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<meta property="og:title" content="July, 2018" />
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<meta property="og:description" content="2018-07-01
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I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:
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$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
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During the mvn package stage on the 5.8 branch I kept getting issues with java running out of memory:
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There is insufficient memory for the Java Runtime Environment to continue.
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" />
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<meta property="og:type" content="article" />
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-07/" />
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<meta property="article:published_time" content="2018-07-01T12:56:54+03:00"/>
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<meta property="article:modified_time" content="2018-07-03T14:37:30+03:00"/>
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="July, 2018"/>
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<meta name="twitter:description" content="2018-07-01
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I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:
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$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
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During the mvn package stage on the 5.8 branch I kept getting issues with java running out of memory:
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There is insufficient memory for the Java Runtime Environment to continue.
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"/>
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<meta name="generator" content="Hugo 0.42.2" />
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"@context": "http://schema.org",
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"@type": "BlogPosting",
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"headline": "July, 2018",
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"datePublished": "2018-07-01T12:56:54+03:00",
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"dateModified": "2018-07-03T14:37:30+03:00",
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"author": {
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"name": "Alan Orth"
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<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/2018-07/">
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<title>July, 2018 | CGSpace Notes</title>
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<header class="blog-header">
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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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</div>
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</header>
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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/2018-07/">July, 2018</a></h2>
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<p class="blog-post-meta"><time datetime="2018-07-01T12:56:54+03:00">Sun Jul 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="2018-07-01">2018-07-01</h2>
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<ul>
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<li>I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:</li>
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</ul>
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<pre><code>$ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
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</code></pre>
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<ul>
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<li>During the <code>mvn package</code> stage on the 5.8 branch I kept getting issues with java running out of memory:</li>
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</ul>
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<pre><code>There is insufficient memory for the Java Runtime Environment to continue.
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</code></pre>
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<p></p>
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<ul>
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<li>As the machine only has 8GB of RAM, I reduced the Tomcat memory heap from 5120m to 4096m so I could try to allocate more to the build process:</li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
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$ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=dspacetest.cgiar.org -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2 clean package
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</code></pre>
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<ul>
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<li>Then I stopped the Tomcat 7 service, ran the ant update, and manually ran the old and ignored SQL migrations:</li>
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</ul>
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<pre><code>$ sudo su - postgres
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$ psql dspace
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...
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dspace=# begin;
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BEGIN
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dspace=# \i Atmire-DSpace-5.8-Schema-Migration.sql
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DELETE 0
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UPDATE 1
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DELETE 1
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dspace=# commit
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dspace=# \q
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$ exit
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$ dspace database migrate ignored
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</code></pre>
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<ul>
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<li>After that I started Tomcat 7 and DSpace seems to be working, now I need to tell our colleagues to try stuff and report issues they have</li>
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</ul>
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<h2 id="2018-07-02">2018-07-02</h2>
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<ul>
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<li>Discuss AgriKnowledge including our Handle identifier on their harvested items from CGSpace</li>
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<li>They seem to be only interested in Gates-funded outputs, for example: <a href="https://www.agriknowledge.org/files/tm70mv21t">https://www.agriknowledge.org/files/tm70mv21t</a></li>
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</ul>
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<h2 id="2018-07-03">2018-07-03</h2>
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<ul>
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<li>Finally finish with the CIFOR Archive records (a total of 2448):
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<ul>
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<li>I mapped the 50 items that were duplicates from elsewhere in CGSpace into <a href="https://cgspace.cgiar.org/handle/10568/16702">CIFOR Archive</a></li>
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<li>I did one last check of the remaining 2398 items and found eight who have a <code>cg.identifier.doi</code> that links to some URL other than a DOI so I moved those to <code>cg.identifier.url</code> and <code>cg.identifier.googleurl</code> as appropriate</li>
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<li>Also, thirteen items had a DOI in their citation, but did not have a <code>cg.identifier.doi</code> field, so I added those</li>
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<li>Then I imported those 2398 items in two batches (to deal with memory issues):</li>
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</ul></li>
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</ul>
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<pre><code>$ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m"
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$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv
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$ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv
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</code></pre>
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<ul>
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<li>I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely:</li>
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</ul>
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<pre><code>dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
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count
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-------
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785
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dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
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count
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-------
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4
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</code></pre>
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<ul>
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<li>I think I should fix that as well as some other garbage values like “test” and “dspace.ilri.org” etc:</li>
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</ul>
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<pre><code>dspace=# begin;
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dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%';
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UPDATE 785
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dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*';
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UPDATE 4
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dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C';
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UPDATE 1
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dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403);
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DELETE 4
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dspace=# commit;
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</code></pre>
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<ul>
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<li>Testing DSpace 5.8 with PostgreSQL 9.6 and Tomcat 8.5.32 (instead of my usual 7.0.88) and for some reason I get autowire errors on Catalina startup with 8.5.32:</li>
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</ul>
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<pre><code>03-Jul-2018 19:51:37.272 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/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$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$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$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:4792)
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at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256)
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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$DeployDescriptor.run(HostConfig.java:1839)
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at java.util.concurrent.Executors$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$Worker.run(ThreadPoolExecutor.java:624)
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at java.lang.Thread.run(Thread.java:748)
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Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' 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#3f6c3e6a': 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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</code></pre>
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<ul>
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<li>Gotta check that out later…</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/2018-07/">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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<li><a href="/cgspace-notes/2018-04/">April, 2018</a></li>
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<li><a href="/cgspace-notes/2018-03/">March, 2018</a></li>
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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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