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Add notes for 2016-12-02
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@ -13,7 +13,7 @@
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<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/post/" />
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<meta property="og:updated_time" content="2016-11-01T09:21:00+03:00"/>
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<meta property="og:updated_time" content="2016-12-02T10:43:00+03:00"/>
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@ -91,6 +91,22 @@
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-12/">December, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-12-02T10:43:00+03:00">Fri Dec 02, 2016</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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2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID="TX157907838689377964651674089851855413607") 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.
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<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>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"><a href="https://alanorth.github.io/cgspace-notes/2016-11/">November, 2016</a></h2>
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@ -323,37 +339,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
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<article class="blog-post">
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<header>
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<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-02/">February, 2016</a></h2>
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<p class="blog-post-meta"><time datetime="2016-02-05T13:18:00+03:00">Fri Feb 05, 2016</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="2016-02-05">2016-02-05</h2>
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<ul>
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<li>Looking at some DAGRIS data for Abenet Yabowork</li>
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<li>Lots of issues with spaces, newlines, etc causing the import to fail</li>
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<li>I noticed we have a very <em>interesting</em> list of countries on CGSpace:</li>
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</ul>
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<p><img src="2016/02/cgspace-countries.png" alt="CGSpace country list" /></p>
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<ul>
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<li>Not only are there 49,000 countries, we have some blanks (25)…</li>
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<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
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</ul>
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<p></p>
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<a href='https://alanorth.github.io/cgspace-notes/2016-02/'>Read more →</a>
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</article>
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<nav class="blog-pagination">
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@ -377,6 +362,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
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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/2016-12/">December, 2016</a></li>
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<li><a href="/cgspace-notes/2016-11/">November, 2016</a></li>
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<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
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@ -385,8 +372,6 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
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<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
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<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
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</ol>
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</section>
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@ -6,9 +6,149 @@
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<description>Recent content in Post-rsses on CGSpace Notes</description>
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<generator>Hugo -- gohugo.io</generator>
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<language>en-us</language>
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<lastBuildDate>Tue, 01 Nov 2016 09:21:00 +0300</lastBuildDate>
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<lastBuildDate>Fri, 02 Dec 2016 10:43:00 +0300</lastBuildDate>
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<atom:link href="https://alanorth.github.io/cgspace-notes/post/index.xml" rel="self" type="application/rss+xml" />
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<item>
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<title>December, 2016</title>
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<link>https://alanorth.github.io/cgspace-notes/2016-12/</link>
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<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
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<description>
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<h2 id="2016-12-02">2016-12-02</h2>
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||||
|
||||
<ul>
|
||||
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
|
||||
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
|
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
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2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
|
||||
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
|
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</code></pre>
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<ul>
|
||||
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
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<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
|
||||
<li>Another worrying error from dspace.log is:</li>
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</ul>
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<pre><code>org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
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at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
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at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
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at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
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at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:789)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
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at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:274)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
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at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
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at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
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at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
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at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
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at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
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at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
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at com.googlecode.psiprobe.Tomcat70AgentValve.invoke(Tomcat70AgentValve.java:44)
|
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at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
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at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:180)
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at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
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at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
|
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at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
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at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
|
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at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
|
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at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
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at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
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at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
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at java.lang.Thread.run(Thread.java:745)
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Caused by: java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
|
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at com.atmire.statistics.generator.TopNDSODatasetGenerator.toDatasetQuery(SourceFile:39)
|
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at com.atmire.statistics.display.StatisticsDataVisitsMultidata.createDataset(SourceFile:108)
|
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at org.dspace.statistics.content.StatisticsDisplay.createDataset(SourceFile:384)
|
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at org.dspace.statistics.content.StatisticsDisplay.getDataset(SourceFile:404)
|
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at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generateJsonData(SourceFile:170)
|
||||
at com.atmire.statistics.mostpopular.JSONStatsMostPopularGenerator.generate(SourceFile:246)
|
||||
at com.atmire.app.xmlui.aspect.statistics.JSONStatsMostPopular.generate(JSONStatsMostPopular.java:145)
|
||||
at sun.reflect.GeneratedMethodAccessor296.invoke(Unknown Source)
|
||||
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
|
||||
at java.lang.reflect.Method.invoke(Method.java:498)
|
||||
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
|
||||
at com.sun.proxy.$Proxy96.process(Unknown Source)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.ReadNode.invoke(ReadNode.java:94)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
|
||||
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
|
||||
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
|
||||
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:117)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:55)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.MatchNode.invoke(MatchNode.java:87)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.PipelineNode.invoke(PipelineNode.java:143)
|
||||
at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
|
||||
at org.apache.cocoon.components.treeprocessor.sitemap.PipelinesNode.invoke(PipelinesNode.java:81)
|
||||
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:239)
|
||||
at org.apache.cocoon.components.treeprocessor.ConcreteTreeProcessor.process(ConcreteTreeProcessor.java:171)
|
||||
at org.apache.cocoon.components.treeprocessor.TreeProcessor.process(TreeProcessor.java:247)
|
||||
at org.apache.cocoon.servlet.RequestProcessor.process(RequestProcessor.java:351)
|
||||
at org.apache.cocoon.servlet.RequestProcessor.service(RequestProcessor.java:169)
|
||||
at org.apache.cocoon.sitemap.SitemapServlet.service(SitemapServlet.java:84)
|
||||
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
|
||||
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:468)
|
||||
at org.apache.cocoon.servletservice.ServletServiceContext$PathDispatcher.forward(ServletServiceContext.java:443)
|
||||
at org.apache.cocoon.servletservice.spring.ServletFactoryBean$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
|
||||
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
|
||||
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
|
||||
at com.sun.proxy.$Proxy89.service(Unknown Source)
|
||||
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
|
||||
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1180)
|
||||
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:950)
|
||||
... 35 more
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>The first error I see in dspace.log this morning is:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>2016-12-02 03:00:46,656 ERROR org.dspace.authority.AuthorityValueFinder @ anonymous::Error while retrieving AuthorityValue from solr:query\colon; id\colon;&quot;b0b541c1-ec15-48bf-9209-6dbe8e338cdc&quot;
|
||||
org.apache.solr.client.solrj.SolrServerException: Server refused connection at: http://localhost:8081/solr/authority
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>Looking through DSpace&rsquo;s solr log I see that about 20 seconds before this, there were a few 30+ KiB solr queries</li>
|
||||
<li>The last logs here right before Solr became unresponsive (and right after I restarted it five hours later) were:</li>
|
||||
</ul>
|
||||
|
||||
<pre><code>2016-12-02 03:00:42,606 INFO org.apache.solr.core.SolrCore @ [statistics] webapp=/solr path=/select params={q=containerItem:72828+AND+type:0&amp;shards=localhost:8081/solr/statistics-2010,localhost:8081/solr/statistics&amp;fq=-isInternal:true&amp;fq=-(author_mtdt:&quot;CGIAR\+Institutional\+Learning\+and\+Change\+Initiative&quot;++AND+subject_mtdt:&quot;PARTNERSHIPS&quot;+AND+subject_mtdt:&quot;RESEARCH&quot;+AND+subject_mtdt:&quot;AGRICULTURE&quot;+AND+subject_mtdt:&quot;DEVELOPMENT&quot;++AND+iso_mtdt:&quot;en&quot;+)&amp;rows=0&amp;wt=javabin&amp;version=2} hits=0 status=0 QTime=19
|
||||
2016-12-02 08:28:23,908 INFO org.apache.solr.servlet.SolrDispatchFilter @ SolrDispatchFilter.init()
|
||||
</code></pre>
|
||||
|
||||
<ul>
|
||||
<li>DSpace&rsquo;s own Solr logs don&rsquo;t give IP addresses, so I will have to enable Nginx&rsquo;s logging of <code>/solr</code> so I can see where this request came from</li>
|
||||
<li>I enabled logging of <code>/rest/</code> and I think I&rsquo;ll leave it on for good</li>
|
||||
</ul>
|
||||
</description>
|
||||
</item>
|
||||
|
||||
<item>
|
||||
<title>November, 2016</title>
|
||||
<link>https://alanorth.github.io/cgspace-notes/2016-11/</link>
|
||||
@ -557,6 +697,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
|
||||
<ul>
|
||||
<li>The <code>maxHttpHeaderSize</code> fix worked on CGSpace (user is able to see the community list on the homepage)</li>
|
||||
<li>The &ldquo;take task&rdquo; cache fix worked on DSpace Test but it&rsquo;s not an official patch, so I&rsquo;ll have to report the bug to DSpace people and try to get advice</li>
|
||||
<li>More work on the KM4Dev Journal article</li>
|
||||
</ul>
|
||||
</description>
|
||||
</item>
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/post/" />
|
||||
|
||||
|
||||
<meta property="og:updated_time" content="2016-01-13T13:18:00+03:00"/>
|
||||
<meta property="og:updated_time" content="2016-02-05T13:18:00+03:00"/>
|
||||
|
||||
|
||||
|
||||
@ -91,6 +91,37 @@
|
||||
|
||||
|
||||
|
||||
<article class="blog-post">
|
||||
<header>
|
||||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-02/">February, 2016</a></h2>
|
||||
<p class="blog-post-meta"><time datetime="2016-02-05T13:18:00+03:00">Fri Feb 05, 2016</time> by Alan Orth in
|
||||
|
||||
<i class="fa fa-tag" aria-hidden="true"></i> <a href="/cgspace-notes/tags/notes" rel="tag">Notes</a>
|
||||
|
||||
</p>
|
||||
</header>
|
||||
<h2 id="2016-02-05">2016-02-05</h2>
|
||||
|
||||
<ul>
|
||||
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
|
||||
<li>Lots of issues with spaces, newlines, etc causing the import to fail</li>
|
||||
<li>I noticed we have a very <em>interesting</em> list of countries on CGSpace:</li>
|
||||
</ul>
|
||||
|
||||
<p><img src="2016/02/cgspace-countries.png" alt="CGSpace country list" /></p>
|
||||
|
||||
<ul>
|
||||
<li>Not only are there 49,000 countries, we have some blanks (25)…</li>
|
||||
<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
|
||||
</ul>
|
||||
|
||||
<p></p>
|
||||
<a href='https://alanorth.github.io/cgspace-notes/2016-02/'>Read more →</a>
|
||||
</article>
|
||||
|
||||
|
||||
|
||||
|
||||
<article class="blog-post">
|
||||
<header>
|
||||
<h2 class="blog-post-title"><a href="https://alanorth.github.io/cgspace-notes/2016-01/">January, 2016</a></h2>
|
||||
@ -195,6 +226,8 @@
|
||||
<h4>Recent Posts</h4>
|
||||
<ol class="list-unstyled">
|
||||
|
||||
<li><a href="/cgspace-notes/2016-12/">December, 2016</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2016-11/">November, 2016</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2016-10/">October, 2016</a></li>
|
||||
@ -203,8 +236,6 @@
|
||||
|
||||
<li><a href="/cgspace-notes/2016-08/">August, 2016</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2016-07/">July, 2016</a></li>
|
||||
|
||||
</ol>
|
||||
</section>
|
||||
|
||||
|
||||
Reference in New Issue
Block a user