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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
|
|
</span></span></code></pre></div><ul>
|
|
<li>Meeting with FAO AGRIS team about how to detect duplicates
|
|
<ul>
|
|
<li>They are currently using a sha256 hash on titles, which will work, but will only return exact matches</li>
|
|
<li>I told them to try to normalize the string, drop stop words, etc to increase the possibility that the hash matches</li>
|
|
</ul>
|
|
</li>
|
|
<li>Meeting with Abenet to discuss CGSpace issues
|
|
<ul>
|
|
<li>She reminded me about needing a metadata field for first author when the affiliation is ILRI</li>
|
|
<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>
|
|
<li>Unless we could do that in AReS reports somehow</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-09">2023-03-09</h2>
|
|
<ul>
|
|
<li>Apply a bunch of corrections to authors, affiliations, and donors on the new items on DSpace Test</li>
|
|
<li>Meeting with Peter and Abenet about future OpenRXV developments, DSpace 7, etc
|
|
<ul>
|
|
<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>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-10">2023-03-10</h2>
|
|
<ul>
|
|
<li>CKM is getting ready to launch their new website and they display CGSpace thumbnails at 255x362px
|
|
<ul>
|
|
<li>Our thumbnails are 300px so they get up-scaled and look bad</li>
|
|
<li>I realized that the last time we <a href="https://github.com/ilri/DSpace/commit/5de61e220124c1d0441c87cd7d36d18cb2293c03">increased the size of our thumbnails was in 2013</a>, from 94x130 to 300px</li>
|
|
<li>I offered to CKM that we increase them again to 400 or 600px</li>
|
|
<li>I did some tests to check the thumbnail file sizes for 300px, 400px, 500px, and 600px on <a href="https://hdl.handle.net/10568/126388">this item</a>:</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>$ ls -lh 10568-126388-*
|
|
</span></span><span style="display:flex;"><span>-rw-r--r-- 1 aorth aorth 31K Mar 10 12:42 10568-126388-300px.jpg
|
|
</span></span><span style="display:flex;"><span>-rw-r--r-- 1 aorth aorth 52K Mar 10 12:41 10568-126388-400px.jpg
|
|
</span></span><span style="display:flex;"><span>-rw-r--r-- 1 aorth aorth 76K Mar 10 12:43 10568-126388-500px.jpg
|
|
</span></span><span style="display:flex;"><span>-rw-r--r-- 1 aorth aorth 106K Mar 10 12:44 10568-126388-600px.jpg
|
|
</span></span></code></pre></div><ul>
|
|
<li>Seems like 600px is 3 to 4 times larger file size, so maybe we should shoot for 400px or 500px
|
|
<ul>
|
|
<li>I decided on 500px</li>
|
|
<li>I started re-generating new thumbnails for the ILRI Publications, CGIAR Initiatives, and other collections</li>
|
|
</ul>
|
|
</li>
|
|
<li>On that note, I also re-worked the XMLUI item display to show larger thumbnails (from a max-width of 128px to 200px)</li>
|
|
<li>And now that I’m looking at thumbnails I am curious what it would take to get DSpace to generate WebP or AVIF thumbnails</li>
|
|
<li>Peter sent me citations and ILRI subjects for the 350 new ILRI publications
|
|
<ul>
|
|
<li>I guess he edited it in Excel because there are a bunch of encoding issues with accents</li>
|
|
<li>I merged Peter’s citations and subjects with the other metadata, ran one last duplicate check (and found one item!), then ran the items through csv-metadata-quality and uploaded them to CGSpace</li>
|
|
<li>In the end it was only 348 items for some reason…</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-12">2023-03-12</h2>
|
|
<ul>
|
|
<li>Start a harvest on AReS</li>
|
|
</ul>
|
|
<h2 id="2023-03-13">2023-03-13</h2>
|
|
<ul>
|
|
<li>Extract a list of DOIs from the Creative Commons licensed ILRI journal articles that I uploaded last week, skipping any that are “no derivatives” (ND):</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>$ csvgrep -c <span style="color:#e6db74">'dc.description.provenance[en]'</span> -m <span style="color:#e6db74">'Made available in DSpace on 2023-03-10'</span> /tmp/ilri-articles.csv <span style="color:#ae81ff">\
|
|
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | csvgrep -c 'dcterms.license[en_US]' -r 'CC(0|\-BY)'
|
|
</span></span><span style="display:flex;"><span> | csvgrep -c 'dcterms.license[en_US]' -i -r '\-ND\-'
|
|
</span></span><span style="display:flex;"><span> | csvcut -c 'id,cg.identifier.doi[en_US],dcterms.type[en_US]' > 2023-03-13-journal-articles.csv
|
|
</span></span></code></pre></div><ul>
|
|
<li>I want to write a script to download the PDFs and create thumbnails for them, then upload to CGSpace
|
|
<ul>
|
|
<li>I wrote one based on <code>post_ciat_pdfs.py</code> but it seems there is an issue uploading anything other than a PDF</li>
|
|
<li>When I upload a JPG or a PNG the file begins with:</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>Content-Disposition: form-data; name="file"; filename="10.1017-s0031182013001625.pdf.jpg"
|
|
</span></span></code></pre></div><ul>
|
|
<li>… this means it is invalid…
|
|
<ul>
|
|
<li>I tried in both the <code>ORIGINAL</code> and <code>THUMBNAIL</code> bundle, and with different filenames</li>
|
|
<li>I tried manually on the command line with <code>http</code> and both PDF and PNG work… hmmmm</li>
|
|
<li>Hmm, this seems to have been due to some difference in behavior between the <code>files</code> and <code>data</code> parameters of <code>requests.get()</code></li>
|
|
<li>I finalized the <code>post_bitstreams.py</code> script and uploaded eighty-five PDF thumbnails</li>
|
|
</ul>
|
|
</li>
|
|
<li>It seems Bizu uploaded covers for a handful so I deleted them and ran them through the script to get proper thumbnails</li>
|
|
</ul>
|
|
<h2 id="2023-03-14">2023-03-14</h2>
|
|
<ul>
|
|
<li>Add twelve IFPRI authors to our controlled vocabulary for authors and ORCID identifiers
|
|
<ul>
|
|
<li>I also tagged their existing items on CGSpace</li>
|
|
</ul>
|
|
</li>
|
|
<li>Export all our ORCIDs and resolve their names to see if any have changed:</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 dspace/config/controlled-vocabularies/cg-creator-identifier.xml | grep -oE <span style="color:#e6db74">'[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}'</span> | sort -u > /tmp/2023-03-14-orcids.txt
|
|
</span></span><span style="display:flex;"><span>$ ./ilri/resolve_orcids.py -i /tmp/2023-03-14-orcids.txt -o /tmp/2023-03-14-orcids-names.txt -d
|
|
</span></span></code></pre></div><ul>
|
|
<li>Then update them in the 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>$ ./ilri/update_orcids.py -i /tmp/2023-03-14-orcids-names.txt -db dspace -u dspace -p <span style="color:#e6db74">'fuuu'</span> -m <span style="color:#ae81ff">247</span>
|
|
</span></span></code></pre></div><h2 id="2023-03-15">2023-03-15</h2>
|
|
<ul>
|
|
<li>Jawoo was asking about possibilities to harvest PDFs from CGSpace for some kind of AI chatbot integration
|
|
<ul>
|
|
<li>I see we have 45,000 PDFs (format ID 2)</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>localhost/dspacetest= ☘ SELECT COUNT(*) FROM bitstream WHERE NOT deleted AND bitstream_format_id=2;
|
|
</span></span><span style="display:flex;"><span> count
|
|
</span></span><span style="display:flex;"><span>───────
|
|
</span></span><span style="display:flex;"><span> 45281
|
|
</span></span><span style="display:flex;"><span>(1 row)
|
|
</span></span></code></pre></div><ul>
|
|
<li>Rework some of my Python scripts to use a common <code>db_connect</code> function from util</li>
|
|
<li>I reworked my <code>post_bitstreams.py</code> script to be able to overwrite bitstreams if requested
|
|
<ul>
|
|
<li>The use case is to upload thumbnails for all the journal articles where we have these horrible pixelated journal covers</li>
|
|
<li>I replaced JPEG thumbnails for ~896 ILRI publications by exporting a list of DOIs from the 10568/3 collection that were CC-BY, getting their PDFs from Sci-Hub, and then posting them with my new script</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-16">2023-03-16</h2>
|
|
<ul>
|
|
<li>Continue working on the ILRI publication thumbnails
|
|
<ul>
|
|
<li>There were about sixty-four that had existing PNG “journal cover” thumbnails that didn’t get replaced because I only overwrote the JPEG ones yesterday</li>
|
|
<li>Now I generated a list of those bitstream UUIDs and deleted them with a shell script via the REST API</li>
|
|
</ul>
|
|
</li>
|
|
<li>I made a <a href="https://github.com/DSpace/DSpace/pull/8722">pull request on DSpace 7 to update the bitstream format registry for PNG, WebP, and AVIF</a></li>
|
|
<li>Export CGSpace to perform mappings to Initiatives collections</li>
|
|
<li>I also used this export to find CC-BY items with DOIs that had JPEGs or PNGs in their provenance, meaning that the submitter likely submitted a low-quality “journal cover” for the item
|
|
<ul>
|
|
<li>I found about 330 of them and got most of their PDFs from Sci-Hub and replaced the crappy thumbnails with real ones where Sci-Hub had them (~245)</li>
|
|
</ul>
|
|
</li>
|
|
<li>In related news, I realized you can get an <a href="https://stackoverflow.com/questions/59202176/python-download-papers-from-sciencedirect-by-doi-with-requests">API key from Elsevier and download the PDFs from their API</a>:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> requests
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>api_key <span style="color:#f92672">=</span> <span style="color:#e6db74">'fuuuuuuuuu'</span>
|
|
</span></span><span style="display:flex;"><span>doi <span style="color:#f92672">=</span> <span style="color:#e6db74">"10.1016/j.foodqual.2021.104362"</span>
|
|
</span></span><span style="display:flex;"><span>request_url <span style="color:#f92672">=</span> <span style="color:#e6db74">f</span><span style="color:#e6db74">'https://api.elsevier.com/content/article/doi:</span><span style="color:#e6db74">{</span>doi<span style="color:#e6db74">}</span><span style="color:#e6db74">'</span>
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>headers <span style="color:#f92672">=</span> {
|
|
</span></span><span style="display:flex;"><span> <span style="color:#e6db74">'X-ELS-APIKEY'</span>: api_key,
|
|
</span></span><span style="display:flex;"><span> <span style="color:#e6db74">'Accept'</span>: <span style="color:#e6db74">'application/pdf'</span>
|
|
</span></span><span style="display:flex;"><span>}
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> requests<span style="color:#f92672">.</span>get(request_url, stream<span style="color:#f92672">=</span><span style="color:#66d9ef">True</span>, headers<span style="color:#f92672">=</span>headers) <span style="color:#66d9ef">as</span> r:
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">if</span> r<span style="color:#f92672">.</span>status_code <span style="color:#f92672">==</span> <span style="color:#ae81ff">200</span>:
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">"article.pdf"</span>, <span style="color:#e6db74">"wb"</span>) <span style="color:#66d9ef">as</span> f:
|
|
</span></span><span style="display:flex;"><span> <span style="color:#66d9ef">for</span> chunk <span style="color:#f92672">in</span> r<span style="color:#f92672">.</span>iter_content(chunk_size<span style="color:#f92672">=</span><span style="color:#ae81ff">1024</span><span style="color:#f92672">*</span><span style="color:#ae81ff">1024</span>):
|
|
</span></span><span style="display:flex;"><span> f<span style="color:#f92672">.</span>write(chunk)
|
|
</span></span></code></pre></div><ul>
|
|
<li>The question is, how do we know if a DOI is Elsevier or not…</li>
|
|
<li>CGIAR Repositories Working Group meeting
|
|
<ul>
|
|
<li>We discussed controlled vocabularies for funders</li>
|
|
<li>I suggested checking our combined lists against Crossref and ROR</li>
|
|
</ul>
|
|
</li>
|
|
<li>Export a list of donors from <code>cg.contributor.donor</code> on CGSpace:</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>localhost/dspacetest= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=248) to /tmp/2023-03-16-donors.txt;
|
|
</span></span><span style="display:flex;"><span>COPY 1521
|
|
</span></span></code></pre></div><ul>
|
|
<li>Then resolve them against Crossref’s funders API:</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>$ ./ilri/crossref_funders_lookup.py -e fuuuu@cgiar.org -i /tmp/2023-03-16-donors.txt -o ~/Downloads/2023-03-16-cgspace-crossref-funders-results.csv -d
|
|
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true ~/Downloads/2023-03-16-cgspace-crossref-funders-results.csv | wc -l
|
|
</span></span><span style="display:flex;"><span>472
|
|
</span></span><span style="display:flex;"><span>$ sed 1d ~/Downloads/2023-03-16-cgspace-crossref-funders-results.csv | wc -l
|
|
</span></span><span style="display:flex;"><span>1521
|
|
</span></span></code></pre></div><ul>
|
|
<li>That’s a 31% hit rate, but I see some simple things like “Bill and Melinda Gates Foundation” instead of “Bill & Melinda Gates Foundation”</li>
|
|
</ul>
|
|
<h2 id="2023-03-17">2023-03-17</h2>
|
|
<ul>
|
|
<li>I did the same lookup of CGSpace donors on ROR’s 2022-12-01 data dump:</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>$ ./ilri/ror_lookup.py -i /tmp/2023-03-16-donors.txt -o ~/Downloads/2023-03-16-cgspace-ror-funders-results.csv -r v1.15-2022-12-01-ror-data.json
|
|
</span></span><span style="display:flex;"><span>$ csvgrep -c matched -m true ~/Downloads/2023-03-16-cgspace-ror-funders-results.csv | wc -l
|
|
</span></span><span style="display:flex;"><span>407
|
|
</span></span><span style="display:flex;"><span>$ sed 1d ~/Downloads/2023-03-16-cgspace-ror-funders-results.csv | wc -l
|
|
</span></span><span style="display:flex;"><span>1521
|
|
</span></span></code></pre></div><ul>
|
|
<li>That’s a 26.7% hit rate</li>
|
|
<li>As for the number of funders in each dataset
|
|
<ul>
|
|
<li>Crossref has about 34,000</li>
|
|
<li>ROR has 15,000 if “FundRef” data is a proxy for that:</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>$ grep -c -rsI FundRef v1.15-2022-12-01-ror-data.json
|
|
</span></span><span style="display:flex;"><span>15162
|
|
</span></span></code></pre></div><ul>
|
|
<li>On a related note, I remembered that DOI.org has a list of DOI prefixes and publishers: <a href="https://doi.crossref.org/getPrefixPublisher">https://doi.crossref.org/getPrefixPublisher</a>
|
|
<ul>
|
|
<li>In Python I can look up publishers by prefix easily, here with a nested list comprehension:</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>In [10]: [publisher for publisher in publishers if '10.3390' in publisher['prefixes']]
|
|
</span></span><span style="display:flex;"><span>Out[10]:
|
|
</span></span><span style="display:flex;"><span>[{'prefixes': ['10.1989', '10.32545', '10.20944', '10.3390', '10.35995'],
|
|
</span></span><span style="display:flex;"><span> 'name': 'MDPI AG',
|
|
</span></span><span style="display:flex;"><span> 'memberId': 1968}]
|
|
</span></span></code></pre></div><ul>
|
|
<li>And in OpenRefine, if I create a new column based on the DOI using Jython:</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-python" data-lang="python"><span style="display:flex;"><span><span style="color:#f92672">import</span> json
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span><span style="color:#66d9ef">with</span> open(<span style="color:#e6db74">"/home/aorth/src/git/DSpace/publisher-doi-prefixes.json"</span>, <span style="color:#e6db74">"rb"</span>) <span style="color:#66d9ef">as</span> f:
|
|
</span></span><span style="display:flex;"><span> publishers <span style="color:#f92672">=</span> json<span style="color:#f92672">.</span>load(f)
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>doi_prefix <span style="color:#f92672">=</span> value<span style="color:#f92672">.</span>split(<span style="color:#e6db74">"/"</span>)[<span style="color:#ae81ff">3</span>]
|
|
</span></span><span style="display:flex;"><span>
|
|
</span></span><span style="display:flex;"><span>publisher <span style="color:#f92672">=</span> [publisher <span style="color:#66d9ef">for</span> publisher <span style="color:#f92672">in</span> publishers <span style="color:#66d9ef">if</span> doi_prefix <span style="color:#f92672">in</span> publisher[<span style="color:#e6db74">'prefixes'</span>]]
|
|
</span></span><span style="display:flex;"><span>
|
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</span></span><span style="display:flex;"><span><span style="color:#66d9ef">return</span> publisher[<span style="color:#ae81ff">0</span>][<span style="color:#e6db74">'name'</span>]
|
|
</span></span></code></pre></div><ul>
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|
<li>… though this is very slow and hung OpenRefine when I tried it</li>
|
|
<li>I added the ability to overwrite multiple bitstream formats at once in <code>post_bitstreams.py</code></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>$ ./ilri/post_bitstreams.py -i test.csv -u https://dspacetest.cgiar.org/rest -e fuuu@example.com -p <span style="color:#e6db74">'fffnjnjn'</span> -d -s 2B40C7C4E34CEFCF5AFAE4B75A8C52E2 --overwrite JPEG --overwrite PNG -n
|
|
</span></span><span style="display:flex;"><span>Session valid: 2B40C7C4E34CEFCF5AFAE4B75A8C52E2
|
|
</span></span><span style="display:flex;"><span>Opened test.csv
|
|
</span></span><span style="display:flex;"><span>384142cb-58b9-4e64-bcdc-0a8cc34888b3: checking for existing bitstreams in THUMBNAIL bundle
|
|
</span></span><span style="display:flex;"><span>> <span style="color:#f92672">(</span>DRY RUN<span style="color:#f92672">)</span> Deleting bitstream: IFPRI Malawi_Maize Market Report_February_202_anonymous.pdf.jpg <span style="color:#f92672">(</span>16883cb0-1fc8-4786-a04f-32132e0617d4<span style="color:#f92672">)</span>
|
|
</span></span><span style="display:flex;"><span>> <span style="color:#f92672">(</span>DRY RUN<span style="color:#f92672">)</span> Deleting bitstream: AgroEcol_Newsletter_2.png <span style="color:#f92672">(</span>7e9cd434-45a6-4d55-8d56-4efa89d73813<span style="color:#f92672">)</span>
|
|
</span></span><span style="display:flex;"><span>> <span style="color:#f92672">(</span>DRY RUN<span style="color:#f92672">)</span> Uploading file: 10568-129666.pdf.jpg
|
|
</span></span></code></pre></div><ul>
|
|
<li>I learned how to use Python’s built-in <code>logging</code> module and it simplifies all my debug and info printing
|
|
<ul>
|
|
<li>I re-factored a few scripts to use the new logging</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-18">2023-03-18</h2>
|
|
<ul>
|
|
<li>I applied changes for publishers on 16,000 items in batches of 5,000</li>
|
|
<li>While working on my <code>post_bitstreams.py</code> script I realized the Tomcat Crawler Session Manager valve that groups bot user agents into sessions is causing my login to fail the first time, every time
|
|
<ul>
|
|
<li>I’ve disabled it for now and will check the Munin session graphs after some time to see if it makes a difference</li>
|
|
<li>In any case I have much better spider user agent lists in DSpace now than I did years ago when I started using the Crawler Session Manager valve</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-19">2023-03-19</h2>
|
|
<ul>
|
|
<li>Start a harvest on AReS</li>
|
|
</ul>
|
|
<h2 id="2023-03-20">2023-03-20</h2>
|
|
<ul>
|
|
<li>Minor updates to a few of my DSpace Python scripts to fix the logging</li>
|
|
<li>Minor updates to some records for Mazingira reported by Sonja</li>
|
|
<li>Upgrade PostgreSQL on DSpace Test from version 12 to 14, the same way I did from 10 to 12 last year:
|
|
<ul>
|
|
<li>First, I installed the new version of PostgreSQL via the Ansible playbook scripts</li>
|
|
<li>Then I stopped Tomcat and all PostgreSQL clusters and used <code>pg_upgrade</code> to upgrade the old version:</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># systemctl stop tomcat7
|
|
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">12</span> main stop
|
|
</span></span><span style="display:flex;"><span># tar -cvzpf var-lib-postgresql-12.tar.gz /var/lib/postgresql/12
|
|
</span></span><span style="display:flex;"><span># tar -cvzpf etc-postgresql-12.tar.gz /etc/postgresql/12
|
|
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main stop
|
|
</span></span><span style="display:flex;"><span># pg_dropcluster <span style="color:#ae81ff">14</span> main
|
|
</span></span><span style="display:flex;"><span># pg_upgradecluster <span style="color:#ae81ff">12</span> main
|
|
</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main start
|
|
</span></span></code></pre></div><ul>
|
|
<li>After that I <a href="https://adamj.eu/tech/2021/04/13/reindexing-all-tables-after-upgrading-to-postgresql-13/">re-indexed the database indexes using a query</a>:</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>$ su - postgres
|
|
</span></span><span style="display:flex;"><span>$ cat /tmp/generate-reindex.sql
|
|
</span></span><span style="display:flex;"><span>SELECT 'REINDEX TABLE CONCURRENTLY ' || quote_ident(relname) || ' /*' || pg_size_pretty(pg_total_relation_size(C.oid)) || '*/;'
|
|
</span></span><span style="display:flex;"><span>FROM pg_class C
|
|
</span></span><span style="display:flex;"><span>LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
|
|
</span></span><span style="display:flex;"><span>WHERE nspname = 'public'
|
|
</span></span><span style="display:flex;"><span> AND C.relkind = 'r'
|
|
</span></span><span style="display:flex;"><span> AND nspname !~ '^pg_toast'
|
|
</span></span><span style="display:flex;"><span>ORDER BY pg_total_relation_size(C.oid) ASC;
|
|
</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/generate-reindex.sql > /tmp/reindex.sql
|
|
</span></span><span style="display:flex;"><span>$ <trim the extra stuff from /tmp/reindex.sql>
|
|
</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/reindex.sql
|
|
</span></span></code></pre></div><ul>
|
|
<li>The index on <code>metadatavalue</code> shrunk by 90MB, and others a bit less
|
|
<ul>
|
|
<li>This is nice, but not as drastic as I noticed last year when upgrading to PostgreSQL 12</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
<h2 id="2023-03-21">2023-03-21</h2>
|
|
<ul>
|
|
<li>Leigh sent me a list of IFPRI authors with ORCID identifiers so I combined them with our list and resolved all their names with <code>resolve_orcids.py</code>
|
|
<ul>
|
|
<li>It adds 154 new ORCID identifiers</li>
|
|
</ul>
|
|
</li>
|
|
<li>I did a follow up to the publisher names from last week using the list from doi.org
|
|
<ul>
|
|
<li>Last week I only updated items with a DOI that had <em>no</em> publisher, but now I was curious to see how our existing publisher information compared</li>
|
|
<li>I checked a dozen or so manually and, other than CIFOR/ICRAF and CIAT/Alliance, the metadata was better than our existing data, so I overwrote them</li>
|
|
</ul>
|
|
</li>
|
|
<li>I spent some time trying to figure out how to get ssimulacra2 running so I could compare thumbnails in JPEG and WebP
|
|
<ul>
|
|
<li>I realized that we can’t directly compare JPEG to WebP, we need to convert to JPEG/WebP, then convert each to lossless PNG</li>
|
|
<li>Also, we shouldn’t be comparing the resulting images against each other, but rather the original, so I need to a straight PDF to lossless PNG version also</li>
|
|
<li>After playing with WebP at Q82 and Q92, I see it has lower ssimulacra2 scores than JPEG Q92 for the dozen test files</li>
|
|
<li>Could it just be something with ImageMagick?</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
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</article>
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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/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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</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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|
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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>
|
|
|
|
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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