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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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<meta property="article:published_time" content="2018-07-01T12:56:54+03:00"/>
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<meta property="article:modified_time" content="2018-07-10T00:22:48+03:00"/>
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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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<title>July, 2018 | CGSpace Notes</title>
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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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<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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<h2 id="2018-07-04">2018-07-04</h2>
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<ul>
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<li>I verified that the autowire error indeed only occurs on Tomcat 8.5, but the application works fine on Tomcat 7</li>
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<li>I have raised this in the <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560">DSpace 5.8 compatibility ticket on Atmire’s tracker</a></li>
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<li>Abenet wants me to add “United Kingdom government” to the sponsors on CGSpace so I created a ticket to track it (<a href="https://github.com/ilri/DSpace/issues/381">#381</a>)</li>
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<li>Also, Udana wants me to add “Enhancing Sustainability Across Agricultural Systems” to the WLE Phase II research themes so I created a ticket to track that (<a href="https://github.com/ilri/DSpace/issues/382">#382</a></li>
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<li>I need to try to finish this DSpace 5.8 business first because I have too many branches with cherry-picks going on right now!</li>
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</ul>
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<h2 id="2018-07-06">2018-07-06</h2>
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<ul>
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<li>CCAFS want me to add “PII-FP2_MSCCCAFS” to their Phase II project tags on CGSpace (<a href="https://github.com/ilri/DSpace/issues/383">#383</a></li>
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<li>I’ll do it in a batch with all the other metadata updates next week</li>
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</ul>
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<h2 id="2018-07-08">2018-07-08</h2>
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<ul>
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<li>I was tempted to do the Linode instance upgrade on CGSpace (linode18), but after looking closely at the system backups I noticed that Solr isn’t being backed up to S3</li>
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<li>I apparently noticed this—and fixed it!—in <a href="/cgspace-notes/2016-07/">2016-07</a>, but it doesn’t look like the backup has been updated since then!</li>
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<li>It looks like I added Solr to the <code>backup_to_s3.sh</code> script, but that script is not even being used (<code>s3cmd</code> is run directly from root’s crontab)</li>
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<li>For now I have just initiated a manual S3 backup of the Solr data:</li>
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</ul>
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<pre><code># s3cmd sync --delete-removed /home/backup/solr/ s3://cgspace.cgiar.org/solr/
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</code></pre>
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<ul>
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<li>But I need to add this to cron!</li>
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<li>I wonder if I should convert some of the cron jobs to systemd services / timers…</li>
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<li>I sent a note to all our users on Yammer to ask them about possible maintenance on Sunday, July 14th</li>
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<li>Abenet wants to be able to search by journal title (dc.source) in the advanced Discovery search so I opened an issue for it (<a href="https://github.com/ilri/DSpace/issues/384">#384</a>)</li>
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<li>I regenerated the list of names for all our ORCID iDs using my <a href="https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b">resolve-orcids.py</a> script:</li>
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</ul>
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<pre><code>$ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml | sort | uniq > /tmp/2018-07-08-orcids.txt
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$ ./resolve-orcids.py -i /tmp/2018-07-08-orcids.txt -o /tmp/2018-07-08-names.txt -d
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</code></pre>
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<ul>
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<li>But after comparing to the existing list of names I didn’t see much change, so I just ignored it</li>
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</ul>
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<h2 id="2018-07-09">2018-07-09</h2>
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<ul>
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<li>Uptime Robot said that CGSpace was down for two minutes early this morning but I don’t see anything in Tomcat logs or dmesg</li>
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<li>Uptime Robot said that CGSpace was down for two minutes again later in the day, and this time I saw a memory error in Tomcat’s <code>catalina.out</code>:</li>
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</ul>
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<pre><code>Exception in thread "http-bio-127.0.0.1-8081-exec-557" java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>I’m not sure if it’s the same error, but I see this in DSpace’s <code>solr.log</code>:</li>
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</ul>
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<pre><code>2018-07-09 06:25:09,913 ERROR org.apache.solr.servlet.SolrDispatchFilter @ null:java.lang.RuntimeException: java.lang.OutOfMemoryError: Java heap space
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</code></pre>
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<ul>
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<li>I see a strange error around that time in <code>dspace.log.2018-07-08</code>:</li>
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</ul>
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<pre><code>2018-07-09 06:23:43,510 ERROR com.atmire.statistics.SolrLogThread @ IOException occured when talking to server at: http://localhost:8081/solr/statistics
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org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr/statistics
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</code></pre>
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<ul>
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<li>But not sure what caused that…</li>
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<li>I got a message from Linode tonight that CPU usage was high on CGSpace for the past few hours around 8PM GMT</li>
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<li>Looking in the nginx logs I see the top ten IP addresses active today:</li>
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "09/Jul/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
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1691 40.77.167.84
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1701 40.77.167.69
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1718 50.116.102.77
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1872 137.108.70.6
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2172 157.55.39.234
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2190 207.46.13.47
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2848 178.154.200.38
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4367 35.227.26.162
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4387 70.32.83.92
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4738 95.108.181.88
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</code></pre>
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<ul>
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<li>Of those, <em>all</em> except <code>70.32.83.92</code> and <code>50.116.102.77</code> are <em>NOT</em> re-using their Tomcat sessions, for example from the XMLUI logs:</li>
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</ul>
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<pre><code>$ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-07-09
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4435
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</code></pre>
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<ul>
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<li><code>95.108.181.88</code> appears to be Yandex, so I dunno why it’s creating so many sessions, as its user agent should match Tomcat’s Crawler Session Manager Valve</li>
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<li><code>70.32.83.92</code> is on MediaTemple but I’m not sure who it is. They are mostly hitting REST so I guess that’s fine</li>
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<li><code>35.227.26.162</code> doesn’t declare a user agent and is on Google Cloud, so I should probably mark them as a bot in nginx</li>
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<li><code>178.154.200.38</code> is Yandex again</li>
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<li><code>207.46.13.47</code> is Bing</li>
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<li><code>157.55.39.234</code> is Bing</li>
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<li><code>137.108.70.6</code> is our old friend CORE bot</li>
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<li><code>50.116.102.77</code> doesn’t declare a user agent and lives on HostGator, but mostly just hits the REST API so I guess that’s fine</li>
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<li><code>40.77.167.84</code> is Bing again</li>
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<li>Interestingly, the first time that I see <code>35.227.26.162</code> was on 2018-06-08</li>
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<li>I’ve added <code>35.227.26.162</code> to the bot tagging logic in the nginx vhost</li>
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</ul>
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<h2 id="2018-07-10">2018-07-10</h2>
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<ul>
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<li>Add “United Kingdom government” to sponsors (<a href="https://github.com/ilri/DSpace/issues/381">#381</a>)</li>
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<li>Add “Enhancing Sustainability Across Agricultural Systems” to WLE Phase II Research Themes (<a href="https://github.com/ilri/DSpace/issues/382">#382</a>)</li>
|
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<li>Add “PII-FP2_MSCCCAFS” to CCAFS Phase II Project Tags (<a href="https://github.com/ilri/DSpace/issues/383">#383</a>)</li>
|
|
<li>Add journal title (dc.source) to Discovery search filters (<a href="https://github.com/ilri/DSpace/issues/384">#384</a>)</li>
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<li>All were tested and merged to the <code>5_x-prod</code> branch and will be deployed on CGSpace this coming weekend when I do the Linode server upgrade</li>
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<li>I need to get them onto the 5.8 testing branch too, either via cherry-picking or by rebasing after we finish testing Atmire’s 5.8 pull request (<a href="https://github.com/ilri/DSpace/pull/378">#378</a>)</li>
|
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<li>Linode sent an alert about CPU usage on CGSpace again, about 13:00UTC</li>
|
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<li>These are the top ten users in the last two hours:</li>
|
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</ul>
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<pre><code># zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "10/Jul/2018:(11|12|13)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
|
|
81 193.95.22.113
|
|
82 50.116.102.77
|
|
112 40.77.167.90
|
|
117 196.190.95.98
|
|
120 178.154.200.38
|
|
215 40.77.167.96
|
|
243 41.204.190.40
|
|
415 95.108.181.88
|
|
695 35.227.26.162
|
|
697 213.139.52.250
|
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</code></pre>
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|
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<ul>
|
|
<li>Looks like <code>213.139.52.250</code> is Moayad testing his new CGSpace vizualization thing:</li>
|
|
</ul>
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<pre><code>213.139.52.250 - - [10/Jul/2018:13:39:41 +0000] "GET /bitstream/handle/10568/75668/dryad.png HTTP/2.0" 200 53750 "http://localhost:4200/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.87 Safari/537.36"
|
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</code></pre>
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<ul>
|
|
<li>He said there was a bug…</li>
|
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<li>I’ll have to keep and eye on this and see how their platform evolves</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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<h4>Recent Posts</h4>
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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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<h4>Links</h4>
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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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