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Start a full harvest on AReS
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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/2022-01/">January, 2022</a></h2>
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<time datetime="2022-01-01T15:20:54+02:00">Sat Jan 01, 2022</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
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</header>
<h2 id="2022-01-01">2022-01-01</h2>
<ul>
<li>Start a full harvest on AReS</li>
</ul>
<h2 id="2022-01-06">2022-01-06</h2>
<ul>
<li>Add ORCID identifier for Chris Jones to CGSpace
<ul>
<li>Also tag eighty-eight of his items in CGSpace:</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>$ cat 2022-01-06-add-orcids.csv
</span></span><span style="display:flex;"><span>dc.contributor.author,cg.creator.identifier
</span></span><span style="display:flex;"><span>&#34;Jones, Chris&#34;,&#34;Chris Jones: 0000-0001-9096-9728&#34;
</span></span><span style="display:flex;"><span>&#34;Jones, Christopher S.&#34;,&#34;Chris Jones: 0000-0001-9096-9728&#34;
</span></span><span style="display:flex;"><span>$ ./ilri/add-orcid-identifiers-csv.py -i 2022-01-06-add-orcids.csv -db dspace63 -u dspacetest -p <span style="color:#e6db74">&#39;dom@in34sniper&#39;</span>
</span></span></code></pre></div><h2 id="2022-01-09">2022-01-09</h2>
<ul>
<li>Validate and register CGSpace on <a href="https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7">OpenArchives</a>
<ul>
<li>Last month IWMI colleagues were asking me to look into this, and after checking the OpenArchives mailing list it seems there was a problem on the server side</li>
<li>Now it has worked and the message is &ldquo;Successfully updated OAI registration database to status COMPLIANT.&rdquo;</li>
<li>I received an email (as the Admin contact on our OAI) that says:</li>
</ul>
</li>
</ul>
<blockquote>
<p>Your repository has been registered in the OAI database of conforming repositories.</p>
</blockquote>
<ul>
<li>Now I&rsquo;m taking a screenshot of the validation page for posterity, because the logs seem to go away after some time</li>
</ul>
<p><img src="/cgspace-notes/2022/01/openarchives-registration.png" alt="OpenArchives.org registration"></p>
<ul>
<li>I tried to re-build the Docker image for OpenRXV and got an error in the backend:</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>...
</span></span><span style="display:flex;"><span>&gt; openrxv-backend@0.0.1 build
</span></span><span style="display:flex;"><span>&gt; nest build
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias &#39;AggregationsAggregate&#39; circularly references itself.
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate&lt;any&gt; | AggregationsTermsAggregate&lt;any&gt; | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate&lt;AggregationsBucket&gt; | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
</span></span><span style="display:flex;"><span> ~~~~~~~~~~~~~~~~~~~~~
</span></span><span style="display:flex;"><span>node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias &#39;AggregationsSingleBucketAggregate&#39; circularly references itself.
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
</span></span><span style="display:flex;"><span> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Found 2 error(s).
</span></span></code></pre></div><ul>
<li>Ah, it seems the code on the server was slightly out of date
<ul>
<li>I checked out the latest master branch and it built</li>
</ul>
</li>
</ul>
<h2 id="2022-01-12">2022-01-12</h2>
<ul>
<li>Fix some citation formatting issues in Gaia&rsquo;s <a href="https://dspacetest.cgiar.org/handle/10568/115230">eighteen CAS Green Cover publications on DSpace Test</a></li>
</ul>
<h2 id="2022-01-19">2022-01-19</h2>
<ul>
<li>Francesca was having issues with a submission on CGSpace this week
<ul>
<li>I checked and see a lot of locks in PostgreSQL:</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">&#34;SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid&#34;</span> | sort | uniq -c | sort -n
</span></span><span style="display:flex;"><span> 1
</span></span><span style="display:flex;"><span> 1 ------------------
</span></span><span style="display:flex;"><span> 1 (3506 rows)
</span></span><span style="display:flex;"><span> 1 application_name
</span></span><span style="display:flex;"><span> 9 psql
</span></span><span style="display:flex;"><span> 10
</span></span><span style="display:flex;"><span> 3487 dspaceWeb
</span></span></code></pre></div><ul>
<li>As before, I see messages from PostgreSQL about processes waiting for locks since I enabled the <code>log_lock_waits</code> setting last month:</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 -E <span style="color:#e6db74">&#39;^2022-01*&#39;</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">&#39;still waiting for&#39;</span>
</span></span><span style="display:flex;"><span>12
</span></span></code></pre></div><ul>
<li>I set a system alert on DSpace and then restarted the server</li>
</ul>
<h2 id="2022-01-20">2022-01-20</h2>
<ul>
<li>Abenet gave me a thumbs up for Gaia&rsquo;s eighteen CAS Green Cover items from last month
<ul>
<li>I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace import --add --eperson<span style="color:#f92672">=</span>aorth@mjanja.ch --source /tmp/SimpleArchiveFormat --mapfile<span style="color:#f92672">=</span>./2022-01-20-green-covers.map
</span></span></code></pre></div><h2 id="2022-01-21">2022-01-21</h2>
<ul>
<li>Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
<ul>
<li>I did some cleanups and standardization of author names</li>
<li>I also noticed that a few dozen items had no dates at all, so I checked the PDFs and found dates for them in the text</li>
<li>Otherwise all items have only a year, which is not great&hellip;</li>
</ul>
</li>
<li>Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
<ul>
<li>I did some basic tests and created a <a href="https://github.com/ilri/OpenRXV/pull/128">pull request</a></li>
</ul>
</li>
</ul>
<h2 id="2022-01-22">2022-01-22</h2>
<ul>
<li>Spend some time adding months to the CGIAR TAC and IWC records from Gaia
<ul>
<li>Most of the PDFs have only YYYY, so this is annoying&hellip;</li>
</ul>
</li>
</ul>
<h2 id="2022-01-23">2022-01-23</h2>
<ul>
<li>Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia</li>
<li>Rebuild AReS and start a fresh harvest</li>
</ul>
<h2 id="2022-01-25">2022-01-25</h2>
<ul>
<li>Help Udana from IWMI answer some questions about licenses on their journal articles
<ul>
<li>I was surprised to see they have 921 total, but only about 200 have a <code>dcterms.license</code> field</li>
<li>I updated about thirty manually, but really Udana should do more&hellip;</li>
</ul>
</li>
<li>Normalize the metadata <code>text_lang</code> attributes on CGSpace database:</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>dspace=# SELECT DISTINCT text_lang, count(text_lang) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) GROUP BY text_lang ORDER BY count DESC;
</span></span><span style="display:flex;"><span> text_lang | count
</span></span><span style="display:flex;"><span>-----------+---------
</span></span><span style="display:flex;"><span> en_US | 2803350
</span></span><span style="display:flex;"><span> en | 6232
</span></span><span style="display:flex;"><span> | 3200
</span></span><span style="display:flex;"><span> fr | 2
</span></span><span style="display:flex;"><span> vn | 2
</span></span><span style="display:flex;"><span> 92 | 1
</span></span><span style="display:flex;"><span> sp | 1
</span></span><span style="display:flex;"><span> | 0
</span></span><span style="display:flex;"><span>(8 rows)
</span></span><span style="display:flex;"><span>dspace=# UPDATE metadatavalue SET text_lang=&#39;en_US&#39; WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN (&#39;en&#39;, &#39;92&#39;, &#39;&#39;);
</span></span><span style="display:flex;"><span>UPDATE 9433
</span></span></code></pre></div><ul>
<li>Then export the WLE Journal Articles collection again so there are fewer columns to mess with</li>
</ul>
<h2 id="2022-01-26">2022-01-26</h2>
<ul>
<li>Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks</li>
</ul>
<h2 id="2022-01-27">2022-01-27</h2>
<ul>
<li>Work on WLE&rsquo;s Journal Articles a bit more
<ul>
<li>I realized that ~130 items have DOIs in their citation, but no <code>cg.identifier.doi</code> field</li>
<li>I used this OpenRefine GREL to copy them:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>cells[&#39;dcterms.bibliographicCitation[en_US]&#39;].value.split(&#34;doi: &#34;)[1]
</code></pre><ul>
<li>I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don&rsquo;t put DOIs in the citation so it&rsquo;s not possible to fix items that are missing DOIs that way
<ul>
<li>And I cleaned up and normalized some licenses</li>
</ul>
</li>
<li>Francesca from Bioversity was having issues with a submission on CGSpace again
<ul>
<li>I looked at PostgreSQL and see an increasing number of locks:</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">&#34;SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid&#34;</span> | sort | uniq -c | sort -n
</span></span><span style="display:flex;"><span> 1
</span></span><span style="display:flex;"><span> 1 ------------------
</span></span><span style="display:flex;"><span> 1 (537 rows)
</span></span><span style="display:flex;"><span> 1 application_name
</span></span><span style="display:flex;"><span> 9 psql
</span></span><span style="display:flex;"><span> 51 dspaceApi
</span></span><span style="display:flex;"><span> 477 dspaceWeb
</span></span><span style="display:flex;"><span>$ grep -E <span style="color:#e6db74">&#39;^2022-01*&#39;</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">&#39;still waiting for&#39;</span>
</span></span><span style="display:flex;"><span>3
</span></span></code></pre></div><ul>
<li>I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
<ul>
<li>The issue in Francesca&rsquo;s case was actually that someone had taken the task, not that PostgreSQL transactions were locked!</li>
</ul>
</li>
</ul>
<h2 id="2022-01-28">2022-01-28</h2>
<ul>
<li>Finalize the last ~100 WLE Journal Article items without licensese and DOIs
<ul>
<li>I did as many as I could, also updating http links to https for many journal links</li>
</ul>
</li>
<li>Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid)
<ul>
<li>She created an account on CGSpace and now we need to see which workflows she should belong to</li>
</ul>
</li>
<li>Start a fresh harvesting on AReS</li>
<li>I adjusted the <code>check-duplicates.py</code> script to write the output to a CSV file including the id, both titles, both dates, and the handle link
<ul>
<li>I included the id because I will need a unique field to join the resulting list of non-duplicates with the original CSV where the rest of the metadata and filenames are</li>
<li>Since these items are not in DSpace yet, I generated simple numeric IDs in OpenRefine using this GREL transform: <code>row.index + 1</code></li>
<li>Then I ran <code>check-duplicates.py</code> on items 1–200 and sent the resulting CSV to Gaia</li>
</ul>
</li>
<li>Delete one duplicate item I saw in IITA&rsquo;s Journal Articles that was uploaded earlier in WLE
<ul>
<li>Also do some general cleanup on IITA&rsquo;s Journal Articles collection in OpenRefine</li>
</ul>
</li>
<li>Delete one duplicate item I saw in ILRI&rsquo;s Journal Articles collection
<ul>
<li>Also do some general cleanup on ILRI&rsquo;s Journal Articles collection in OpenRefine and csv-metadata-quality</li>
</ul>
</li>
</ul>
<h2 id="2022-01-29">2022-01-29</h2>
<ul>
<li>I did some more cleanup on the ILRI Journal Articles
<ul>
<li>I added missing journal titles for items that had ISSNs</li>
<li>Then I added pages for items that had them in the citation</li>
<li>First, I faceted the citation field based on whether or not the item had something like &ldquo;: 232-234&rdquo; present:</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>value.contains(/:\s?\d+(-|–)\d+/)
</span></span></code></pre></div><ul>
<li>Then I faceted by blank on <code>dcterms.extent</code> and did a transform to extract the page information for over 1,000 items!</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>&#39;p. &#39; +
</span></span><span style="display:flex;"><span>cells[&#39;dcterms.bibliographicCitation[en_US]&#39;].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[0] +
</span></span><span style="display:flex;"><span>&#39;-&#39; +
</span></span><span style="display:flex;"><span>cells[&#39;dcterms.bibliographicCitation[en_US]&#39;].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[2]
</span></span></code></pre></div><ul>
<li>Then I did similar for <code>cg.volume</code> and <code>cg.issue</code>, also based on the citation, for example to extract the &ldquo;16&rdquo; from &ldquo;Journal of Blah 16(1)&rdquo;, where &ldquo;16&rdquo; is the second capture group in a zero-based match:</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>cells[&#39;dcterms.bibliographicCitation[en_US]&#39;].value.match(/.*( |;)(\d+)\((\d+)\).*/)[1]
</span></span></code></pre></div><ul>
<li>This was 3,000 items so I imported the changes on CGSpace 1,000 at a time&hellip;</li>
</ul>
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<li><a href="/cgspace-notes/2022-06/">June, 2022</a></li>
<li><a href="/cgspace-notes/2022-05/">May, 2022</a></li>
<li><a href="/cgspace-notes/2022-04/">April, 2022</a></li>
<li><a href="/cgspace-notes/2022-03/">March, 2022</a></li>
<li><a href="/cgspace-notes/2022-02/">February, 2022</a></li>
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<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>
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