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<meta property="og:title" content="September, 2018" />
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<meta property="og:description" content="2018-09-02
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New PostgreSQL JDBC driver version 42.2.5
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I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
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Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
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I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-09/" /><meta property="article:published_time" content="2018-09-02T09:55:54+03:00"/>
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<meta property="article:modified_time" content="2018-09-04T13:25:13+03:00"/>
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<meta name="twitter:title" content="September, 2018"/>
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<meta name="twitter:description" content="2018-09-02
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New PostgreSQL JDBC driver version 42.2.5
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I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
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Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
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I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
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"/>
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-09/">
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<title>September, 2018 | 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"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
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<p class="lead blog-description">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
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<article class="blog-post">
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2018-09/">September, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-09-02T09:55:54+03:00">Sun Sep 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="2018-09-02">2018-09-02</h2>
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<ul>
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<li>New <a href="https://jdbc.postgresql.org/documentation/changelog.html#version_42.2.5">PostgreSQL JDBC driver version 42.2.5</a></li>
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<li>I’ll update the DSpace role in our <a href="https://github.com/ilri/rmg-ansible-public">Ansible infrastructure playbooks</a> and run the updated playbooks on CGSpace and DSpace Test</li>
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<li>Also, I’ll re-run the <code>postgresql</code> tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month</li>
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<li>I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:</li>
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</ul>
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<p></p>
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<pre><code>02-Sep-2018 11:18:52.678 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener]
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java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/dspacetest.cgiar.org/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)}
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at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92)
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at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4776)
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at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5240)
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at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
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at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754)
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at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730)
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at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
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at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:629)
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at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1838)
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at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
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at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
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at java.lang.Thread.run(Thread.java:748)
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Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/dspacetest.cgiar.org/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#4c5d5a2': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations:
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</code></pre>
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<ul>
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<li>Full log here: <a href="https://gist.github.com/alanorth/1e4ae567b853fea9d9dbf1a030ecd8c2">https://gist.github.com/alanorth/1e4ae567b853fea9d9dbf1a030ecd8c2</a></li>
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<li>XMLUI fails to load, but the REST, SOLR, JSPUI, etc work</li>
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<li>The old <code>5_x-prod-dspace-5.5</code> branch does work in Ubuntu 18.04 with Tomcat 8.5.30-1ubuntu1.4, however!</li>
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<li>And the <code>5_x-prod</code> DSpace 5.8 branch does work in Tomcat 8.5.x on my Arch Linux laptop…</li>
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<li>I’m not sure where the issue is then!</li>
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</ul>
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<h2 id="2018-09-03">2018-09-03</h2>
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<ul>
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<li>Abenet says she’s getting three emails about periodic statistics reports every day since the DSpace 5.8 upgrade last week</li>
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<li>They are from the CUA module</li>
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<li>Two of them have “no data” and one has a “null” title</li>
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<li>The last one is a report of the top downloaded items, and includes a graph</li>
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<li>She will try to click the “Unsubscribe” link in the first two to see if it works, otherwise we should contact Atmire</li>
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<li>The only one she remembers subscribing to is the top downloads one</li>
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</ul>
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<h2 id="2018-09-04">2018-09-04</h2>
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<ul>
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<li>I’m looking over the latest round of IITA records from Sisay: <a href="https://dspacetest.cgiar.org/handle/10568/104230">Mercy1806_August_29</a>
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<ul>
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<li>All fields are split with multiple columns like <code>cg.authorship.types</code> and <code>cg.authorship.types[]</code></li>
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<li>This makes it super annoying to do the checks and cleanup, so I will merge them (also time consuming)</li>
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<li>Five items had <code>dc.date.issued</code> values like <code>2013-5</code> so I corrected them to be <code>2013-05</code></li>
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<li>Several metadata fields had values with newlines in them (even in some titles!), which I fixed by trimming the consecutive whitespaces in Open Refine</li>
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<li>Many (196!) items from before 2011 are indicated as having a CRP, but CRPs didn’t exist then so this is impossible</li>
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<li>I got all items that were from 2011 and onwards using a custom facet with this GREL on the <code>dc.date.issued</code> column: <code>isNotNull(value.match(/201[1-8].*/))</code> and then blanking their CRPs</li>
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<li>Some affiliations with only one separator (|) for multiple values</li>
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<li>I replaced smart quotes like <code>’</code> with plain ones</li>
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<li>Some inconsitencies in <code>cg.subject.iita</code> like COWPEA and COWPEAS, and YAM and YAMS, etc, as well as some spelling mistakes like IMPACT ASSESSMENTN</li>
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<li>Some values in the <code>dc.identifier.isbn</code> are actually ISSNs so I moved them to the <code>dc.identifier.issn</code> column</li>
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<li>I found one invalid ISSN using a custom text facet with the regex from the <a href="https://en.wikipedia.org/wiki/International_Standard_Serial_Number#Code_format">ISSN page on Wikipedia</a>: <code>isNotBlank(value.match(/^\d{4}-\d{3}[\dxX]$/))</code></li>
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<li>One invalid value for <code>dc.type</code></li>
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</ul></li>
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</ul>
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<!-- vim: set sw=2 ts=2: -->
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</article>
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</div> <!-- /.blog-main -->
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<aside class="col-sm-3 ml-auto blog-sidebar">
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<section class="sidebar-module">
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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/2018-09/">September, 2018</a></li>
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<li><a href="/cgspace-notes/2018-08/">August, 2018</a></li>
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<li><a href="/cgspace-notes/2018-07/">July, 2018</a></li>
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<li><a href="/cgspace-notes/2018-06/">June, 2018</a></li>
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<li><a href="/cgspace-notes/2018-05/">May, 2018</a></li>
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</ol>
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</section>
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<section class="sidebar-module">
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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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</ol>
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</section>
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</aside>
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