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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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<div class="container">
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-02/">February, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-02-01T16:28:54+02:00">Thu Feb 01, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-02-01">2018-02-01</h2>
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<ul>
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<li>Peter gave feedback on the <code>dc.rights</code> proof of concept that I had sent him last week</li>
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<li>We don’t need to distinguish between internal and external works, so that makes it just a simple list</li>
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<li>Yesterday I figured out how to monitor DSpace sessions using JMX</li>
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<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>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-02/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2018-01/">January, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-01-02T08:35:54-08:00">Tue Jan 02, 2018</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2018-01-02">2018-01-02</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time</li>
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<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>
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<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>
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<li>In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”</li>
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<li><p>And just before that I see this:</p>
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<pre><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].
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</code></pre></li>
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<li><p>Ah hah! So the pool was actually empty!</p></li>
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<li><p>I need to increase that, let’s try to bump it up from 50 to 75</p></li>
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<li><p>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</p></li>
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<li><p>I notice this error quite a few times in dspace.log:</p>
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<pre><code>2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
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org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
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</code></pre></li>
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<li><p>And there are many of these errors every day for the past month:</p>
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<pre><code>$ grep -c "Error while searching for sidebar facets" dspace.log.*
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dspace.log.2017-11-21:4
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dspace.log.2017-11-22:1
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dspace.log.2017-11-23:4
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dspace.log.2017-11-24:11
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dspace.log.2017-11-25:0
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dspace.log.2017-11-26:1
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dspace.log.2017-11-27:7
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dspace.log.2017-11-28:21
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dspace.log.2017-11-29:31
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dspace.log.2017-11-30:15
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dspace.log.2017-12-01:15
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dspace.log.2017-12-02:20
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dspace.log.2017-12-03:38
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dspace.log.2017-12-04:65
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dspace.log.2017-12-05:43
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dspace.log.2017-12-06:72
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dspace.log.2017-12-07:27
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dspace.log.2017-12-08:15
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dspace.log.2017-12-09:29
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dspace.log.2017-12-10:35
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dspace.log.2017-12-11:20
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dspace.log.2017-12-12:44
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dspace.log.2017-12-13:36
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dspace.log.2017-12-14:59
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dspace.log.2017-12-15:104
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dspace.log.2017-12-16:53
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dspace.log.2017-12-17:66
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dspace.log.2017-12-18:83
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dspace.log.2017-12-19:101
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dspace.log.2017-12-20:74
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dspace.log.2017-12-21:55
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dspace.log.2017-12-22:66
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dspace.log.2017-12-23:50
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dspace.log.2017-12-24:85
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dspace.log.2017-12-25:62
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dspace.log.2017-12-26:49
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dspace.log.2017-12-27:30
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dspace.log.2017-12-28:54
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dspace.log.2017-12-29:68
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dspace.log.2017-12-30:89
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dspace.log.2017-12-31:53
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dspace.log.2018-01-01:45
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dspace.log.2018-01-02:34
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</code></pre></li>
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<li><p>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</p></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2018-01/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-12/">December, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-12-01T13:53:54+03:00">Fri Dec 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-12-01">2017-12-01</h2>
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<ul>
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<li>Uptime Robot noticed that CGSpace went down</li>
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<li>The logs say “Timeout waiting for idle object”</li>
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<li>PostgreSQL activity says there are 115 connections currently</li>
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<li>The list of connections to XMLUI and REST API for today:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-12/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-11/">November, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-11-02T09:37:54+02:00">Thu Nov 02, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-11-01">2017-11-01</h2>
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<ul>
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<li>The CORE developers responded to say they are looking into their bot not respecting our robots.txt</li>
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</ul>
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<h2 id="2017-11-02">2017-11-02</h2>
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<ul>
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<li><p>Today there have been no hits by CORE and no alerts from Linode (coincidence?)</p>
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<pre><code># grep -c "CORE" /var/log/nginx/access.log
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0
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</code></pre></li>
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<li><p>Generate list of authors on CGSpace for Peter to go through and correct:</p>
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<pre><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;
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COPY 54701
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</code></pre></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-11/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-10/">October, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-10-01T08:07:54+03:00">Sun Oct 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-10-01">2017-10-01</h2>
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<ul>
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<li><p>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:</p>
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<pre><code>http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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</code></pre></li>
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<li><p>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</p></li>
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<li><p>Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections</p></li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-10/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/">CGIAR Library Migration</a></h2>
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<p class="blog-post-meta"><time datetime="2017-09-18T16:38:35+03:00">Mon Sep 18, 2017</time> by Alan Orth in
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<i class="fa fa-folder" aria-hidden="true"></i> <a href="/cgspace-notes/categories/notes" rel="category tag">Notes</a>
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</p>
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</header>
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<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>
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<a href='https://alanorth.github.io/cgspace-notes/cgiar-library-migration/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-09/">September, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-09-07T16:54:52+07:00">Thu Sep 07, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-09-06">2017-09-06</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two hours</li>
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</ul>
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<h2 id="2017-09-07">2017-09-07</h2>
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<ul>
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<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>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-09/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-08/">August, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-08-01T11:51:52+03:00">Tue Aug 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-08-01">2017-08-01</h2>
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<ul>
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<li>Linode sent an alert that CGSpace (linode18) was using 350% CPU for the past two hours</li>
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<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>
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<li>The good thing is that, according to <code>dspace.log.2017-08-01</code>, they are all using the same Tomcat session</li>
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<li>This means our Tomcat Crawler Session Valve is working</li>
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<li>But many of the bots are browsing dynamic URLs like:
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<ul>
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<li>/handle/10568/3353/discover</li>
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<li>/handle/10568/16510/browse</li>
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</ul></li>
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<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>
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<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>
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<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>
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<li>Also, the bot has to successfully browse the page first so it can receive the HTTP header…</li>
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<li>We might actually have to <em>block</em> these requests with HTTP 403 depending on the user agent</li>
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<li>Abenet pointed out that the CGIAR Library Historical Archive collection I sent July 20th only had ~100 entries, instead of 2415</li>
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<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>
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<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>
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<li>Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-08/'>Read more →</a>
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</article>
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-07/">July, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-07-01T18:03:52+03:00">Sat Jul 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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</p>
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</header>
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<h2 id="2017-07-01">2017-07-01</h2>
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<ul>
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<li>Run system updates and reboot DSpace Test</li>
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</ul>
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<h2 id="2017-07-04">2017-07-04</h2>
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<ul>
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<li>Merge changes for WLE Phase II theme rename (<a href="https://github.com/ilri/DSpace/pull/329">#329</a>)</li>
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<li>Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace</li>
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<li>We can use PostgreSQL’s extended output format (<code>-x</code>) plus <code>sed</code> to format the output into quasi XML:</li>
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</ul>
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<a href='https://alanorth.github.io/cgspace-notes/2017-07/'>Read more →</a>
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</article>
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<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2017-06/">June, 2017</a></h2>
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<p class="blog-post-meta"><time datetime="2017-06-01T10:14:52+03:00">Thu Jun 01, 2017</time> by Alan Orth in
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<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
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2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we’ll create a new sub-community for Phase II and create collections for the research themes there The current “Research Themes” community will be renamed to “WLE Phase I Research Themes” Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg.
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<a href='https://alanorth.github.io/cgspace-notes/2017-06/'>Read more →</a>
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<li><a href="/cgspace-notes/2019-10/">October, 2019</a></li>
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<li><a href="/cgspace-notes/2019-06/">June, 2019</a></li>
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