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Last night I re-synced DSpace 7 Test from CGSpace
I also updated all my local 7_x-dev branches on the latest upstreams
I spent some time updating the authorizations in Alliance collections
I want to make sure they use groups instead of individuals where possible!
I reverted the Cocoon autosave change because it was more of a nuissance that Peter can&rsquo;t upload CSVs from the web interface and is a very low severity security issue
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Last night I re-synced DSpace 7 Test from CGSpace
I also updated all my local 7_x-dev branches on the latest upstreams
I spent some time updating the authorizations in Alliance collections
I want to make sure they use groups instead of individuals where possible!
I reverted the Cocoon autosave change because it was more of a nuissance that Peter can&rsquo;t upload CSVs from the web interface and is a very low severity security issue
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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/2022-11/">November, 2022</a></h2>
<p class="blog-post-meta">
<time datetime="2022-11-01T09:11:36+03:00">Tue Nov 01, 2022</time>
in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2022-11-01">2022-11-01</h2>
<ul>
<li>Last night I re-synced DSpace 7 Test from CGSpace
<ul>
<li>I also updated all my local <code>7_x-dev</code> branches on the latest upstreams</li>
</ul>
</li>
<li>I spent some time updating the authorizations in Alliance collections
<ul>
<li>I want to make sure they use groups instead of individuals where possible!</li>
</ul>
</li>
<li>I reverted the Cocoon autosave change because it was more of a nuissance that Peter can&rsquo;t upload CSVs from the web interface and is a very low severity security issue</li>
</ul>
<ul>
<li>I ran FixLowQualityThumbnails from cgspace-java-helpers on some large collections on CGSpace and ended up fixing 194 items!</li>
<li>I did some minor checking and uploaded twenty-four IFPRI outputs for the Initiatives to DSpace Test</li>
<li>Tim merged my <a href="https://github.com/DSpace/DSpace/pull/8553">pull request to override the ImageMagick PDF density in DSpace 7</a>
<ul>
<li>I ported it to DSpace 6.x and submitted a pull request: <a href="https://github.com/DSpace/DSpace/pull/8560">https://github.com/DSpace/DSpace/pull/8560</a></li>
</ul>
</li>
</ul>
<h2 id="2022-11-02">2022-11-02</h2>
<ul>
<li>I joined the FAO–CGIAR AGROVOC results sharing meeting
<ul>
<li>From June to October, 2022 we suggested 39 new keywords, added 27 to AGROVOC, 4 rejected, and 9 still under discussion</li>
</ul>
</li>
<li>Doing duplicate check on IFPRI&rsquo;s batch upload and I found one duplicate uploaded by IWMI earlier this year
<ul>
<li>I will update the metadata of that item and map it to the correct Initiative collection</li>
</ul>
</li>
</ul>
<h2 id="2022-11-03">2022-11-03</h2>
<ul>
<li>I added countries to the twenty-three IFPRI items in OpenRefine based on their titles and abstracts (using the Jython trick I learned a few months ago), then added regions using csv-metadata-quality, and uploaded them to CGSpace</li>
<li>I exported a list of collections from CGSpace so I can run the thumbnail fixes on each, as we seem to have issues when doing it on (some) large communities like the CRP community:</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/dspace= ☘ \COPY (SELECT ds6_collection2collectionhandle(uuid) AS collection FROM collection) to /tmp/collections.txt
</span></span><span style="display:flex;"><span>COPY 1268
</span></span></code></pre></div><ul>
<li>Then I started a test run on DSpace Test:</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>$ <span style="color:#66d9ef">while</span> read -r collection; <span style="color:#66d9ef">do</span> chrt -b <span style="color:#ae81ff">0</span> dspace dsrun io.github.ilri.cgspace.scripts.FixLowQualityThumbnails $collection | tee -a /tmp/FixLowQualityThumbnails.log; <span style="color:#66d9ef">done</span> &lt; /tmp/collections.txt
</span></span></code></pre></div><ul>
<li>I&rsquo;ll be curious to check the log after it&rsquo;s all done.
<ul>
<li>After a few hours I see:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ grep -c <span style="color:#e6db74">&#39;Action: remove&#39;</span> /tmp/FixLowQualityThumbnails.log
</span></span><span style="display:flex;"><span>626
</span></span></code></pre></div><ul>
<li>Not bad, because last week I did a more manual selection of collections and deleted ~200
<ul>
<li>I will replicate this on CGSpace soon, and also try the FixJpgJpgThumbnails tool</li>
</ul>
</li>
<li>I see that the CIAT Library is still up, so I should really grab all the PDFs before they shut that old server down
<ul>
<li>Export a list of items with PDFs linked there:</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= ☘ \COPY (SELECT dspace_object_id,text_value FROM metadatavalue WHERE metadata_field_id=219 AND text_value LIKE &#39;%ciat-library%&#39;) to /tmp/ciat-library-items.csv;
</span></span><span style="display:flex;"><span>COPY 4621
</span></span></code></pre></div><ul>
<li>After stripping the page numbers off I see there are only about 2,700 unique files, and we have to filter the dead JSPUI ones&hellip;</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>$ csvcut -c url 2022-11-03-CIAT-Library-items.csv | sed 1d | grep -v jspui | sort -u | wc -l
</span></span><span style="display:flex;"><span>2752
</span></span></code></pre></div><ul>
<li>I&rsquo;m not sure how we&rsquo;ll handle the duplicates because many items are book chapters or something where they share a PDF</li>
</ul>
<h2 id="2022-11-04">2022-11-04</h2>
<ul>
<li>I decided to check for old pre-ImageMagick thumbnails on CGSpace by finding any bitstreams with the description &ldquo;Generated Thumbnail&rdquo;:</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 ds6_bitstream2itemhandle(dspace_object_id) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND text_value=&#39;Generated Thumbnail&#39;) to /tmp/old-thumbnails.txt;
</span></span><span style="display:flex;"><span>COPY 1147
</span></span><span style="display:flex;"><span>$ grep -v <span style="color:#e6db74">&#39;\\N&#39;</span> /tmp/old-thumbnails.txt &gt; /tmp/old-thumbnail-handles.txt
</span></span><span style="display:flex;"><span>$ wc -l /tmp/old-thumbnail-handles.txt
</span></span><span style="display:flex;"><span>987 /tmp/old-thumbnail-handles.txt
</span></span></code></pre></div><ul>
<li>A bunch of these have <code>\N</code> for some reason when I use the <code>ds6_bitstream2itemhandle</code> function to get their handles so I had to exclude those&hellip;
<ul>
<li>I forced the media-filter for these items on CGSpace:</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>$ <span style="color:#66d9ef">while</span> read -r handle; <span style="color:#66d9ef">do</span> JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx512m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -i $handle -f -v; <span style="color:#66d9ef">done</span> &lt; /tmp/old-thumbnail-handles.txt
</span></span></code></pre></div><ul>
<li>Upload some batch records via CSV for Peter</li>
<li>Update the about page on CGSpace with new text from Peter</li>
<li>Add a few more ORCID identifiers and names to my growing file <code>2022-09-22-add-orcids.csv</code>
<ul>
<li>I tagged fifty-four new authors using this list</li>
</ul>
</li>
<li>I deleted and mapped one duplicate item for Maria Garruccio</li>
<li>I updated the CG Core website from Bootstrap v4.6 to v5.2</li>
</ul>
<h2 id="2022-11-07">2022-11-07</h2>
<ul>
<li>I did a harvest on AReS last night but it seems that MELSpace&rsquo;s sitemap is broken again because we have 10,000 fewer records</li>
<li>I filed <a href="https://github.com/ecrmnn/iso-3166-1/issues/10">an issue</a> on the iso-3166-1 npm package to update the name of Turkey to Türkiye
<ul>
<li>I also filed <a href="https://github.com/flyingcircusio/pycountry/issues/148">an issue</a> and <a href="https://github.com/flyingcircusio/pycountry/pull/149">a pull request</a> on the pycountry package</li>
<li>I also filed <a href="https://github.com/konstantinstadler/country_converter/issues/121">an issue</a> and <a href="https://github.com/konstantinstadler/country_converter/pull/122">a pull request</a> on the country-converter package</li>
<li>I also changed one item on CGSpace that had been submitted since the name was changed</li>
<li>I also imported the new iso-codes 4.12.0 into cgspace-java-helpers</li>
<li>I also updated it in the DSpace <code>input-forms.xml</code></li>
<li>I also forked the iso-3166-1 package from npm and updated Swaziland, Macedonia, and Turkey in my fork
<ul>
<li>I submitted a <a href="https://github.com/ecrmnn/iso-3166-1/pull/11">pull request</a> to update this upstream</li>
</ul>
</li>
</ul>
</li>
<li>Since I was making all these pull requests I also made <a href="https://github.com/konstantinstadler/country_converter/pull/123">one on country-converter for the UN M.49 region &ldquo;South-eastern Asia&rdquo;</a></li>
<li>Port the <a href="https://github.com/DSpace/DSpace/pull/8550">ImageMagick PDF cropbox fix</a> to DSpace 6.x
<ul>
<li>I deployed it on CGSpace, ran all updates, and rebooted the host</li>
<li>I ran the filter-media script on one large collection where many of these PDFs with cropbox issues exist:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -v -f -i 10568/78 &gt;&amp; /tmp/filter-media-cropbox.log
</span></span></code></pre></div><ul>
<li>But looking at the items it processed, I&rsquo;m not sure it&rsquo;s working as expected
<ul>
<li>I looked at a few dozen</li>
</ul>
</li>
<li>I found some links to the Bioversity website on CGSpace that are not redirecting properly:</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>$ http --print Hh http://www.bioversityinternational.org/nc/publications/publication/issue/geneflow_2004.html
</span></span><span style="display:flex;"><span>GET /nc/publications/publication/issue/geneflow_2004.html HTTP/1.1
</span></span><span style="display:flex;"><span>Accept: */*
</span></span><span style="display:flex;"><span>Accept-Encoding: gzip, deflate
</span></span><span style="display:flex;"><span>Connection: keep-alive
</span></span><span style="display:flex;"><span>Host: www.bioversityinternational.org
</span></span><span style="display:flex;"><span>User-Agent: HTTPie/3.2.1
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>HTTP/1.1 302 Found
</span></span><span style="display:flex;"><span>Connection: Keep-Alive
</span></span><span style="display:flex;"><span>Content-Length: 275
</span></span><span style="display:flex;"><span>Content-Type: text/html; charset=iso-8859-1
</span></span><span style="display:flex;"><span>Date: Mon, 07 Nov 2022 16:35:21 GMT
</span></span><span style="display:flex;"><span>Keep-Alive: timeout=15, max=100
</span></span><span style="display:flex;"><span>Location: https://www.bioversityinternational.orgnc/publications/publication/issue/geneflow_2004.html
</span></span><span style="display:flex;"><span>Server: Apache
</span></span></code></pre></div><ul>
<li>The <code>Location</code> header is clearly wrong, and if I try https directly I get an HTTP 500</li>
</ul>
<h2 id="2022-11-08">2022-11-08</h2>
<ul>
<li>Looking at the Solr statistics hits on CGSpace for 2022-11
<ul>
<li>I see 221.219.100.42 is on China Unicom and was making thousands of requests to XMLUI in a few hours, using a normal user agent</li>
<li>I see 122.10.101.60 is in Hong Kong and making thousands of requests to XMLUI handles in a few hours, using a normal user agent</li>
<li>I see 135.125.21.38 on OVH is making thousands of requests trying to do SQL injection</li>
<li>I see 163.237.216.11 is somewhere in California making thousands of requests with a normal user agent</li>
<li>I see 51.254.154.148 on OVH is making thousands of requests trying to do SQL injection</li>
<li>I see 221.219.103.211 is on China Unicom and was making thousands of requests to XMLUI in a few hours, using a normal user agent</li>
<li>I see 216.218.223.53 on Hurricane Electric making thousands of requests to XMLUI in a few minutes using a normal user agent</li>
<li>I will purge all these hits and proably add China Unicom&rsquo;s subnet mask to my nginx <code>bot-network.conf</code> file to tag them as bots since there are SO many bad and malicious requests coming from there</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>$ ./ilri/check-spider-ip-hits.sh -f /tmp/ips.txt -p
</span></span><span style="display:flex;"><span>Purging 8975 hits from 221.219.100.42 in statistics
</span></span><span style="display:flex;"><span>Purging 7577 hits from 122.10.101.60 in statistics
</span></span><span style="display:flex;"><span>Purging 6536 hits from 135.125.21.38 in statistics
</span></span><span style="display:flex;"><span>Purging 23950 hits from 163.237.216.11 in statistics
</span></span><span style="display:flex;"><span>Purging 4093 hits from 51.254.154.148 in statistics
</span></span><span style="display:flex;"><span>Purging 2797 hits from 221.219.103.211 in statistics
</span></span><span style="display:flex;"><span>Purging 2618 hits from 216.218.223.53 in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 56546
</span></span></code></pre></div><ul>
<li>Also interesting to see a few new user agents:
<ul>
<li><code>RStudio Desktop (2022.7.1.554); R (4.2.1 x86_64-w64-mingw32 x86_64 mingw32)</code></li>
<li><code>rstudio.cloud R (4.2.1 x86_64-pc-linux-gnu x86_64 linux-gnu)</code></li>
<li><code>MEL</code></li>
<li><code>Gov employment data scraper ([[your email]])</code></li>
<li><code>RStudio Desktop (2021.9.0.351); R (4.1.1 x86_64-w64-mingw32 x86_64 mingw32)</code></li>
</ul>
</li>
<li>I will purge all these:</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/check-spider-hits.sh -f /tmp/agents.txt -p
</span></span><span style="display:flex;"><span>Purging 6155 hits from RStudio in statistics
</span></span><span style="display:flex;"><span>Purging 1929 hits from rstudio in statistics
</span></span><span style="display:flex;"><span>Purging 1454 hits from MEL in statistics
</span></span><span style="display:flex;"><span>Purging 1094 hits from Gov employment data scraper in statistics
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 10632
</span></span></code></pre></div><ul>
<li>Work on the CIAT Library items a bit again in OpenRefine
<ul>
<li>I flagged items with:
<ul>
<li>URL containing &ldquo;#page&rdquo; at the end (these are linking to book chapters, but we don&rsquo;t want to upload the PDF multiple times)</li>
<li>Same URL used by more than one item (&ldquo;Duplicates&rdquo; facet in OpenRefine, these are some corner case I don&rsquo;t want to handle right now)</li>
<li>URL containing &ldquo;:8080&rdquo; to CIAT&rsquo;s old DSpace (this server is no longer live)</li>
</ul>
</li>
<li>I want to try to handle the simple cases that should cover most of the items first</li>
</ul>
</li>
</ul>
<h2 id="2022-11-09">2022-11-09</h2>
<ul>
<li>Continue working on the Python script to upload PDFs from CIAT Library to the relevant item on CGSpace
<ul>
<li>I got the basic functionality working</li>
</ul>
</li>
</ul>
<h2 id="2022-11-12">2022-11-12</h2>
<ul>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2022-11-15">2022-11-15</h2>
<ul>
<li>Meeting with Marie-Angelique, Sara, and Valentina about CG Core types
<ul>
<li>We agreed to continue adding the feedback for each of the proposed actions</li>
<li>The others will start filling in definitions for the types</li>
<li>Sara had some good questions about duplicates on CGSpace and how we can possibly prevent them now that several systems are submitting items directly into the repository
<ul>
<li>We need to be careful especially with regards to author&rsquo;s outputs that will be reported in the PRMS</li>
</ul>
</li>
</ul>
</li>
</ul>
<h2 id="2022-11-16">2022-11-16</h2>
<ul>
<li>Maria asked if we can extend the timeout for XMLUI sessions
<ul>
<li>According to <a href="https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44">this issue</a> it seems to be 30 minutes by default, as a Tomcat default</li>
<li>I think we could extend this to an hour, as there is no real security risk (we&rsquo;re not a bank) and most user&rsquo;s lock screens would have activated after ten minutes or so anyways</li>
</ul>
</li>
</ul>
<h2 id="2022-11-20">2022-11-20</h2>
<ul>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2022-11-22">2022-11-22</h2>
<ul>
<li>Check and upload some items to CGSpace for Peter
<ul>
<li>I am waiting for some feedback from him about some duplicates and metadata issues for the rest</li>
</ul>
</li>
</ul>
<h2 id="2022-11-23">2022-11-23</h2>
<ul>
<li>Fix some authorization issues for ABC&rsquo;s TIP submit tool on DSpace Test (the groups were correct on CGSpace, but not on test)</li>
<li>Peter sent me feedback about the duplicates and metadata questions from yesterday
<ul>
<li>I uploaded the eight items for COHESA and sixty-two for Gender</li>
</ul>
</li>
<li>I ran the script to tag ORCID identifiers with my <code>2022-09-22-add-orcids.csv</code> file and tagged twenty-seven</li>
<li>Maria asked for help uploading a large PDF to CGSpace
<ul>
<li>The PDF is only two pages, but it is 139MB!</li>
<li>I decided to compress it with GhostScript, first with the screen profile (72dpi), then with the ebook profile (150dpi):</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>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>Key<span style="color:#ae81ff">\ </span>facts<span style="color:#ae81ff">\ </span>from<span style="color:#ae81ff">\ </span>a<span style="color:#ae81ff">\ </span>traditional<span style="color:#ae81ff">\ </span>colombian<span style="color:#ae81ff">\ </span>food<span style="color:#ae81ff">\ </span>market-screen.pdf Key<span style="color:#ae81ff">\ </span>facts<span style="color:#ae81ff">\ </span>from<span style="color:#ae81ff">\ </span>a<span style="color:#ae81ff">\ </span>traditional<span style="color:#ae81ff">\ </span>colombian<span style="color:#ae81ff">\ </span>food<span style="color:#ae81ff">\ </span>market.pdf
</span></span><span style="display:flex;"><span>$ gs -sDEVICE<span style="color:#f92672">=</span>pdfwrite -dCompatibilityLevel<span style="color:#f92672">=</span>1.4 -dPDFSETTINGS<span style="color:#f92672">=</span>/ebook -dNOPAUSE -dQUIET -dBATCH -sOutputFile<span style="color:#f92672">=</span>Key<span style="color:#ae81ff">\ </span>facts<span style="color:#ae81ff">\ </span>from<span style="color:#ae81ff">\ </span>a<span style="color:#ae81ff">\ </span>traditional<span style="color:#ae81ff">\ </span>colombian<span style="color:#ae81ff">\ </span>food<span style="color:#ae81ff">\ </span>market-ebook.pdf Key<span style="color:#ae81ff">\ </span>facts<span style="color:#ae81ff">\ </span>from<span style="color:#ae81ff">\ </span>a<span style="color:#ae81ff">\ </span>traditional<span style="color:#ae81ff">\ </span>colombian<span style="color:#ae81ff">\ </span>food<span style="color:#ae81ff">\ </span>market.pdf
</span></span></code></pre></div><ul>
<li>The ebook one looks really good and is only 2.4MB&hellip;</li>
<li>But for reference, this free Adobe tool seems to work: <a href="https://www.adobe.com/acrobat/online/compress-pdf.html">https://www.adobe.com/acrobat/online/compress-pdf.html</a></li>
</ul>
<h2 id="2022-11-24">2022-11-24</h2>
<ul>
<li>My script finished downloading the CIAT Library PDFs
<ul>
<li>I did some more work on my <code>post-ciat-pdfs.py</code> script and tested uploading the items to my local DSpace and DSpace Test</li>
<li>Then I ran the script on CGSpace, uploading ~1,500 PDFs to to existing items</li>
</ul>
</li>
</ul>
<h2 id="2022-11-25">2022-11-25</h2>
<ul>
<li>Tony Murray, who is working on IFPRI&rsquo;s CGSpace integration, emailed me to ask some questions about the REST API</li>
<li>Oh no, I realized there is a logic issue with the PDFbox cropbox code I added a few weeks ago:</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>$ JAVA_OPTS<span style="color:#f92672">=</span><span style="color:#e6db74">&#34;-Xmx1024m -Dfile.encoding=UTF-8&#34;</span> dspace filter-media -p <span style="color:#e6db74">&#34;ImageMagick PDF Thumbnail&#34;</span> -v -f -i 10568/77010
</span></span><span style="display:flex;"><span>The following MediaFilters are enabled:
</span></span><span style="display:flex;"><span>Full Filter Name: org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
</span></span><span style="display:flex;"><span>org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter
</span></span><span style="display:flex;"><span>Loading @mire database changes for module MQM
</span></span><span style="display:flex;"><span>Changes have been processed
</span></span><span style="display:flex;"><span>IM Thumbnail tropentag2016_marshall.pdf is replacable.
</span></span><span style="display:flex;"><span>File: tropentag2016_marshall.pdf.jpg
</span></span><span style="display:flex;"><span>ERROR filtering, skipping bitstream:
</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span> Item Handle: 10568/77010
</span></span><span style="display:flex;"><span> Bundle Name: ORIGINAL
</span></span><span style="display:flex;"><span> File Size: 1486580
</span></span><span style="display:flex;"><span> Checksum: 1ad66d918a56a5e84667386e1a32e352 (MD5)
</span></span><span style="display:flex;"><span> Asset Store: 0
</span></span><span style="display:flex;"><span>java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
</span></span><span style="display:flex;"><span>java.lang.IndexOutOfBoundsException: 1-based index out of bounds: 2
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:325)
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:248)
</span></span><span style="display:flex;"><span> at org.apache.pdfbox.pdmodel.PDDocument.getPage(PDDocument.java:1543)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.ImageMagickThumbnailFilter.getImageFile(ImageMagickThumbnailFilter.java:167)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.ImageMagickPdfThumbnailFilter.getDestinationStream(ImageMagickPdfThumbnailFilter.java:27)
</span></span><span style="display:flex;"><span> at com.atmire.dspace.app.mediafilter.AtmireMediaFilter.processBitstream(AtmireMediaFilter.java:103)
</span></span><span style="display:flex;"><span> at com.atmire.dspace.app.mediafilter.AtmireMediaFilterServiceImpl.filterBitstream(AtmireMediaFilterServiceImpl.java:61)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterServiceImpl.filterItem(MediaFilterServiceImpl.java:181)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterServiceImpl.applyFiltersItem(MediaFilterServiceImpl.java:159)
</span></span><span style="display:flex;"><span> at org.dspace.app.mediafilter.MediaFilterCLITool.main(MediaFilterCLITool.java:232)
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
</span></span><span style="display:flex;"><span> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
</span></span><span style="display:flex;"><span> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
</span></span><span style="display:flex;"><span> at java.lang.reflect.Method.invoke(Method.java:498)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
</span></span></code></pre></div><ul>
<li>Salem gave me a list of CGSpace collections that have double spaces in the names
<ul>
<li>Normally this would only be a minor annoyance, but he discovered that the REST API seems to trim the spaces, which causes an issue when trying to reference them!</li>
<li>He sent me a list of about ten collection UUIDs so I fixed them</li>
</ul>
</li>
<li>I found a bunch of LIVES presentations on CGSpace that have presentations on SlideShare with incorrect licenses&hellip; I updated about fifty of them</li>
</ul>
<h2 id="2022-11-26">2022-11-26</h2>
<ul>
<li>Sync DSpace Test with CGSpace</li>
<li>I increased the session timeout in Tomcat from thirty minutes to sixty, as requested by Maria a few weeks ago
<ul>
<li>See: <a href="https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44">https://gitlab.inf.unibz.it/commul/docker/clarin-dspace/-/issues/44</a></li>
</ul>
</li>
<li>I re-built DSpace on CGSpace, ran all updates, and rebooted the machine
<ul>
<li>Then after coming back up the handle server won&rsquo;t start</li>
<li>The <code>handle-server.log</code> file shows:</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>Shutting down...
</span></span><span style="display:flex;"><span>&#34;2022/11/26 02:12:17 CET&#34; 25 Rotating log files
</span></span><span style="display:flex;"><span>Error: null
</span></span><span style="display:flex;"><span> (see the error log for details.)
</span></span></code></pre></div><ul>
<li>In the <code>error.log</code> file I see:</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>&#34;2022/11/26 02:12:18 CET&#34; 25 Started new run.
</span></span><span style="display:flex;"><span>java.lang.UnsupportedOperationException
</span></span><span style="display:flex;"><span> at java.lang.Runtime.runFinalizersOnExit(Runtime.java:287)
</span></span><span style="display:flex;"><span> at java.lang.System.runFinalizersOnExit(System.java:1059)
</span></span><span style="display:flex;"><span> at net.handle.server.Main.initialize(Main.java:124)
</span></span><span style="display:flex;"><span> at net.handle.server.Main.main(Main.java:75)
</span></span><span style="display:flex;"><span>Shutting down...
</span></span></code></pre></div><ul>
<li>Ah, it seems to be due to an <a href="https://groups.google.com/g/dspace-tech/c/PqjfA5mqG4w/m/FhxI5oXhFwAJ?pli=1">issue in OpenJDK 1.8.0_352</a></li>
<li>I see the server upgraded to the new JDK version on 2022-11-10:</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>Upgrade: openjdk-8-jdk-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04), openjdk-8-jre-headless:amd64 (8u342-b07-0ubuntu1~20.04, 8u352-ga-1~20.04)
</span></span><span style="display:flex;"><span>End-Date: 2022-11-10 04:10:45
</span></span></code></pre></div><ul>
<li>As highlighted in the dspace-tech mailing list thread above, <a href="https://mail.openjdk.org/pipermail/jdk8u-dev/2022-October/015706.html">this OpenJDK release deprecated <code>Runtime.runFinalizersOnExit</code></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> - JDK-8287132: Retire Runtime.runFinalizersOnExit so that it always throws UOE
</span></span></code></pre></div><ul>
<li>I downloaded the previous versions of the packages from Launchpad:</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># wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jdk-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
</span></span><span style="display:flex;"><span># wget https://launchpad.net/~openjdk-security/+archive/ubuntu/ppa/+build/24195357/+files/openjdk-8-jre-headless_8u342-b07-0ubuntu1~20.04_amd64.deb
</span></span><span style="display:flex;"><span># dpkg -i openjdk-8-j*8u342-b07*.deb
</span></span></code></pre></div><ul>
<li>Then the handle-server process starts up fine, so I held these OpenJDK versions for now:</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># apt-mark hold openjdk-8-jdk-headless:amd64 apt-mark hold openjdk-8-jre-headless:amd64
</span></span><span style="display:flex;"><span>openjdk-8-jdk-headless set on hold.
</span></span><span style="display:flex;"><span>openjdk-8-jre-headless set on hold.
</span></span></code></pre></div><ul>
<li>Start a harvest on AReS</li>
</ul>
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