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<meta property="og:title" content="January, 2024" />
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<meta property="og:description" content="2024-01-02
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Work on preparation of new server for DSpace 7 migration
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I’m not quite sure what we need to do for the Handle server
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For now I just ran the dspace make-handle-config script and diffed it with the one from DSpace 6
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I sent the bundle to the Handle admins to make sure it’s OK before we do the migration
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Continue testing and debugging the cgspace-java-helpers on DSpace 7
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Work on IFPRI ISNAR archive cleanup
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<meta property="article:published_time" content="2024-01-02T10:08:00+03:00" />
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<meta property="article:modified_time" content="2024-01-10T08:34:16+03:00" />
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<meta name="twitter:title" content="January, 2024"/>
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<meta name="twitter:description" content="2024-01-02
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Work on preparation of new server for DSpace 7 migration
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I’m not quite sure what we need to do for the Handle server
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For now I just ran the dspace make-handle-config script and diffed it with the one from DSpace 6
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I sent the bundle to the Handle admins to make sure it’s OK before we do the migration
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Continue testing and debugging the cgspace-java-helpers on DSpace 7
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Work on IFPRI ISNAR archive cleanup
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<title>January, 2024 | CGSpace Notes</title>
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<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
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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/2024-01/">January, 2024</a></h2>
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<p class="blog-post-meta">
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<time datetime="2024-01-02T10:08:00+03:00">Tue Jan 02, 2024</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="2024-01-02">2024-01-02</h2>
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<ul>
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<li>Work on preparation of new server for DSpace 7 migration
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<ul>
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<li>I’m not quite sure what we need to do for the Handle server</li>
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<li>For now I just ran the <code>dspace make-handle-config</code> script and diffed it with the one from DSpace 6</li>
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<li>I sent the bundle to the Handle admins to make sure it’s OK before we do the migration</li>
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</ul>
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</li>
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<li>Continue testing and debugging the cgspace-java-helpers on DSpace 7</li>
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<li>Work on IFPRI ISNAR archive cleanup</li>
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</ul>
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<h2 id="2024-01-03">2024-01-03</h2>
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<ul>
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<li>I haven’t heard from the Handle admins so I’m preparing a backup solution using nginx streams</li>
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<li>This seems to work in my simple tests (this must be outside the <code>http {}</code> block):</li>
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</ul>
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<pre tabindex="0"><code>stream {
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upstream handle_tcp_9000 {
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server 188.34.177.10:9000;
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}
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server {
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listen 9000;
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proxy_connect_timeout 1s;
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proxy_timeout 3s;
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proxy_pass handle_tcp_9000;
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}
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}
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</code></pre><ul>
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<li>Here I forwarded a test TCP port 9000 from one server to another and was able to retrieve a test HTML that was running on the target
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<ul>
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<li>I will have to do TCP and UDP on port 2641, and TCP/HTTP on port 8000.</li>
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</ul>
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</li>
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<li>I did some more minor work on the IFPRI ISNAR archive
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<ul>
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<li>I got some PDFs from the UMN AgEcon search and fixed some metadata</li>
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<li>Then I did some duplicate checking and found five items already on CGSpace</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-01-04">2024-01-04</h2>
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<ul>
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<li>Upload 692 items for the ISNAR archive to CGSpace: <a href="https://cgspace.cgiar.org/handle/10568/136192">https://cgspace.cgiar.org/handle/10568/136192</a></li>
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<li>Help Peter proof and upload 252 items from the 2023 Gender conference to CGSpace</li>
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<li>Meeting with IFPRI to discuss their migration to CGSpace
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<ul>
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<li>We agreed to add two new fields, one for IFPRI project and one for IFPRI publication ranking</li>
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<li>Most likely we will use <code>cg.identifier.project</code> as a general field and consolidate other project fields there</li>
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<li>Not sure which field to use for the publication rank…</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-01-05">2024-01-05</h2>
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<ul>
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<li>Proof and upload 51 items in bulk for IFPRI</li>
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<li>I did a big cleanup of user groups in anticipation of complaints about slow workflow tasks etc in DSpace 7
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<ul>
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<li>I removed ILRI editors from all the dozens of CCAFS community and collection groups, and I should do the same for other CRPs since they are closed for two years now</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-01-06">2024-01-06</h2>
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<ul>
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<li>Migrate CGSpace to DSpace 7</li>
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</ul>
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<h2 id="2024-01-07">2024-01-07</h2>
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<ul>
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<li>High load on the server and UptimeRobot saying the frontend is flapping
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<ul>
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<li>I noticed tons of logs from pm2 in the systemd journal, so I disabled those in the systemd unit because they are available from pm2’s log directory anyway</li>
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<li>I also noticed the same for Solr, so I disabled stdout for that systemd unit as well</li>
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</ul>
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</li>
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<li>I spent a lot of time bringing back the nginx rate limits we used in DSpace 6 and it seems to have helped</li>
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<li>I see some client doing weird HEAD requests to search pages:</li>
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</ul>
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<pre tabindex="0"><code>47.76.35.19 - - [07/Jan/2024:00:00:02 +0100] "HEAD /search/?f.accessRights=Open+Access%2Cequals&f.actionArea=Resilient+Agrifood+Systems%2Cequals&f.author=Burkart%2C+Stefan%2Cequals&f.country=Kenya%2Cequals&f.impactArea=Climate+adaptation+and+mitigation%2Cequals&f.itemtype=Brief%2Cequals&f.publisher=CGIAR+System+Organization%2Cequals&f.region=Asia%2Cequals&f.sdg=SDG+12+-+Responsible+consumption+and+production%2Cequals&f.sponsorship=CGIAR+Trust+Fund%2Cequals&f.subject=environmental+factors%2Cequals&spc.page=1 HTTP/1.1" 499 0 "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/74.0.2504.63 Safari/537.36"
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</code></pre><ul>
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<li>I will add their network blocks (AS45102) and regenerate my list of bot networks:</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>$ wget https://asn.ipinfo.app/api/text/list/AS16276 <span style="color:#ae81ff">\
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</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> https://asn.ipinfo.app/api/text/list/AS23576 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS24940 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS13238 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS14061 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS12876 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS55286 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS203020 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS204287 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS50245 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS6939 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS45102 \
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</span></span><span style="display:flex;"><span> https://asn.ipinfo.app/api/text/list/AS21859
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</span></span><span style="display:flex;"><span>$ cat AS* | sort | uniq | wc -l
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</span></span><span style="display:flex;"><span>4897
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</span></span><span style="display:flex;"><span>$ cat AS* | ~/go/bin/mapcidr -a > /tmp/networks.txt
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/networks.txt
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</span></span><span style="display:flex;"><span>2017 /tmp/networks.txt
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</span></span></code></pre></div><ul>
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<li>I’m surprised to see the number of networks reduced from my current ones… hmmm.</li>
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<li>I will also update my list of Bing networks:</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>$ ./ilri/bing-networks-to-ips.sh
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</span></span><span style="display:flex;"><span>$ ~/go/bin/mapcidr -a < /tmp/bing-ips.txt > /tmp/bing-networks.txt
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/bing-networks.txt
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</span></span><span style="display:flex;"><span>250 /tmp/bing-networks.txt
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</span></span></code></pre></div><h2 id="2024-01-08">2024-01-08</h2>
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<ul>
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<li>Export list of publishers for Peter to select some amount to use as a controlled vocabulary:</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/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "dcterms.publisher", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 178 GROUP BY "dcterms.publisher" ORDER BY count DESC) to /tmp/2024-01-publishers.csv WITH CSV HEADER;
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</span></span><span style="display:flex;"><span>COPY 4332
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</span></span></code></pre></div><ul>
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<li>Address some feedback on DSpace 7 from users, including fileing some issues on GitHub
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<ul>
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<li><a href="https://github.com/DSpace/dspace-angular/issues/2730">https://github.com/DSpace/dspace-angular/issues/2730</a>: List of available metadata fields is truncated when adding new metadata in “Edit Item”</li>
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</ul>
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</li>
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<li>The Alliance TIP team was having issues posting to one collection via the legacy DSpace 6 REST API
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<ul>
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<li>In the DSpace logs I see the same issue that they had last month:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>ERROR unknown unknown org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.
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</code></pre><h2 id="2024-01-09">2024-01-09</h2>
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<ul>
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<li>I restarted Tomcat to see if it helps the REST issue</li>
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<li>After talking with Peter about publishers we decided to get a clean list of the top ~100 publishers and then make sure all CGIAR centers, Initiatives, and Impact Platforms are there as well
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<ul>
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<li>I exported a list from PostgreSQL and then filtered by count > 40 in OpenRefine and then extracted the metadata values:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>$ csvcut -c dcterms.publisher ~/Downloads/2024-01-09-publishers4.csv | sed -e 1d -e 's/"//g' > /tmp/top-publishers.txt
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</code></pre><ul>
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<li>Export a list of ORCID identifiers from PostgreSQL to look them up on ORCID and update our controlled vocabulary:</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/dspace7= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=247) to /tmp/2024-01-09-orcid-identifiers.txt;
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</span></span><span style="display:flex;"><span>localhost/dspace7= ☘ \q
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</span></span><span style="display:flex;"><span>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/2024-01-09-orcid-identifiers.txt | 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/2024-01-09-orcids.txt
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</span></span><span style="display:flex;"><span>$ ./ilri/resolve_orcids.py -i /tmp/2024-01-09-orcids.txt -o /tmp/2024-01-09-orcids-names.txt -d
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</span></span></code></pre></div><ul>
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<li>Then I updated existing ORCID identifiers in CGSpace:</li>
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</ul>
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<pre tabindex="0"><code>$ ./ilri/update_orcids.py -i /tmp/2024-01-09-orcids-names.txt -db dspace -u dspace -p bahhhh
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</code></pre><ul>
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<li>Bizu seems to be having issues due to belonging to too many groups
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<ul>
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<li>I see some messages from Solr in the DSpace log:</li>
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</ul>
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</li>
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</ul>
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<pre tabindex="0"><code>2024-01-09 06:23:35,893 ERROR unknown unknown org.dspace.authorize.AuthorizeServiceImpl @ Failed getting getting community/collection admin status for bahhhhh@cgiar.org The search error is: Error from server at http://localhost:8983/solr/search: org.apache.solr.search.SyntaxError: Cannot parse 'search.resourcetype:Community AND (admin:eef481147-daf3-4fd2-bb8d-e18af8131d8c OR admin:g80199ef9-bcd6-4961-9512-501dea076607 OR admin:g4ac29263-cf0c-48d0-8be7-7f09317d50ec OR admin:g0e594148-a0f6-4f00-970d-6b7812f89540 OR admin:g0265b87a-2183-4357-a971-7a5b0c7add3a OR admin:g371ae807-f014-4305-b4ec-f2a8f6f0dcfa OR admin:gdc5cb27c-4a5a-45c2-b656-a399fded70de OR admin:ge36d0ece-7a52-4925-afeb-6641d6a348cc OR admin:g15dc1173-7ddf-43cf-a89a-77a7f81c4cfc OR admin:gc3a599d3-c758-46cd-9855-c98f6ab58ae4 OR admin:g3d648c3e-58c3-4342-b500-07cba10ba52d OR admin:g82bf5168-65c1-4627-8eb4-724fa0ea51a7 OR admin:ge751e973-697d-419c-b59b-5a5644702874 OR admin:g44dd0a80-c1e6-4274-9be4-9f342d74928c OR admin:g4842f9c2-73ed-476a-a81a-7167d8aa7946 OR admin:g5f279b3f-c2ce-4c75-b151-1de52c1a540e OR admin:ga6df8adc-2e1d-40f2-8f1e-f77796d0eecd OR admin:gfdfc1621-382e-437a-8674-c9007627565c OR admin:g15cd114a-0b89-442b-a1b4-1febb6959571 OR admin:g12aede99-d018-4c00-b4d4-a732541d0017 OR admin:gc59529d7-002a-4216-b2e1-d909afd2d4a9 OR admin:gd0806714-bc13-460d-bedd-121bdd5436a4 OR admin:gce70739a-8820-4d56-b19c-f191855479e4 OR admin:g7d3409eb-81e3-4156-afb1-7f02de22065f OR admin:g54bc009e-2954-4dad-8c30-be6a09dc5093 OR admin:gc5e1d6b7-4603-40d7-852f-6654c159dec9 OR admin:g0046214d-c85b-4f12-a5e6-2f57a2c3abb0 OR admin:g4c7b4fd0-938f-40e9-ab3e-447c317296c1 OR admin:gcfae9b69-d8dd-4cf3-9a4e-d6e31ff68731 OR ... admin:g20f366c0-96c0-4416-ad0b-46884010925f)': too many boolean clauses The search resourceType filter was: search.resourcetype:Community
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</code></pre><ul>
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<li>There are 1,805 OR clauses in the full log!
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<ul>
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<li>We previous had this issue in 2020-01 and 2020-02 with DSpace 5 and DSpace 6</li>
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<li>At the time the solution was to increase the <code>maxBooleanClauses</code> in Solr and to disable access rights awareness, but I don’t think we want to do the second one now</li>
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<li>I saw many users of Solr in other applications increasing this to obscenely high numbers, so I think we should be OK to increase it from 1024 to 2048</li>
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</ul>
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</li>
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<li>Re-visiting the DSpace user groomer to delete inactive users
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<ul>
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<li>In 2023-08 I noticed that this was now <a href="https://github.com/DSpace/DSpace/pull/2928">possible in DSpace 7</a></li>
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<li>As a test I tried to delete all users who have been inactive since six years ago (Janury 9, 2018):</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>$ dspace dsrun org.dspace.eperson.Groomer -a -b 01/09/2018 -d
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</span></span></code></pre></div><ul>
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<li>I tested it on DSpace 7 Test and it worked… I am debating running it on CGSpace…
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<ul>
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<li>I see we have almost 9,000 users:</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>$ dspace user -L > /tmp/users-before.txt
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</span></span><span style="display:flex;"><span>$ wc -l /tmp/users-before.txt
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</span></span><span style="display:flex;"><span>8943 /tmp/users-before.txt
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</span></span></code></pre></div><ul>
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<li>I decided to do the same on CGSpace and it worked without errors</li>
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<li>I finished working on the controlled vocabulary for publishers</li>
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</ul>
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<h2 id="2024-01-10">2024-01-10</h2>
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<ul>
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<li>I spent some time deleting old groups on CGSpace</li>
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<li>I looked into the use of the <code>cg.identifier.ciatproject</code> field and found there are only a handful of uses, with some even seeming to be a mistake:</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/dspace7= ☘ SELECT DISTINCT text_value AS "cg.identifier.ciatproject", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata
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</span></span><span style="display:flex;"><span>_field_id = 232 GROUP BY "cg.identifier.ciatproject" ORDER BY count DESC;
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</span></span><span style="display:flex;"><span> cg.identifier.ciatproject │ count
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</span></span><span style="display:flex;"><span>───────────────────────────┼───────
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</span></span><span style="display:flex;"><span> D145 │ 4
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</span></span><span style="display:flex;"><span> LAM_LivestockPlus │ 2
|
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</span></span><span style="display:flex;"><span> A215 │ 1
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</span></span><span style="display:flex;"><span> A217 │ 1
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</span></span><span style="display:flex;"><span> A220 │ 1
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</span></span><span style="display:flex;"><span> A223 │ 1
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|
</span></span><span style="display:flex;"><span> A224 │ 1
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</span></span><span style="display:flex;"><span> A227 │ 1
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</span></span><span style="display:flex;"><span> A229 │ 1
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</span></span><span style="display:flex;"><span> A230 │ 1
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</span></span><span style="display:flex;"><span> CLIMATE CHANGE MITIGATION │ 1
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</span></span><span style="display:flex;"><span> LIVESTOCK │ 1
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</span></span><span style="display:flex;"><span>(12 rows)
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</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
|
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Time: 240.041 ms
|
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</span></span></code></pre></div><ul>
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<li>I think we can move those to a new <code>cg.identifier.project</code> if we create one</li>
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<li>The <code>cg.identifier.cpwfproject</code> field is similarly sparse, but the CCAFS ones are widely used</li>
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</ul>
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