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Upgrade CGSpace to DSpace 7.6.2
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Upgrade CGSpace to DSpace 7.6.2
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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/2024-09/">September, 2024</a></h2>
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<p class="blog-post-meta">
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<time datetime="2024-09-01T21:16:00-07:00">Sun Sep 01, 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="2024-09-01">2024-09-01</h2>
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<ul>
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<li>Upgrade CGSpace to DSpace 7.6.2</li>
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</ul>
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<h2 id="2024-09-05">2024-09-05</h2>
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<ul>
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<li>Finalize work on migrating DSpace Angular from Yarn to NPM</li>
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</ul>
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<h2 id="2024-09-06">2024-09-06</h2>
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<ul>
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<li>This morning Tomcat crashed due to an OOM kill:</li>
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</ul>
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<pre tabindex="0"><code>Sep 06 00:00:24 server systemd[1]: tomcat9.service: A process of this unit has been killed by the OOM killer.
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Sep 06 00:00:25 server systemd[1]: tomcat9.service: Main process exited, code=killed, status=9/KILL
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Sep 06 00:00:25 server systemd[1]: tomcat9.service: Failed with result 'oom-kill'.
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</code></pre><ul>
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<li>According to the system journal, it was a Node.js dspace-angular process that tried to allocate memory and failed, thus invoking the OOM killer</li>
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<li>Currently I see high memory usage in those processes:</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>$ pm2 status
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</span></span><span style="display:flex;"><span>┌────┬──────────────┬─────────────┬─────────┬─────────┬──────────┬────────┬──────┬───────────┬──────────┬──────────┬──────────┬──────────┐
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</span></span><span style="display:flex;"><span>│ id │ name │ namespace │ version │ mode │ pid │ uptime │ ↺ │ status │ cpu │ mem │ user │ watching │
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</span></span><span style="display:flex;"><span>├────┼──────────────┼─────────────┼─────────┼─────────┼──────────┼────────┼──────┼───────────┼──────────┼──────────┼──────────┼──────────┤
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</span></span><span style="display:flex;"><span>│ 0 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 994 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
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</span></span><span style="display:flex;"><span>│ 1 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1015 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
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</span></span><span style="display:flex;"><span>│ 2 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1029 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
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</span></span><span style="display:flex;"><span>│ 3 │ dspace-ui │ default │ 7.6.3-… │ cluster │ 1042 │ 4D │ 0 │ online │ 0% │ 3.4gb │ dspace │ disabled │
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</span></span><span style="display:flex;"><span>└────┴──────────────┴─────────────┴─────────┴─────────┴──────────┴────────┴──────┴───────────┴──────────┴──────────┴──────────┴──────────┘
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</span></span></code></pre></div><ul>
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<li>I bet if I look in the logs I’d find some kind of heavy traffic on the frontend, causing high caching for Angular SSR</li>
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</ul>
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<h2 id="2024-09-08">2024-09-08</h2>
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<ul>
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<li>Analyzing memory use in our DSpace hosts, which have 32GB of memory
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<ul>
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<li>Effective cache of PostgreSQL is estimated at 11GB, which seems way high since the database is only 2GB</li>
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<li>Realistically this should be how we adjust, with PostgreSQL using ~8GB (or less) and each dspace-angular process pinned at 2GB…</li>
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</ul>
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</li>
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</ul>
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<blockquote>
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<p>Total - Solr - Tomcat Postgres - Nginx - Angular
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31366 − (1024×4.4) − 7168 − (8×1024) − 512 - (4x2048) = 2796.4 left…</p>
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</blockquote>
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<ul>
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<li>I put some of these changes in on DSpace Test and will monitor this week</li>
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</ul>
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<h2 id="2024-09-10">2024-09-10</h2>
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<ul>
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<li>Some bot in South Africa made a ton of requests on the API and made the load hit the roof:</li>
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</ul>
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<pre tabindex="0"><code># grep -E '10/Sep/2024:[10-11]' /var/log/nginx/api-access.log | awk '{print $1}' | sort | uniq -c | sort -h
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...
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149720 102.182.38.90
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</code></pre><ul>
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<li>They are using several user agents so are obviously a bot:</li>
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</ul>
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<pre tabindex="0"><code>Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:130.0) Gecko/20100101 Firefox/130.0
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Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/111.0
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Mozilla/5.0 (Windows; U; Windows NT 6.1; rv:11.0) Gecko/20100101 Firefox/11.0
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</code></pre><ul>
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<li>I added them to the list of bot networks in nginx and the load went down</li>
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</ul>
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<h2 id="2024-09-11">2024-09-11</h2>
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<ul>
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<li>Upgrade DSpace 7 Test to Ubuntu 24.04</li>
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<li>I did some minor maintenance to test dspace-statistics-api with Python 3.12
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<ul>
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<li>I tagged version 1.4.4 and released it on GitHub</li>
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</ul>
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</li>
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</ul>
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<h2 id="2024-09-14">2024-09-14</h2>
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<ul>
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<li>Noticed a persistent higher than usual load on CGSpace and checked the server logs
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<ul>
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<li>Found some new data center subnets to block because they were making thousands of requests with normal user agents</li>
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</ul>
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</li>
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<li>I enabled HTTP/3 in nginx</li>
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<li>I enabled the SSR patch in Angular: <a href="https://github.com/DSpace/dspace-angular/issues/3110">https://github.com/DSpace/dspace-angular/issues/3110</a></li>
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</ul>
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<h2 id="2024-09-16">2024-09-16</h2>
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<ul>
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<li>Experiment with the <!-- raw HTML omitted -->dspace-statistics-api-js<!-- raw HTML omitted --> on DSpace 7 Test
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<ul>
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<li>In the past it always caused Solr to run out of memory, but I increased Solr’s heap from 2g to 3g and it runs without crashing</li>
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<li>I attached VisualVM to Solr with a 3g and 4g heap and iterated over 1260 pages of results in the dspace-statistics-api-js:</li>
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</ul>
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</li>
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</ul>
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<p><img src="/cgspace-notes/2024/09/2024-09-16-Solr-3g-heap.png" alt="Solr with 3g heap"></p>
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<p><img src="/cgspace-notes/2024/09/2024-09-16-Solr-4g-heap.png" alt="Solr with 4g heap"></p>
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<h2 id="2024-09-23">2024-09-23</h2>
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<ul>
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<li>Upgrade PostgreSQL from version 14 to 15 on DSpace Test the same way I did last year:</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># apt update
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</span></span><span style="display:flex;"><span># apt install postgresql-15
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</span></span><span style="display:flex;"><span># Update configs with Ansible
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</span></span><span style="display:flex;"><span># systemctl stop tomcat9
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</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">14</span> main stop
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</span></span><span style="display:flex;"><span># tar -cvzpf var-lib-postgresql-14.tar.gz /var/lib/postgresql/14
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</span></span><span style="display:flex;"><span># tar -cvzpf etc-postgresql-14.tar.gz /etc/postgresql/14
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</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">15</span> main stop
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</span></span><span style="display:flex;"><span># pg_dropcluster <span style="color:#ae81ff">15</span> main
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</span></span><span style="display:flex;"><span># pg_upgradecluster <span style="color:#ae81ff">14</span> main
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</span></span><span style="display:flex;"><span># pg_ctlcluster <span style="color:#ae81ff">15</span> main start
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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:#960050;background-color:#1e0010">
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</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>ERROR: could not find function "xml_is_well_formed" in file "/usr/lib/postgresql/15/lib/pgxml.so"
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</span></span><span style="display:flex;"><span>ERROR: function public.xml_is_well_formed(text) does not exist
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</span></span><span style="display:flex;"><span>ERROR: could not find function "xml_is_well_formed" in file "/usr/lib/postgresql/15/lib/pgxml.so"
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</span></span><span style="display:flex;"><span>ERROR: function public.xml_valid(text) does not exist
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</span></span></code></pre></div><ul>
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<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</a> using a query:</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>$ su - postgres
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</span></span><span style="display:flex;"><span>$ cat /tmp/generate-reindex.sql
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</span></span><span style="display:flex;"><span>SELECT 'REINDEX TABLE CONCURRENTLY ' || quote_ident(relname) || ' /*' || pg_size_pretty(pg_total_relation_size(C.oid)) || '*/;'
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</span></span><span style="display:flex;"><span>FROM pg_class C
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</span></span><span style="display:flex;"><span>LEFT JOIN pg_namespace N ON (N.oid = C.relnamespace)
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</span></span><span style="display:flex;"><span>WHERE nspname = 'public'
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</span></span><span style="display:flex;"><span> AND C.relkind = 'r'
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</span></span><span style="display:flex;"><span> AND nspname !~ '^pg_toast'
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</span></span><span style="display:flex;"><span>ORDER BY pg_total_relation_size(C.oid) ASC;
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</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/generate-reindex.sql > /tmp/reindex.sql
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</span></span><span style="display:flex;"><span>$ <trim the extra stuff from /tmp/reindex.sql>
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</span></span><span style="display:flex;"><span>$ psql dspace < /tmp/reindex.sql
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</span></span></code></pre></div><ul>
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<li>The database shrunk by 186MB!</li>
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</ul>
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<h2 id="2024-09-29">2024-09-29</h2>
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<ul>
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<li>I upgraded the database on CGSpace to PostgreSQL 15</li>
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</ul>
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<!-- raw HTML omitted -->
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</article>
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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/2024-10/">October, 2024</a></li>
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<li><a href="/cgspace-notes/2024-09/">September, 2024</a></li>
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<li><a href="/cgspace-notes/2024-08/">August, 2024</a></li>
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<li><a href="/cgspace-notes/2024-07/">July, 2024</a></li>
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<li><a href="/cgspace-notes/2024-06/">June, 2024</a></li>
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<h4>Links</h4>
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<ol class="list-unstyled">
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<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
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<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
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<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
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