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Start a full harvest on AReS
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Start a full harvest on AReS
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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/2022-01/">January, 2022</a></h2>
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<p class="blog-post-meta">
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<time datetime="2022-01-01T15:20:54+02:00">Sat Jan 01, 2022</time>
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in
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<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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</p>
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</header>
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<h2 id="2022-01-01">2022-01-01</h2>
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<ul>
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<li>Start a full harvest on AReS</li>
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</ul>
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<h2 id="2022-01-06">2022-01-06</h2>
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<ul>
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<li>Add ORCID identifier for Chris Jones to CGSpace
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<ul>
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<li>Also tag eighty-eight of his items in CGSpace:</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>$ cat 2022-01-06-add-orcids.csv
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</span></span><span style="display:flex;"><span>dc.contributor.author,cg.creator.identifier
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</span></span><span style="display:flex;"><span>"Jones, Chris","Chris Jones: 0000-0001-9096-9728"
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</span></span><span style="display:flex;"><span>"Jones, Christopher S.","Chris Jones: 0000-0001-9096-9728"
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</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">'dom@in34sniper'</span>
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</span></span></code></pre></div><h2 id="2022-01-09">2022-01-09</h2>
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<ul>
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<li>Validate and register CGSpace on <a href="https://www.openarchives.org/Register/ValidateSite?log=Z2V7WCT7">OpenArchives</a>
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<ul>
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<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>
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<li>Now it has worked and the message is “Successfully updated OAI registration database to status COMPLIANT.”</li>
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<li>I received an email (as the Admin contact on our OAI) that says:</li>
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</ul>
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</li>
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</ul>
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<blockquote>
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<p>Your repository has been registered in the OAI database of conforming repositories.</p>
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</blockquote>
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<ul>
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<li>Now I’m taking a screenshot of the validation page for posterity, because the logs seem to go away after some time</li>
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</ul>
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<p><img src="/cgspace-notes/2022/01/openarchives-registration.png" alt="OpenArchives.org registration"></p>
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<ul>
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<li>I tried to re-build the Docker image for OpenRXV and got an error in the backend:</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>...
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</span></span><span style="display:flex;"><span>> openrxv-backend@0.0.1 build
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</span></span><span style="display:flex;"><span>> nest build
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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>node_modules/@elastic/elasticsearch/api/types.d.ts:2454:13 - error TS2456: Type alias 'AggregationsAggregate' circularly references itself.
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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>2454 export type AggregationsAggregate = AggregationsSingleBucketAggregate | AggregationsAutoDateHistogramAggregate | AggregationsFiltersAggregate | AggregationsSignificantTermsAggregate<any> | AggregationsTermsAggregate<any> | AggregationsBucketAggregate | AggregationsCompositeBucketAggregate | AggregationsMultiBucketAggregate<AggregationsBucket> | AggregationsMatrixStatsAggregate | AggregationsKeyedValueAggregate | AggregationsMetricAggregate
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</span></span><span style="display:flex;"><span> ~~~~~~~~~~~~~~~~~~~~~
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</span></span><span style="display:flex;"><span>node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.
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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>3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
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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>Found 2 error(s).
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</span></span></code></pre></div><ul>
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<li>Ah, it seems the code on the server was slightly out of date
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<ul>
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<li>I checked out the latest master branch and it built</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-01-12">2022-01-12</h2>
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<ul>
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<li>Fix some citation formatting issues in Gaia’s <a href="https://dspacetest.cgiar.org/handle/10568/115230">eighteen CAS Green Cover publications on DSpace Test</a></li>
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</ul>
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<h2 id="2022-01-19">2022-01-19</h2>
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<ul>
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<li>Francesca was having issues with a submission on CGSpace this week
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<ul>
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<li>I checked and see a lot of locks in PostgreSQL:</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>$ psql -c <span style="color:#e6db74">"SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
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</span></span><span style="display:flex;"><span> 1
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</span></span><span style="display:flex;"><span> 1 ------------------
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</span></span><span style="display:flex;"><span> 1 (3506 rows)
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</span></span><span style="display:flex;"><span> 1 application_name
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</span></span><span style="display:flex;"><span> 9 psql
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</span></span><span style="display:flex;"><span> 10
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</span></span><span style="display:flex;"><span> 3487 dspaceWeb
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</span></span></code></pre></div><ul>
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<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>
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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>$ grep -E <span style="color:#e6db74">'^2022-01*'</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">'still waiting for'</span>
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</span></span><span style="display:flex;"><span>12
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</span></span></code></pre></div><ul>
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<li>I set a system alert on DSpace and then restarted the server</li>
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</ul>
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<h2 id="2022-01-20">2022-01-20</h2>
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<ul>
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<li>Abenet gave me a thumbs up for Gaia’s eighteen CAS Green Cover items from last month
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<ul>
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<li>I created a SimpleArchiveFormat bundle with SAFBuilder and then imported them on CGSpace:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">"-Xmx1024m -Dfile.encoding=UTF-8"</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
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</span></span></code></pre></div><h2 id="2022-01-21">2022-01-21</h2>
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<ul>
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<li>Start working on the rest of the ~980 CGIAR TAC and ICW documents from Gaia
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<ul>
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<li>I did some cleanups and standardization of author names</li>
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<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>
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<li>Otherwise all items have only a year, which is not great…</li>
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</ul>
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</li>
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<li>Proof of concept upgrade of OpenRXV from Angular 9 to Angular 10
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<ul>
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<li>I did some basic tests and created a <a href="https://github.com/ilri/OpenRXV/pull/128">pull request</a></li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-01-22">2022-01-22</h2>
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<ul>
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<li>Spend some time adding months to the CGIAR TAC and IWC records from Gaia
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<ul>
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<li>Most of the PDFs have only YYYY, so this is annoying…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-01-23">2022-01-23</h2>
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<ul>
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<li>Finalize cleaning up the dates on the CGIAR TAC and IWC records from Gaia</li>
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<li>Rebuild AReS and start a fresh harvest</li>
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</ul>
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<h2 id="2022-01-25">2022-01-25</h2>
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<ul>
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<li>Help Udana from IWMI answer some questions about licenses on their journal articles
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<ul>
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<li>I was surprised to see they have 921 total, but only about 200 have a <code>dcterms.license</code> field</li>
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<li>I updated about thirty manually, but really Udana should do more…</li>
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</ul>
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</li>
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<li>Normalize the metadata <code>text_lang</code> attributes on CGSpace database:</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>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;
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</span></span><span style="display:flex;"><span> text_lang | count
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</span></span><span style="display:flex;"><span>-----------+---------
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</span></span><span style="display:flex;"><span> en_US | 2803350
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</span></span><span style="display:flex;"><span> en | 6232
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</span></span><span style="display:flex;"><span> | 3200
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</span></span><span style="display:flex;"><span> fr | 2
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</span></span><span style="display:flex;"><span> vn | 2
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</span></span><span style="display:flex;"><span> 92 | 1
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</span></span><span style="display:flex;"><span> sp | 1
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</span></span><span style="display:flex;"><span> | 0
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</span></span><span style="display:flex;"><span>(8 rows)
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</span></span><span style="display:flex;"><span>dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_lang IN ('en', '92', '');
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</span></span><span style="display:flex;"><span>UPDATE 9433
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</span></span></code></pre></div><ul>
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<li>Then export the WLE Journal Articles collection again so there are fewer columns to mess with</li>
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</ul>
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<h2 id="2022-01-26">2022-01-26</h2>
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<ul>
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<li>Send Gaia an example of the duplicate report for the first 200 TAC items to see what she thinks</li>
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</ul>
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<h2 id="2022-01-27">2022-01-27</h2>
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<ul>
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<li>Work on WLE’s Journal Articles a bit more
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<ul>
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<li>I realized that ~130 items have DOIs in their citation, but no <code>cg.identifier.doi</code> field</li>
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<li>I used this OpenRefine GREL to copy them:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>cells['dcterms.bibliographicCitation[en_US]'].value.split("doi: ")[1]
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</code></pre><ul>
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<li>I also spent a bit of time cleaning up ILRI Journal Articles, but I notice that we don’t put DOIs in the citation so it’s not possible to fix items that are missing DOIs that way
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<ul>
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<li>And I cleaned up and normalized some licenses</li>
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</ul>
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</li>
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<li>Francesca from Bioversity was having issues with a submission on CGSpace again
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<ul>
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<li>I looked at PostgreSQL and see an increasing number of locks:</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>$ psql -c <span style="color:#e6db74">"SELECT application_name FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON pl.pid = psa.pid"</span> | sort | uniq -c | sort -n
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</span></span><span style="display:flex;"><span> 1
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</span></span><span style="display:flex;"><span> 1 ------------------
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</span></span><span style="display:flex;"><span> 1 (537 rows)
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</span></span><span style="display:flex;"><span> 1 application_name
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</span></span><span style="display:flex;"><span> 9 psql
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</span></span><span style="display:flex;"><span> 51 dspaceApi
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</span></span><span style="display:flex;"><span> 477 dspaceWeb
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</span></span><span style="display:flex;"><span>$ grep -E <span style="color:#e6db74">'^2022-01*'</span> /var/log/postgresql/postgresql-10-main.log | grep -c <span style="color:#e6db74">'still waiting for'</span>
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</span></span><span style="display:flex;"><span>3
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</span></span></code></pre></div><ul>
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<li>I set a system alert on CGSpace and then restarted Tomcat and PostgreSQL
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<ul>
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<li>The issue in Francesca’s case was actually that someone had taken the task, not that PostgreSQL transactions were locked!</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-01-28">2022-01-28</h2>
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<ul>
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<li>Finalize the last ~100 WLE Journal Article items without licensese and DOIs
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<ul>
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<li>I did as many as I could, also updating http links to https for many journal links</li>
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</ul>
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</li>
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<li>Federica Bottamedi contacted us from the system office to say that she took over for Vini (Abhilasha Vaid)
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<ul>
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<li>She created an account on CGSpace and now we need to see which workflows she should belong to</li>
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</ul>
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</li>
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<li>Start a fresh harvesting on AReS</li>
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<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
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<ul>
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<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>
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<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>
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<li>Then I ran <code>check-duplicates.py</code> on items 1–200 and sent the resulting CSV to Gaia</li>
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</ul>
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</li>
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<li>Delete one duplicate item I saw in IITA’s Journal Articles that was uploaded earlier in WLE
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<ul>
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<li>Also do some general cleanup on IITA’s Journal Articles collection in OpenRefine</li>
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</ul>
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</li>
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<li>Delete one duplicate item I saw in ILRI’s Journal Articles collection
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<ul>
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<li>Also do some general cleanup on ILRI’s Journal Articles collection in OpenRefine and csv-metadata-quality</li>
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</ul>
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</li>
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</ul>
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<h2 id="2022-01-29">2022-01-29</h2>
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<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 “: 232-234” 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>'p. ' +
|
||
</span></span><span style="display:flex;"><span>cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-|–)(\d+).*/)[0] +
|
||
</span></span><span style="display:flex;"><span>'-' +
|
||
</span></span><span style="display:flex;"><span>cells['dcterms.bibliographicCitation[en_US]'].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 “16” from “Journal of Blah 16(1)”, where “16” 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['dcterms.bibliographicCitation[en_US]'].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…</li>
|
||
</ul>
|
||
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|
||
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|
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|
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</article>
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<h4>Recent Posts</h4>
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<ol class="list-unstyled">
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<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
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<li><a href="/cgspace-notes/2022-11/">November, 2022</a></li>
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<li><a href="/cgspace-notes/2022-10/">October, 2022</a></li>
|
||
|
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<li><a href="/cgspace-notes/2022-09/">September, 2022</a></li>
|
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|
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<li><a href="/cgspace-notes/2022-08/">August, 2022</a></li>
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</ol>
|
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</section>
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|
||
<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>
|
||
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|
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|
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|
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