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Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
I finally got through with porting the input form from DSpace 6 to DSpace 7
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Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)
iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
I finally got through with porting the input form from DSpace 6 to DSpace 7
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<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
<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/2023-03/">March, 2023</a></h2>
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<time datetime="2023-03-01T07:58:36+03:00">Wed Mar 01, 2023</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
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<h2 id="2023-03-01">2023-03-01</h2>
<ul>
<li>Remove <code>cg.subject.wle</code> and <code>cg.identifier.wletheme</code> from CGSpace input form after confirming with IWMI colleagues that they no longer need them (WLE closed in 2021)</li>
<li><a href="https://salsa.debian.org/iso-codes-team/iso-codes/-/blob/main/CHANGELOG.md#4130-2023-02-28">iso-codes 4.13.0 was released</a>, which incorporates my changes to the common names for Iran, Laos, and Syria</li>
<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
</ul>
<ul>
<li>I can’t put my finger on it, but the input form has to be formatted very particularly, for example if your rows have more than two fields in them with out a sufficient Bootstrap grid style, or if you use a <code>twobox</code>, etc, the entire form step appears blank</li>
</ul>
<h2 id="2023-03-02">2023-03-02</h2>
<ul>
<li>I did some experiments with the new <a href="https://datapythonista.me/blog/pandas-20-and-the-arrow-revolution-part-i">Pandas 2.0.0rc0 Apache Arrow support</a>
<ul>
<li>There is a change to the way nulls are handled and it causes my tests for <code>pd.isna(field)</code> to fail</li>
<li>I think we need consider blanks as null, but I’m not sure</li>
</ul>
</li>
<li>I made some adjustments to the Discovery sidebar facets on DSpace 6 while I was looking at the DSpace 7 configuration
<ul>
<li>I downgraded CIFOR subject, Humidtropics subject, Drylands subject, ICARDA subject, and Language from DiscoverySearchFilterFacet to DiscoverySearchFilter in <code>discovery.xml</code> since we are no longer using them in sidebar facets</li>
</ul>
</li>
</ul>
<h2 id="2023-03-03">2023-03-03</h2>
<ul>
<li>Atmire merged one of my old pull requests into COUNTER-Robots:
<ul>
<li><a href="https://github.com/atmire/COUNTER-Robots/pull/54">COUNTER_Robots_list.json: Add new bots</a></li>
</ul>
</li>
<li>I will update the local ILRI overrides in our DSpace spider agents file</li>
</ul>
<h2 id="2023-03-04">2023-03-04</h2>
<ul>
<li>Submit a <a href="https://github.com/flyingcircusio/pycountry/pull/156">pull request on pycountry to use iso-codes 4.13.0</a></li>
</ul>
<h2 id="2023-03-05">2023-03-05</h2>
<ul>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-03-06">2023-03-06</h2>
<ul>
<li>Export CGSpace to do Initiative collection mappings
<ul>
<li>There were thirty-three that needed updating</li>
</ul>
</li>
<li>Send Abenet and Sam a list of twenty-one CAS publications that had been marked as “multiple documents” that we uploaded as metadata-only items
<ul>
<li>Goshu will download the PDFs for each and upload them to the items on CGSpace manually</li>
</ul>
</li>
<li>I spent some time trying to get csv-metadata-quality working with the new Arrow backend for Pandas 2.0.0rc0
<ul>
<li>It seems there is a problem recognizing empty strings as na with <code>pd.isna()</code></li>
<li>If I do <code>pd.isna(field) or field == ""</code> then it works as expected, but that feels hacky</li>
<li>I’m going to test again on the next release…</li>
<li>Note that I had been setting both of these global options:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>pd.options.mode.dtype_backend = 'pyarrow'
pd.options.mode.nullable_dtypes = True
</code></pre><ul>
<li>Then reading the CSV like this:</li>
</ul>
<pre tabindex="0"><code>df = pd.read_csv(args.input_file, engine='pyarrow', dtype='string[pyarrow]'
</code></pre><h2 id="2023-03-07">2023-03-07</h2>
<ul>
<li>Create a PostgreSQL 14 instance on my local environment to start testing compatibility with DSpace 6 as well as all my scripts:</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>$ podman pull docker.io/library/postgres:14-alpine
</span></span><span style="display:flex;"><span>$ podman run --name dspacedb14 -v dspacedb14_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD<span style="color:#f92672">=</span>postgres -p 5432:5432 -d postgres:14-alpine
</span></span><span style="display:flex;"><span>$ createuser -h localhost -p <span style="color:#ae81ff">5432</span> -U postgres --pwprompt dspacetest
</span></span><span style="display:flex;"><span>$ createdb -h localhost -p <span style="color:#ae81ff">5432</span> -U postgres -O dspacetest --encoding<span style="color:#f92672">=</span>UNICODE dspacetest
</span></span></code></pre></div><ul>
<li>Peter sent me a list of items that had ILRI affiation on Altmetric, but that didn’t have Handles
<ul>
<li>I ran a duplicate check on them to find if they exist or if we can import them</li>
<li>There were about ninety matches, but a few dozen of those were pre-prints!</li>
<li>After excluding those there were about sixty-one items we already have on CGSpace so I will add their DOIs to the existing items
<ul>
<li>After joining these with the records from CGSpace and inspecting the DOIs I found that only forty-four were new DOIs</li>
<li>Surprisingly some of the DOIs on Altmetric were not working, though we also had some that were not working (specifically the Journal of Agricultural Economics seems to have reassigned DOIs)</li>
</ul>
</li>
</ul>
</li>
<li>An unscientific comparison of duplicate checking Peter’s file with ~500 titles on PostgreSQL 12 and PostgreSQL 14:
<ul>
<li>PostgreSQL 12: <code>0.11s user 0.04s system 0% cpu 19:24.65 total</code></li>
<li>PostgreSQL 14: <code>0.12s user 0.04s system 0% cpu 18:13.47 total</code></li>
</ul>
</li>
</ul>
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<h4>Recent Posts</h4>
<ol class="list-unstyled">
<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>
<li><a href="/cgspace-notes/2022-12/">December, 2022</a></li>
<li><a href="/cgspace-notes/2022-11/">November, 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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