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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)
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iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
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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)
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iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
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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>
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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/2023-03/">March, 2023</a></h2>
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<time datetime="2023-03-01T07:58:36+03:00">Wed Mar 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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</p>
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</header>
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<h2 id="2023-03-01">2023-03-01</h2>
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<ul>
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<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>
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<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>
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<li>I finally got through with porting the input form from DSpace 6 to DSpace 7</li>
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</ul>
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<ul>
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<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>
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</ul>
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<h2 id="2023-03-02">2023-03-02</h2>
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<ul>
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<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>
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<ul>
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<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>
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<li>I think we need consider blanks as null, but I’m not sure</li>
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</ul>
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</li>
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<li>I made some adjustments to the Discovery sidebar facets on DSpace 6 while I was looking at the DSpace 7 configuration
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<ul>
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<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>
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</ul>
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</li>
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</ul>
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<h2 id="2023-03-03">2023-03-03</h2>
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<ul>
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<li>Atmire merged one of my old pull requests into COUNTER-Robots:
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<ul>
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<li><a href="https://github.com/atmire/COUNTER-Robots/pull/54">COUNTER_Robots_list.json: Add new bots</a></li>
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</ul>
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</li>
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<li>I will update the local ILRI overrides in our DSpace spider agents file</li>
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</ul>
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<h2 id="2023-03-04">2023-03-04</h2>
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<ul>
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<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>
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</ul>
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<h2 id="2023-03-05">2023-03-05</h2>
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<ul>
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<li>Start a harvest on AReS</li>
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</ul>
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<h2 id="2023-03-06">2023-03-06</h2>
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<ul>
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<li>Export CGSpace to do Initiative collection mappings
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<ul>
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<li>There were thirty-three that needed updating</li>
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</ul>
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</li>
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<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
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<ul>
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<li>Goshu will download the PDFs for each and upload them to the items on CGSpace manually</li>
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</ul>
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</li>
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<li>I spent some time trying to get csv-metadata-quality working with the new Arrow backend for Pandas 2.0.0rc0
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<ul>
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<li>It seems there is a problem recognizing empty strings as na with <code>pd.isna()</code></li>
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<li>If I do <code>pd.isna(field) or field == ""</code> then it works as expected, but that feels hacky</li>
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<li>I’m going to test again on the next release…</li>
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<li>Note that I had been setting both of these global options:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>pd.options.mode.dtype_backend = 'pyarrow'
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pd.options.mode.nullable_dtypes = True
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</code></pre><ul>
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<li>Then reading the CSV like this:</li>
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</ul>
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<pre tabindex="0"><code>df = pd.read_csv(args.input_file, engine='pyarrow', dtype='string[pyarrow]'
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</code></pre><h2 id="2023-03-07">2023-03-07</h2>
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<ul>
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<li>Create a PostgreSQL 14 instance on my local environment to start testing compatibility with DSpace 6 as well as all my scripts:</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>$ podman pull docker.io/library/postgres:14-alpine
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</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
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</span></span><span style="display:flex;"><span>$ createuser -h localhost -p <span style="color:#ae81ff">5432</span> -U postgres --pwprompt dspacetest
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</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
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</span></span></code></pre></div><ul>
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<li>Peter sent me a list of items that had ILRI affiation on Altmetric, but that didn’t have Handles
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<ul>
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<li>I ran a duplicate check on them to find if they exist or if we can import them</li>
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<li>There were about ninety matches, but a few dozen of those were pre-prints!</li>
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<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
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<ul>
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<li>After joining these with the records from CGSpace and inspecting the DOIs I found that only forty-four were new DOIs</li>
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<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>
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</ul>
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</li>
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<li>For the rest of the ~359 items I extracted their DOIs and looked up the metadata on Crossref using my <code>crossref-doi-lookup.py</code> script
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<ul>
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<li>After spending some time cleaning the data in OpenRefine I realized we don’t get access status from Crossref</li>
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<li>We can imply it if the item is Creative Commons, but otherwise I might be able to use <a href="https://unpaywall.org/products/api">Unpaywall’s API</a></li>
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<li>I found some false positives in Unpaywall, so I might only use their data when it says the DOI is not OA…</li>
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</ul>
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</li>
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</ul>
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</li>
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<li>During this process I updated my <code>crossref-doi-lookup.py</code> script to get more information from Crossref like ISSNs, ISBNs, full journal title, and subjects</li>
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<li>An unscientific comparison of duplicate checking Peter’s file with ~500 titles on PostgreSQL 12 and PostgreSQL 14:
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<ul>
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<li>PostgreSQL 12: <code>0.11s user 0.04s system 0% cpu 19:24.65 total</code></li>
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<li>PostgreSQL 14: <code>0.12s user 0.04s system 0% cpu 18:13.47 total</code></li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-03-08">2023-03-08</h2>
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<ul>
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<li>I am wondering how to speed up PostgreSQL trgm searches more
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<ul>
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<li>I see my local PostgreSQL is using vanilla configuration and I should update some configs:</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/dspacetest= ☘ SELECT setting, unit FROM pg_settings WHERE name = 'shared_buffers';
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</span></span><span style="display:flex;"><span> setting │ unit
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</span></span><span style="display:flex;"><span>─────────┼──────
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</span></span><span style="display:flex;"><span> 16384 │ 8kB
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</span></span><span style="display:flex;"><span>(1 row)
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</span></span></code></pre></div><ul>
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<li>I re-created my PostgreSQL 14 container with some extra memory settings:</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>$ 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 -c shared_buffers<span style="color:#f92672">=</span>1024MB -c random_page_cost<span style="color:#f92672">=</span>1.1
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</span></span></code></pre></div><ul>
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<li>Then I created a GiST <a href="https://alexklibisz.com/2022/02/18/optimizing-postgres-trigram-search">index on the <code>metadatavalue</code> table to try to speed up the trgm similarity operations</a>:</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/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gist_idx ON metadatavalue USING gist(text_value gist_trgm_ops(siglen=64)); # \di+ shows index size is 795MB
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</span></span></code></pre></div><ul>
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<li>That took a few minutes to build… then the duplicate checker ran in 12 minutes: <code>0.07s user 0.02s system 0% cpu 12:43.08 total</code></li>
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<li>On a hunch, I tried with a GIN index:</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/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gin_idx ON metadatavalue USING gin(text_value gin_trgm_ops); # \di+ shows index size is 274MB
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</span></span></code></pre></div><ul>
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<li>This ran in 19 minutes: <code>0.08s user 0.01s system 0% cpu 19:49.73 total</code>
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<ul>
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<li>So clearly the GiST index is better for this task</li>
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<li>I am curious if I increase the signature length in the GiST index from 64 to 256 (which will for sure increase the size taken):</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/dspacetest= ☘ CREATE INDEX metadatavalue_text_value_trgm_gist_idx ON metadatavalue USING gist(text_value gist_trgm_ops(siglen=256)); # \di+ shows index size is 716MB, which is less than the previous GiST index...
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</span></span></code></pre></div><ul>
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<li>This one finished in ten minutes: <code>0.07s user 0.02s system 0% cpu 10:04.04 total</code></li>
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<li>I might also want to <a href="https://stackoverflow.com/questions/43008382/postgresql-gin-index-slower-than-gist-for-pg-trgm">increase my <code>work_mem</code></a> (default 4MB):</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/dspacetest= ☘ SELECT setting, unit FROM pg_settings WHERE name = 'work_mem';
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</span></span><span style="display:flex;"><span> setting │ unit
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</span></span><span style="display:flex;"><span>─────────┼──────
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</span></span><span style="display:flex;"><span> 4096 │ kB
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</span></span><span style="display:flex;"><span>(1 row)
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</span></span></code></pre></div><ul>
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<li>After updating my Crossref lookup script and checking the remaining ~359 items I found a eight more duplicates already existing on CGSpace</li>
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<li>Wow, I found a <a href="https://programminghistorian.org/en/lessons/fetch-and-parse-data-with-openrefine#example-1-fetching-and-parsing-html">really cool way to fetch URLs in OpenRefine</a>
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<ul>
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<li>I used this to fetch the open access status for each DOI from Unpaywall</li>
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</ul>
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</li>
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<li>First, create a new column called “url” based on the DOI that builds the request URL. I used a Jython expression:</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-python" data-lang="python"><span style="display:flex;"><span>unpaywall_baseurl <span style="color:#f92672">=</span> <span style="color:#e6db74">'https://api.unpaywall.org/v2/'</span>
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</span></span><span style="display:flex;"><span>email <span style="color:#f92672">=</span> <span style="color:#e6db74">"a.orth+unpaywall@cgiar.org"</span>
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</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> value<span style="color:#f92672">.</span>replace(<span style="color:#e6db74">"https://doi.org/"</span>, <span style="color:#e6db74">""</span>)
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</span></span><span style="display:flex;"><span>request_url <span style="color:#f92672">=</span> unpaywall_baseurl <span style="color:#f92672">+</span> doi <span style="color:#f92672">+</span> <span style="color:#e6db74">'?email='</span> <span style="color:#f92672">+</span> email
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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:#66d9ef">return</span> request_url
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</span></span></code></pre></div><ul>
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<li>Then create a new column based on fetching the values in that column. I called it “unpaywall_status”</li>
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<li>Then you get a JSON blob in each and you can extract the Open Access status with a GREL like <code>value.parseJson()['is_oa']</code>
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<ul>
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<li>I checked a handful of results manually and found that the limited access status was more trustworthy from Unpaywall than the open access, so I will just tag the limited access ones</li>
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</ul>
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</li>
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<li>I merged the funders and affiliations from Altmetric into my file, then used the same technique to get Crossref data for open access items directly into OpenRefine and parsed the abstracts
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<ul>
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<li>The syntax was hairy because it’s marked up with tags like <code><jats:p></code>, but this got me most of the way there:</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>value.replace("jats:p", "jats-p").parseHtml().select("jats-p")[0].innerHtml()
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</span></span><span style="display:flex;"><span>value.replace("<jats:italic>","").replace("</jats:italic>", "")
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</span></span><span style="display:flex;"><span>value.replace("<jats:sub>","").replace("</jats:sub>", "").replace("<jats:sup>","").replace("</jats:sup>", "")
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</span></span></code></pre></div><ul>
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<li>I uploaded the 350 items to DSpace Test so Peter and Abenet can explore them</li>
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<li>I exported a list of authors, affiliations, and funders from the new items to let Peter correct them:</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 dc.contributor.author /tmp/new-items.csv | sed -e 1d -e <span style="color:#e6db74">'s/"//g'</span> -e <span style="color:#e6db74">'s/||/\n/g'</span> | sort | uniq -c | sort -nr | awk <span style="color:#e6db74">'{$1=""; print $0}'</span> | sed -e <span style="color:#e6db74">'s/^ //'</span> > /tmp/new-authors.csv
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</span></span></code></pre></div><ul>
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<li>Meeting with FAO AGRIS team about how to detect duplicates
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<ul>
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<li>They are currently using a sha256 hash on titles, which will work, but will only return exact matches</li>
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<li>I told them to try to normalize the string, drop stop words, etc to increase the possibility that the hash matches</li>
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</ul>
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</li>
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<li>Meeting with Abenet to discuss CGSpace issues
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<ul>
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<li>She reminded me about needing a metadata field for first author when the affiliation is ILRI</li>
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<li>I said I prefer to write a small script for her that will check the first author and first affiliation… I could do it easily in Python, but would need to put a web frontend on it for her</li>
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<li>Unless we could do that in AReS reports somehow</li>
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</ul>
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</li>
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</ul>
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<h2 id="2023-03-09">2023-03-09</h2>
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<ul>
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<li>Apply a bunch of corrections to authors, affiliations, and donors on the new items on DSpace Test</li>
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<li>Meeting with Peter and Abenet about future OpenRXV developments, DSpace 7, etc
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<ul>
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<li>I submitted an <a href="https://github.com/CodeObia/MEL/issues/11173">issue on MEL asking them to add provenance metadata when submitting to CGSpace</a></li>
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</ul>
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</li>
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</ul>
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<h4>Recent Posts</h4>
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<li><a href="/cgspace-notes/2023-03/">March, 2023</a></li>
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<li><a href="/cgspace-notes/2023-02/">February, 2023</a></li>
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<li><a href="/cgspace-notes/2023-01/">January, 2023</a></li>
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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="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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