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<meta property="og:title" content="January, 2022" />
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<meta property="og:description" content="2022-01-01
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Start a full harvest on AReS
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" />
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<meta property="article:modified_time" content="2022-01-12T19:55:47+02:00" />
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<meta name="twitter:title" content="January, 2022"/>
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<meta name="twitter:description" content="2022-01-01
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Start a full harvest on AReS
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<meta name="generator" content="Hugo 0.92.0" />
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{
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "January, 2022",
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"url": "https://alanorth.github.io/cgspace-notes/2022-01/",
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"name": "Alan Orth"
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<title>January, 2022 | CGSpace Notes</title>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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<header class="blog-header">
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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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</header>
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<div class="container">
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<article class="blog-post">
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<header>
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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="/cgspace-notes/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">$ cat 2022-01-06-add-orcids.csv
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dc.contributor.author,cg.creator.identifier
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"Jones, Chris","Chris Jones: 0000-0001-9096-9728"
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"Jones, Christopher S.","Chris Jones: 0000-0001-9096-9728"
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$ ./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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</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">...
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> openrxv-backend@0.0.1 build
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> nest build
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<span style="color:#960050;background-color:#1e0010">
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</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 style="color:#960050;background-color:#1e0010">
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</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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~~~~~~~~~~~~~~~~~~~~~
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node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type alias 'AggregationsSingleBucketAggregate' circularly references itself.
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<span style="color:#960050;background-color:#1e0010">
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</span><span style="color:#960050;background-color:#1e0010"></span>3209 export type AggregationsSingleBucketAggregate = AggregationsSingleBucketAggregateKeys
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<span style="color:#960050;background-color:#1e0010">
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</span><span style="color:#960050;background-color:#1e0010"></span>Found 2 error(s).
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</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">$ 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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1
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1 ------------------
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1 (3506 rows)
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1 application_name
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9 psql
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10
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3487 dspaceWeb
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</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">$ 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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12
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</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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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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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/2022-01/">January, 2022</a></li>
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<li><a href="/cgspace-notes/2021-12/">December, 2021</a></li>
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<li><a href="/cgspace-notes/2021-11/">November, 2021</a></li>
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<li><a href="/cgspace-notes/2021-10/">October, 2021</a></li>
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<li><a href="/cgspace-notes/2021-09/">September, 2021</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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</ol>
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</section>
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