<!DOCTYPE html> <html lang="en" > <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <meta property="og:title" content="CGSpace Notes" /> <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." /> <meta property="og:type" content="website" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" /> <meta property="og:updated_time" content="2023-01-04T10:53:02+03:00" /> <meta name="twitter:card" content="summary"/> <meta name="twitter:title" content="CGSpace Notes"/> <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/> <meta name="generator" content="Hugo 0.108.0"> <script type="application/ld+json"> { "@context": "http://schema.org", "@type": "Blog", "headline": "CGSpace Notes", "url" : "https://alanorth.github.io/cgspace-notes/", "author": { "@type": 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href="https://alanorth.github.io/cgspace-notes/index.xml" title="CGSpace Notes" /> </head> <body> <div class="blog-masthead"> <div class="container"> <nav class="nav blog-nav"> <a class="nav-link active" href="https://alanorth.github.io/cgspace-notes/">Home</a> </nav> </div> </div> <header class="blog-header"> <div class="container"> <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> </div> </header> <div class="container"> <div class="row"> <div class="col-sm-8 blog-main"> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-03/">March, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-03-02T16:07:54+02:00">Fri Mar 02, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-03-02">2018-03-02</h2> <ul> <li>Export a CSV of the IITA community metadata for Martin Mueller</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-03/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-02-01">2018-02-01</h2> <ul> <li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li> <li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li> <li>Yesterday I figured out how to monitor DSpace sessions using JMX</li> <li>I copied the logic in the <code>jmx_tomcat_dbpools</code> provided by Ubuntu’s <code>munin-plugins-java</code> package and used the stuff I discovered about JMX <a href="/cgspace-notes/2018-01/">in 2018-01</a></li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2> <p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2018-01-02">2018-01-02</h2> <ul> <li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li> <li>I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary</li> <li>The nginx logs show HTTP 200s until <code>02/Jan/2018:11:27:17 +0000</code> when Uptime Robot got an HTTP 500</li> <li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li> <li>And just before that I see this:</li> </ul> <pre tabindex="0"><code>Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000]. </code></pre><ul> <li>Ah hah! So the pool was actually empty!</li> <li>I need to increase that, let’s try to bump it up from 50 to 75</li> <li>After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw</li> <li>I notice this error quite a few times in dspace.log:</li> </ul> <pre tabindex="0"><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32. </code></pre><ul> <li>And there are many of these errors every day for the past month:</li> </ul> <pre tabindex="0"><code>$ grep -c "Error while searching for sidebar facets" dspace.log.* dspace.log.2017-11-21:4 dspace.log.2017-11-22:1 dspace.log.2017-11-23:4 dspace.log.2017-11-24:11 dspace.log.2017-11-25:0 dspace.log.2017-11-26:1 dspace.log.2017-11-27:7 dspace.log.2017-11-28:21 dspace.log.2017-11-29:31 dspace.log.2017-11-30:15 dspace.log.2017-12-01:15 dspace.log.2017-12-02:20 dspace.log.2017-12-03:38 dspace.log.2017-12-04:65 dspace.log.2017-12-05:43 dspace.log.2017-12-06:72 dspace.log.2017-12-07:27 dspace.log.2017-12-08:15 dspace.log.2017-12-09:29 dspace.log.2017-12-10:35 dspace.log.2017-12-11:20 dspace.log.2017-12-12:44 dspace.log.2017-12-13:36 dspace.log.2017-12-14:59 dspace.log.2017-12-15:104 dspace.log.2017-12-16:53 dspace.log.2017-12-17:66 dspace.log.2017-12-18:83 dspace.log.2017-12-19:101 dspace.log.2017-12-20:74 dspace.log.2017-12-21:55 dspace.log.2017-12-22:66 dspace.log.2017-12-23:50 dspace.log.2017-12-24:85 dspace.log.2017-12-25:62 dspace.log.2017-12-26:49 dspace.log.2017-12-27:30 dspace.log.2017-12-28:54 dspace.log.2017-12-29:68 dspace.log.2017-12-30:89 dspace.log.2017-12-31:53 dspace.log.2018-01-01:45 dspace.log.2018-01-02:34 </code></pre><ul> <li>Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-12-01T13:53:54+03:00">Fri Dec 01, 2017</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2017-12-01">2017-12-01</h2> <ul> <li>Uptime Robot noticed that CGSpace went down</li> <li>The logs say “Timeout waiting for idle object”</li> <li>PostgreSQL activity says there are 115 connections currently</li> <li>The list of connections to XMLUI and REST API for today:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-12/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2017-11-01">2017-11-01</h2> <ul> <li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li> </ul> <h2 id="2017-11-02">2017-11-02</h2> <ul> <li>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</li> </ul> <pre tabindex="0"><code># grep -c "CORE" /var/log/nginx/access.log 0 </code></pre><ul> <li>Generate list of authors on CGSpace for Peter to go through and correct:</li> </ul> <pre tabindex="0"><code>dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv; COPY 54701 </code></pre> <a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> </p> </header> <h2 id="2017-10-01">2017-10-01</h2> <ul> <li>Peter emailed to point out that many items in the <a href="https://cgspace.cgiar.org/handle/10568/2703">ILRI archive collection</a> have multiple handles:</li> </ul> <pre tabindex="0"><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336 </code></pre><ul> <li>There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine</li> <li>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2> <p class="blog-post-meta"><time datetime="2017-09-18T16:38:35+03:00">Mon Sep 18, 2017</time> by Alan Orth in <span class="fas fa-folder" aria-hidden="true"></span> <a href="/categories/notes/" rel="category tag">Notes</a> <span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/migration/" rel="tag">Migration</a> </p> </header> <p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p> <a href='https://alanorth.github.io/cgspace-notes/cgiar-library-migration/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-09/">September, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-09-07T16:54:52+07:00">Thu Sep 07, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2017-09-06">2017-09-06</h2> <ul> <li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li> </ul> <h2 id="2017-09-07">2017-09-07</h2> <ul> <li>Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-09/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-08/">August, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-08-01T11:51:52+03:00">Tue Aug 01, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2017-08-01">2017-08-01</h2> <ul> <li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li> <li>I looked in the Activity pane of the Admin Control Panel and it seems that Google, Baidu, Yahoo, and Bing are all crawling with massive numbers of bots concurrently (~100 total, mostly Baidu and Google)</li> <li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li> <li>This means our Tomcat Crawler Session Valve is working</li> <li>But many of the bots are browsing dynamic URLs like: <ul> <li>/handle/10568/3353/discover</li> <li>/handle/10568/16510/browse</li> </ul> </li> <li>The <code>robots.txt</code> only blocks the top-level <code>/discover</code> and <code>/browse</code> URLs… we will need to find a way to forbid them from accessing these!</li> <li>Relevant issue from DSpace Jira (semi resolved in DSpace 6.0): <a href="https://jira.duraspace.org/browse/DS-2962">https://jira.duraspace.org/browse/DS-2962</a></li> <li>It turns out that we’re already adding the <code>X-Robots-Tag "none"</code> HTTP header, but this only forbids the search engine from <em>indexing</em> the page, not crawling it!</li> <li>Also, the bot has to successfully browse the page first so it can receive the HTTP header…</li> <li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li> <li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li> <li>This was due to newline characters in the <code>dc.description.abstract</code> column, which caused OpenRefine to choke when exporting the CSV</li> <li>I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using <code>g/^$/d</code></li> <li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-08/'>Read more →</a> </article> <article class="blog-post"> <header> <h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2> <p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in <span class="fas fa-tag" aria-hidden="true"></span> <a href="/tags/notes/" rel="tag">Notes</a> </p> </header> <h2 id="2017-07-01">2017-07-01</h2> <ul> <li>Run system updates and reboot DSpace Test</li> </ul> <h2 id="2017-07-04">2017-07-04</h2> <ul> <li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li> <li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li> <li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li> </ul> <a href='https://alanorth.github.io/cgspace-notes/2017-07/'>Read more →</a> </article> <nav class="blog-pagination"> <a class="btn btn-outline-primary" href="/cgspace-notes/page/6/" rel="prev" role="button">Previous page</a> <a class="btn btn-outline-primary" href="/cgspace-notes/page/8/" rel="next" role="button">Next page</a> </nav> </div> <!-- /.blog-main --> <aside class="col-sm-3 ml-auto blog-sidebar"> <section class="sidebar-module"> <h4>Recent Posts</h4> <ol class="list-unstyled"> <li><a href="/cgspace-notes/2023-01/">January, 2023</a></li> <li><a href="/cgspace-notes/2022-12/">December, 2022</a></li> <li><a href="/cgspace-notes/2022-11/">November, 2022</a></li> <li><a href="/cgspace-notes/2022-10/">October, 2022</a></li> <li><a href="/cgspace-notes/2022-09/">September, 2022</a></li> </ol> </section> <section class="sidebar-module"> <h4>Links</h4> <ol class="list-unstyled"> <li><a href="https://cgspace.cgiar.org">CGSpace</a></li> <li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li> <li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li> </ol> </section> </aside> </div> <!-- /.row --> </div> <!-- /.container --> <footer class="blog-footer"> <p dir="auto"> Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>. </p> <p> <a href="#">Back to top</a> </p> </footer> </body> </html>