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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2023-12/">December, 2023</a></h2>
<p class="blog-post-meta">
<time datetime="2023-12-01T08:48:36+03:00">Fri Dec 01, 2023</time>
in
<span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2023-12-01">2023-12-01</h2>
<ul>
<li>There is still high load on CGSpace and I don’t know why
<ul>
<li>I don’t see a high number of sessions compared to previous days in the last few weeks</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
<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">for</span> file in dspace.log.2023-11-<span style="color:#f92672">[</span>23<span style="color:#f92672">]</span>*; <span style="color:#66d9ef">do</span> echo <span style="color:#e6db74">"</span>$file<span style="color:#e6db74">"</span>; grep -a -oE <span style="color:#e6db74">'session_id=[A-Z0-9]{32}'</span> <span style="color:#e6db74">"</span>$file<span style="color:#e6db74">"</span> | sort | uniq | wc -l; <span style="color:#66d9ef">done</span>
</span></span><span style="display:flex;"><span>dspace.log.2023-11-20
</span></span><span style="display:flex;"><span>22865
</span></span><span style="display:flex;"><span>dspace.log.2023-11-21
</span></span><span style="display:flex;"><span>20296
</span></span><span style="display:flex;"><span>dspace.log.2023-11-22
</span></span><span style="display:flex;"><span>19688
</span></span><span style="display:flex;"><span>dspace.log.2023-11-23
</span></span><span style="display:flex;"><span>17906
</span></span><span style="display:flex;"><span>dspace.log.2023-11-24
</span></span><span style="display:flex;"><span>18453
</span></span><span style="display:flex;"><span>dspace.log.2023-11-25
</span></span><span style="display:flex;"><span>17513
</span></span><span style="display:flex;"><span>dspace.log.2023-11-26
</span></span><span style="display:flex;"><span>19037
</span></span><span style="display:flex;"><span>dspace.log.2023-11-27
</span></span><span style="display:flex;"><span>21103
</span></span><span style="display:flex;"><span>dspace.log.2023-11-28
</span></span><span style="display:flex;"><span>23023
</span></span><span style="display:flex;"><span>dspace.log.2023-11-29
</span></span><span style="display:flex;"><span>23545
</span></span><span style="display:flex;"><span>dspace.log.2023-11-30
</span></span><span style="display:flex;"><span>21298
</span></span></code></pre></div><ul>
<li>Even the number of unique IPs is not very high compared to the last week or so:</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># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.1 | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>17023
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.2.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>17294
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.3.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>22057
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.4.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>32956
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.5.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>11415
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.6.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>15444
</span></span><span style="display:flex;"><span># awk <span style="color:#e6db74">'{print $1}'</span> /var/log/nginx/<span style="color:#f92672">{</span>access,library-access,oai,rest<span style="color:#f92672">}</span>.log.7.gz | sort | uniq | wc -l
</span></span><span style="display:flex;"><span>12648
</span></span></code></pre></div><ul>
<li>It doesn’t make any sense so I think I’m going to restart the server…
<ul>
<li>After restarting the server the load went down to normal levels… who knows…</li>
</ul>
</li>
<li>I started trying to see how I’m going to generate the fake statistics for the Alliance bitstream that was replaced
<ul>
<li>I exported all the statistics for the owningItem now:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/stats-export.json -f <span style="color:#e6db74">'owningItem:b5862bfa-9799-4167-b1cf-76f0f4ea1e18'</span> -k uid
</span></span></code></pre></div><ul>
<li>Importing them into DSpace Test didn’t show the statistics in the Atmire module, but I see them in Solr…</li>
</ul>
<h2 id="2023-12-02">2023-12-02</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-12-04">2023-12-04</h2>
<ul>
<li>Send a message to Altmetric support because the item IWMI highlighted last month still doesn’t show the attention score for the Handle after I tweeted it several times weeks ago</li>
<li>Spent some time writing a Python script to fix the literal MaxMind City JSON objects in our Solr statistics
<ul>
<li>There are about 1.6 million of these, so I exported them using solr-import-export-json with the query <code>city:com*</code> but ended up finding many that have missing bundles, container bitstreams, etc:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>city:com* AND -bundleName:[* TO *] AND -containerBitstream:[* TO *] AND -file_id:[* TO *] AND -owningItem:[* TO *] AND -version_id:[* TO *]
</code></pre><ul>
<li>(Note the negation to find fields that are missing)</li>
<li>I don’t know what I want to do with these yet</li>
</ul>
<h2 id="2023-12-05">2023-12-05</h2>
<ul>
<li>I finished the <code>fix_maxmind_stats.py</code> script and fixed 1.6 million records and imported them on CGSpace after testing on DSpace 7 Test</li>
<li>Altmetric said there was a glitch regarding the Handle and DOI linking and they successfully re-scraped the item page and linked them
<ul>
<li>They sent me a list of current production IPs and I notice that some of them are in our nginx bot network list:</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">for</span> network in <span style="color:#66d9ef">$(</span>csvcut -c network /tmp/ips.csv | sed 1d | sort -u<span style="color:#66d9ef">)</span>; <span style="color:#66d9ef">do</span> grepcidr $network ~/src/git/rmg-ansible-public/roles/dspace/files/nginx/bot-networks.conf; <span style="color:#66d9ef">done</span>
</span></span><span style="display:flex;"><span>108.128.0.0/13 'bot';
</span></span><span style="display:flex;"><span>46.137.0.0/16 'bot';
</span></span><span style="display:flex;"><span>52.208.0.0/13 'bot';
</span></span><span style="display:flex;"><span>52.48.0.0/13 'bot';
</span></span><span style="display:flex;"><span>54.194.0.0/15 'bot';
</span></span><span style="display:flex;"><span>54.216.0.0/14 'bot';
</span></span><span style="display:flex;"><span>54.220.0.0/15 'bot';
</span></span><span style="display:flex;"><span>54.228.0.0/15 'bot';
</span></span><span style="display:flex;"><span>63.32.242.35/32 'bot';
</span></span><span style="display:flex;"><span>63.32.0.0/14 'bot';
</span></span><span style="display:flex;"><span>99.80.0.0/15 'bot'
</span></span></code></pre></div><ul>
<li>I will remove those for now so that Altmetric doesn’t have any unexpected issues harvesting</li>
</ul>
<h2 id="2023-12-08">2023-12-08</h2>
<ul>
<li>Finalized the script to generate Solr statistics for Alliance research Mirjam
<ul>
<li>The script is <code>ilri/generate_solr_statistics.py</code></li>
<li>I generated ~3,200 statistics based on her records of the download statistics of <a href="https://hdl.handle.net/10568/131997">that item</a> and imported them on CGSpace</li>
</ul>
</li>
<li>Did some work on the DSpace 7 submission form</li>
<li>Peter asked for lists of affiliations, investors, and publishers to do some cleanups
<ul>
<li>I generated a list from a CSV export instead of doing it based on a SQL dump…</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ csvcut -c <span style="color:#e6db74">'cg.contributor.affiliation[en_US]'</span> /tmp/initiatives.csv <span style="color:#ae81ff">\
</span></span></span><span style="display:flex;"><span><span style="color:#ae81ff"></span> | sed -e 1d -e 's/^"//' -e 's/"$//' -e 's/||/\n/g' -e '/^$/d' \
</span></span><span style="display:flex;"><span> | sort | uniq -c | sort -hr \
</span></span><span style="display:flex;"><span> | awk 'BEGIN { FS = "^[[:space:]]+[[:digit:]]+[[:space:]]+" } {print $2}'\
</span></span><span style="display:flex;"><span> | sed -e '1i cg.contributor.affiliation' -e 's/^\(.*\)$/"\1"/' \
</span></span><span style="display:flex;"><span> > /tmp/2023-12-08-initiatives-affiliations.csv
</span></span></code></pre></div><ul>
<li>Export a list of authors as well:</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/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "dc.contributor.author", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 3 GROUP BY "dc.contributor.author" ORDER BY count DESC) to /tmp/2023-12-08-authors.csv WITH CSV HEADER;
</span></span><span style="display:flex;"><span>COPY 102435
</span></span></code></pre></div><h2 id="2023-12-11">2023-12-11</h2>
<ul>
<li>Work on OpenRXV dependencies and podman a bit</li>
<li>Peter noticed that the statistics for this month are very very low on CGSpace
<ul>
<li>I don’t know what is going on, perhaps it is related to me adjusting the nginx config last week?</li>
<li>Ah, it’s probably because of the spider patterns I updated on 2023-11</li>
</ul>
</li>
</ul>
<h2 id="2023-12-16">2023-12-16</h2>
<ul>
<li>Export CGSpace to check for missing Initiative collection mappings</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-12-17">2023-12-17</h2>
<ul>
<li>Pull latest master branch for OpenRXV and deploy on the server
<ul>
<li>I threw away some changes in the tree regarding the Angular base ref, and it broke AReS</li>
<li>So note to self: we need to set the base ref in <code>frontend/Dockerfile</code> before building!</li>
</ul>
</li>
<li>Now Salem fixed the country map</li>
</ul>
<h2 id="2023-12-18">2023-12-18</h2>
<ul>
<li>Work a bit on the IFPRI-ISNAR archive from Leigh</li>
<li>More work on the DSpace 7 home page</li>
</ul>
<h2 id="2023-12-19">2023-12-19</h2>
<ul>
<li>More work on the DSpace 7 home page</li>
<li>The Alliance TIP team is testing deposits to the DSpace 7 REST API and getting an HTTP 500 error
<ul>
<li>In the DSpace logs I see this after they log in, create the item, and update the metadata:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>2023-12-19 17:49:28,022 ERROR unknown unknown org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.
</code></pre><ul>
<li>I found some messages on the dspace-tech mailing list suggesting this might be an old bug: <a href="https://groups.google.com/g/dspace-tech/c/My1GUFYFGoU/m/tS7-WAJPAwAJ">https://groups.google.com/g/dspace-tech/c/My1GUFYFGoU/m/tS7-WAJPAwAJ</a>
<ul>
<li>I restarted Tomcat and told the Alliance TIP team to try again</li>
</ul>
</li>
</ul>
<h2 id="2023-12-20">2023-12-20</h2>
<ul>
<li>The Alliance guys said that submitting via REST works now… sigh, so that’s just some old DSpace 5/6 REST API bug</li>
<li>I lowercased all our AGROVOC keywords in <code>dcterms.subject</code> in SQL:</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>dspace=# BEGIN;
</span></span><span style="display:flex;"><span>BEGIN
</span></span><span style="display:flex;"><span>dspace=*# UPDATE metadatavalue SET text_value=LOWER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=187 AND text_value ~ '[[:upper:]]';
</span></span><span style="display:flex;"><span>UPDATE 462
</span></span><span style="display:flex;"><span>dspace=*# COMMIT;
</span></span><span style="display:flex;"><span>COMMIT
</span></span></code></pre></div><h2 id="2023-12-25">2023-12-25</h2>
<ul>
<li>Looking into <a href="https://solr.apache.org/guide/8_11/making-and-restoring-backups.html">Solr backups</a>
<ul>
<li>Since we are not running in Solr Cloud mode we need to use the replication endpoint for Solr standalone</li>
<li>This works:</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>$ curl <span style="color:#e6db74">'http://localhost:8983/solr/statistics/replication?command=backup'</span>
</span></span><span style="display:flex;"><span>{
</span></span><span style="display:flex;"><span> "responseHeader":{
</span></span><span style="display:flex;"><span> "status":0,
</span></span><span style="display:flex;"><span> "QTime":26},
</span></span><span style="display:flex;"><span> "status":"OK"}
</span></span></code></pre></div><ul>
<li>Then I saw the size of the snapshot reach the size of the index…</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># du -sh /var/solr/data/configsets/statistics/data/*
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/index
</span></span><span style="display:flex;"><span>16G /var/solr/data/configsets/statistics/data/snapshot.20231225074111671
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/snapshot_metadata
</span></span><span style="display:flex;"><span># du -sh /var/solr/data/configsets/statistics/data/*
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/index
</span></span><span style="display:flex;"><span>20G /var/solr/data/configsets/statistics/data/snapshot.20231225074111671
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/snapshot_metadata
</span></span><span style="display:flex;"><span># du -sh /var/solr/data/configsets/statistics/data/*
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/index
</span></span><span style="display:flex;"><span>21G /var/solr/data/configsets/statistics/data/snapshot.20231225074111671
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/snapshot_metadata
</span></span><span style="display:flex;"><span># du -sh /var/solr/data/configsets/statistics/data/*
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/index
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/snapshot.20231225074111671
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/snapshot_metadata
</span></span></code></pre></div><ul>
<li>Then I deleted the core and restored from the snapshot backup:</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>$ curl http://localhost:8983/solr/statistics/update -H <span style="color:#e6db74">"Content-type: text/xml"</span> --data-binary <span style="color:#e6db74">'<delete><query>*:*</query></delete>'</span>
</span></span><span style="display:flex;"><span>$ curl http://localhost:8983/solr/statistics/update -H <span style="color:#e6db74">"Content-type: text/xml"</span> --data-binary <span style="color:#e6db74">'<commit />'</span>
</span></span><span style="display:flex;"><span>$ curl <span style="color:#e6db74">'http://localhost:8983/solr/statistics/replication?command=restore&name=statistics'</span>
</span></span></code></pre></div><ul>
<li>Interestingly the import worked fine, but created a new data index:</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># du -sh /var/solr/data/configsets/statistics/data/*
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/index.properties
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/restore.20231225154626463
</span></span><span style="display:flex;"><span>4.0K /var/solr/data/configsets/statistics/data/snapshot_metadata
</span></span><span style="display:flex;"><span>22G /var/solr/data/configsets/statistics/data/snapshot.statistics
</span></span></code></pre></div><ul>
<li>Not sure the implications of that—Solr uses the data just fine</li>
<li>I can surely use this for atomic Solr backups</li>
</ul>
<h2 id="2023-12-27">2023-12-27</h2>
<ul>
<li>Delete duplicate metadata as described in my DSpace issue from last year: <a href="https://github.com/DSpace/DSpace/issues/8253">https://github.com/DSpace/DSpace/issues/8253</a></li>
<li>Do some other metadata cleanups on CGSpace
<ul>
<li>I also looked up our DOIs on Crossref to get some missing abstracts and correct licenses and dates</li>
</ul>
</li>
<li>Some minor work on the CGSpace DSpace 7 theme to fix the navbar on mobile</li>
<li>Some work on the IFPRI ISNAR archive</li>
</ul>
<h2 id="2023-12-28">2023-12-28</h2>
<ul>
<li>I started porting the <a href="https://github.com/ilri/cgspace-java-helpers">cgspace-java-helpers</a> to DSpace 7</li>
<li>Some work on the IFPRI ISNAR archive
<ul>
<li>I ended up going through most of the PDFs to get better dates and abstracts</li>
</ul>
</li>
</ul>
<h2 id="2023-12-29">2023-12-29</h2>
<ul>
<li>I created a new Hetzner server to replace the current DSpace 6 CGSpace next week when we migrate to DSpace 7</li>
<li>Interesting, I haven’t checked for content pointing to legacy domains in several years (!)
<ul>
<li><code>inurl:mahider.cgiar.org</code>: 0 results on Google!</li>
<li><code>inurl:mahider.ilri.org</code>: 2,100 results on Google</li>
<li><code>inurl:mahider.ilri.org inurl:https</code>: 2 results on Google (!)</li>
<li><code>inurl:dspace.ilri.org:</code> 1,390 results on Google</li>
<li><code>inurl:dspace.ilri.org inurl:https</code>: 0 results on Google (!)</li>
</ul>
</li>
<li>So it seems I can do away with the HTTPS virtual hosts finally
<ul>
<li>Well my current certificates expired on 2021-02-13 and nobody noticed… so…</li>
</ul>
</li>
</ul>
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