagging everything: I had overridden the <code>force</code> parameter last week!</li>
|
||
<li>Start a harvest on AReS</li>
|
||
</ul>
|
||
<h2 id="2023-02-20">2023-02-20</h2>
|
||
<ul>
|
||
<li>IWMI is concerned that some of their items with top Altmetric attention scores don’t show up in the AReS Explorer
|
||
<ul>
|
||
<li>I looked into it for one and found that AReS is using the Handle, but Altmetric hasn’t associated the Handle with the DOI</li>
|
||
</ul>
|
||
</li>
|
||
<li>Looking into country and region issues for the PRMS team
|
||
<ul>
|
||
<li>Last week they had some questions about some invalid countries that ended up being typos</li>
|
||
<li>I realized my cgspace-java-helpers country-code-tagger curation task is not using the latest version, so it was missing Türkiye</li>
|
||
<li>I compiled the new version and ran it manually, but I have to upload a new version to Maven Central and then update the dependency in <code>dspace/modules/additions/pom.xml</code> ughhhhhh</li>
|
||
<li>I tagged version 6.2 with the change for Türkiye and uploaded to to Maven Central with <code>mvn clean deploy</code></li>
|
||
</ul>
|
||
</li>
|
||
<li>I’m having second thoughts about switching to UN M.49 for countries because there are just too many tradeoffs
|
||
<ul>
|
||
<li>I want to find a way to keep our existing list, and codify some rules for it</li>
|
||
<li>There are several discussions related to the shortcomings of ISO themselves and the iso-codes project, for example:
|
||
<ul>
|
||
<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/33">Inconsistency with articles in ISO-3166-1 English short names</a> (this one was filed by me two years ago!)</li>
|
||
<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/issues/44">ISO 3166-1: What’s the policy for <code>common_name</code>?</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>I almost want to say fuck it, let’s just use iso-codes and tell everyone to deal with it, but make sure we handle ISO 3166-1 Alpha2 or probably Alpha3 in the future</li>
|
||
<li>Something like:
|
||
<ul>
|
||
<li>Prefer <code>common_name</code> if it exists</li>
|
||
<li>Prefer the shorter of <code>name</code> and <code>official name</code></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-21">2023-02-21</h2>
|
||
<ul>
|
||
<li>Continue working on my <code>parse-iso-codes.py</code> script to parse the iso-codes JSON for ISO 3166-1
|
||
<ul>
|
||
<li>I also started a spreadsheet to track current CGSpace country names, proposed new names using the compromise above, and UN M.49 names</li>
|
||
<li>I proposed this to Peter but he wasn’t happy because there are still some stupidly long and political names there</li>
|
||
</ul>
|
||
</li>
|
||
<li>I bumped the version of cgspace-java-helpers to 6.2-SNAPSHOT and pushed it to Maven Central because I can’t figure out how to get non-snapshot releases to go there</li>
|
||
<li>Ouch, grunt 1.6.0 was released a few weeks ago, which relies on Node.js v16, thus breaking the Mirage 2 build in DSpace 6
|
||
<ul>
|
||
<li>I filed <a href="https://github.com/DSpace/DSpace/issues/8676">an issue in DSpace</a></li>
|
||
</ul>
|
||
</li>
|
||
<li>Help Moises from CIP troubleshoot harvesting issues on their WordPress site
|
||
<ul>
|
||
<li>I see 2,000 requests with the user agent “RTB website BOT” today and they are all HTTP 200</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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># grep <span style="color:#e6db74">'RTB website BOT'</span> /var/log/nginx/rest.log | awk <span style="color:#e6db74">'{print $9}'</span> | sort | uniq -c | sort -h
|
||
</span></span><span style="display:flex;"><span> 2023 200
|
||
</span></span></code></pre></div><ul>
|
||
<li>Start reviewing and fixing metadata for Sam’s ~250 CAS publications from last year
|
||
<ul>
|
||
<li>Both Abenet and Peter have already looked at them and Sam has been waiting for months on this</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-22">2023-02-22</h2>
|
||
<ul>
|
||
<li>Continue proofing CAS records for Sam
|
||
<ul>
|
||
<li>I downloaded all the PDFs manually and checked the issue dates for each from the PDF, noting some that had licenses, ISBNs, etc</li>
|
||
<li>I combined the title, abstract, and system subjects into one column to mine them for AGROVOC terms:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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>toLowercase(value) + toLowercase(cells["dcterms.abstract"].value) + toLowercase(cells["cg.subject.system"].value.replace("||", " "))
|
||
</span></span></code></pre></div><ul>
|
||
<li>Then I extracted a list of AGROVOC terms the same way I did in <a href="/cgspace-notes/2022-08/">August, 2022</a> and used this Jython code to extract matching terms:</li>
|
||
</ul>
|
||
<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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> re
|
||
</span></span><span style="display:flex;"><span>
|
||
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">r</span><span style="color:#e6db74">"/tmp/agrovoc-subjects.txt"</span>,<span style="color:#e6db74">'r'</span>) <span style="color:#66d9ef">as</span> f :
|
||
</span></span><span style="display:flex;"><span> terms <span style="color:#f92672">=</span> [name<span style="color:#f92672">.</span>rstrip()<span style="color:#f92672">.</span>lower() <span style="color:#66d9ef">for</span> name <span style="color:#f92672">in</span> f]
|
||
</span></span><span style="display:flex;"><span>
|
||
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> <span style="color:#e6db74">"||"</span><span style="color:#f92672">.</span>join([term <span style="color:#66d9ef">for</span> term <span style="color:#f92672">in</span> terms <span style="color:#66d9ef">if</span> re<span style="color:#f92672">.</span><span style="color:#66d9ef">match</span>(<span style="color:#e6db74">r</span><span style="color:#e6db74">".*\b"</span> <span style="color:#f92672">+</span> term <span style="color:#f92672">+</span> <span style="color:#e6db74">r</span><span style="color:#e6db74">"\b.*"</span>, value<span style="color:#f92672">.</span>lower())])
|
||
</span></span></code></pre></div><ul>
|
||
<li>Then I used <a href="https://stackoverflow.com/questions/15419080/openrefine-remove-duplicates-from-list-with-jython">this cool Jython to remove duplicate metadata values</a>:</li>
|
||
</ul>
|
||
<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-python" data-lang="python"><span style="display:flex;"><span>deduped_list <span style="color:#f92672">=</span> list(set(value<span style="color:#f92672">.</span>split(<span style="color:#e6db74">"||"</span>)))
|
||
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> <span style="color:#e6db74">'||'</span><span style="color:#f92672">.</span>join(map(str, deduped_list))
|
||
</span></span></code></pre></div><ul>
|
||
<li>Then I did the same with countries, woooooo!</li>
|
||
<li>I checked for duplicates and found forty-one</li>
|
||
<li>I just stumbled upon UNTERM, which provides the official list of countries for the UN General Assembly, including a downloadable Excel with the short and formal names in all UN languages: <a href="https://unterm.un.org/unterm2/en/country">https://unterm.un.org/unterm2/en/country</a></li>
|
||
<li>I created a <a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/merge_requests/32">pull request to add common names for Iran, Laos, and Syria on the Debian iso-codes package</a>
|
||
<ul>
|
||
<li>These are remarked upon in the ISO.org online browsing platform for ISO 3166-1</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-23">2023-02-23</h2>
|
||
<ul>
|
||
<li>Tag v0.6.1 of csv-metadata-quality</li>
|
||
<li>Weekly meeting about CG Core types
|
||
<ul>
|
||
<li>I need to get some definitions from Peter for some types</li>
|
||
</ul>
|
||
</li>
|
||
<li>Peter sent some of the feedback from Indira to XMLUI
|
||
<ul>
|
||
<li>I removed some old facets, limited others to less values, and adjusted the recent submissions from 5 to 10</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-24">2023-02-24</h2>
|
||
<ul>
|
||
<li>More work on understanding Sam’s CAS publications to prepare for uploading them to CGSpace
|
||
<ul>
|
||
<li>I need to reconcile the duplicates and Peter’s type re-classifications in the final version of the spreadsheet</li>
|
||
<li>I flagged all the duplicates by creating a custom text facet matching all their titles like:</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<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>or(
|
||
</span></span><span style="display:flex;"><span> isNotNull(value.match("Evaluation of the CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS)")),
|
||
</span></span><span style="display:flex;"><span> isNotNull(value.match("Report of the IEA Workshop on Development, Use and Assessment of TOC in CGIAR Research, Rome, 12-13 January 2017")),
|
||
</span></span><span style="display:flex;"><span> isNotNull(value.match("Report of the IEA Workshop on Evaluating the Quality of Science, Rome, 10-11 December 2015")),
|
||
</span></span><span style="display:flex;"><span> isNotNull(value.match("Review of CGIAR’s Intellectual Assets Principles")),
|
||
</span></span><span style="display:flex;"><span>...
|
||
</span></span><span style="display:flex;"><span>)
|
||
</span></span></code></pre></div><ul>
|
||
<li>Annoyingly this seems to miss the ones with parenthesis so I had to do those manually
|
||
<ul>
|
||
<li>This matched thirty-seven items, then I flagged them so I can handle them separately after uploading the others</li>
|
||
<li>Then I used the URL field in the old version of the file to match the items with types <code>Evaluation</code> and <code>Independent Commentary</code> since Peter changed them</li>
|
||
<li>I added extent, volume, issue, number, and affiliation to a few journal articles</li>
|
||
<li>Then I did some last minute checks to make sure we’re not uploading files for items marked as having “multiple documents”</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-25">2023-02-25</h2>
|
||
<ul>
|
||
<li>Oh nice, my <a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/merge_requests/32">pull request adding common names for Iran, Laos, and Syria to iso-codes</a> was merged</li>
|
||
<li>I did a test import of the 198 CAS Publications on DSpace Test, then inspected Abenet’s file with Gaia’s “multiple documents” field one more time and decided to do the import on CGSpace
|
||
<ul>
|
||
<li>Gaia’s “multiple documents” column had some text like “E6” and “F7” that didn’t make any sense, and those files were not in the Sharepoint even</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-26">2023-02-26</h2>
|
||
<ul>
|
||
<li>Start a harvest on AReS</li>
|
||
</ul>
|
||
<h2 id="2023-02-27">2023-02-27</h2>
|
||
<ul>
|
||
<li>I found two items for the CAS Publications that were marked as a duplicates, but upon second inspection were not, so I uploaded it to CGSpace
|
||
<ul>
|
||
<li>That makes the total number of items for CAS 200…</li>
|
||
</ul>
|
||
</li>
|
||
<li>I did some CSV joining and inspections with the remaining thirty-six duplicates with the metadata for their existing items on CGSpace and uploaded them</li>
|
||
<li>Do some work on the new DSpace 7 submission forms
|
||
<ul>
|
||
<li>I ended up reverting to the stock configuration to use some new techniques like the style and type bind</li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
<h2 id="2023-02-28">2023-02-28</h2>
|
||
<ul>
|
||
<li>Keep working on the DSpace 7 submission forms
|
||
<ul>
|
||
<li>As part of this I asked Maria and Francesca if they are still using the <code>cg.link.permalink</code> (Bioversity publications permalink) and they said no, so we can remove it from the submission form</li>
|
||
<li>I also removed <code>cg.subject.ccafs</code> since the CRP ended over a year ago and <code>cg.subject.pabra</code> since there have only been a handful of new items in <a href="https://hdl.handle.net/10568/80211">their collection</a> and they seem to be using Alliance subjects instead</li>
|
||
</ul>
|
||
</li>
|
||
<li>I filed <a href="https://github.com/DSpace/DSpace/issues/8686">a bug</a> on DSpace regarding the inability to add freetext values from an input field that uses a vocabulary</li>
|
||
</ul>
|
||
<!-- raw HTML omitted -->
|
||
|
||
|
||
|
||
|
||
|
||
</article>
|
||
|
||
|
||
|
||
</div> <!-- /.blog-main -->
|
||
|
||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Recent Posts</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
|
||
<li><a href="/cgspace-notes/2023-05/">May, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-04/">April, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
|
||
|
||
<li><a href="/cgspace-notes/2023-01/">January, 2023</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
|
||
|
||
|
||
<section class="sidebar-module">
|
||
<h4>Links</h4>
|
||
<ol class="list-unstyled">
|
||
|
||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||
|
||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||
|
||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||
|
||
</ol>
|
||
</section>
|
||
|
||
</aside>
|
||
|
||
|
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|
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<p dir="auto">
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