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Add notes for 2023-04-18

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Alan Orth 2023-04-18 11:08:15 -07:00
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@ -91,4 +91,361 @@ $ for file in $(csvjoin -c doi /tmp/donald-doi-pdfs.csv /tmp/donald-open-dois.cs
- I ran out of time and had to stop the process around 3,127 PDFs - I ran out of time and had to stop the process around 3,127 PDFs
- I zipped them up and sent them to the others, along with a CSV of the DOIs, PDF filenames, and licenses - I zipped them up and sent them to the others, along with a CSV of the DOIs, PDF filenames, and licenses
## 2023-04-17
- Abenet noticed a weird issue with [this item](https://cgspace.cgiar.org/handle/10568/75611)
- The item has metadata, but the page is blank
- When I try to edit the item's authorization policies in XMLUI I get a nullPointerException:
```
Java stacktrace: java.lang.NullPointerException
at org.dspace.app.xmlui.aspect.administrative.authorization.EditItemPolicies.addBody(EditItemPolicies.java:166)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:234)
at sun.reflect.GeneratedMethodAccessor347.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy201.startElement(Unknown Source)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.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.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.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.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.components.sax.AbstractXMLByteStreamInterpreter.parse(AbstractXMLByteStreamInterpreter.java:117)
at org.apache.cocoon.components.sax.XMLByteStreamInterpreter.deserialize(XMLByteStreamInterpreter.java:44)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:324)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:326)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:326)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.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.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:439)
at sun.reflect.GeneratedMethodAccessor255.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.treeprocessor.sitemap.SerializeNode.invoke(SerializeNode.java:147)
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.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:117)
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:728)
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$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at com.sun.proxy.$Proxy186.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1216)
at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:1001)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:853)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:160)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:165)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:235)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:1025)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:451)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1201)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:654)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:750)
```
- I don't see anything on the DSpace issue tracker or mailing list so I asked about it on the DSpace Slack...
- Peter said CGSpace was slow and I see a lot of locks from the XMLUI
- I looked and found many locks that were many hours and days old so I killed some:
```console
$ psql < locks-age.sql | grep -E "[[:digit:]] days" | awk -F\| '{print $10}' | sort -u
1050672
1053773
1054602
1054702
1056782
1057629
1057630
$ psql < locks-age.sql | grep -E "[[:digit:]] days" | awk -F\| '{print $10}' | sort -u | xargs kill
```
- I'm also running a `dspace cleanup -v`, but it doesn't seem to be finishing
- I recall something like there being errors in the logs rather than on the command line in DSpace 6...
- I found it in the DSpace log:
```console
2023-04-17 21:09:46,004 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle"
Detail: Key (uuid)=(a7ddf477-1c04-4de0-9c7a-4d3c84a875bc) is still referenced from table "bundle".
```
- If I mark the primary bitstream as null manually the cleanup script continues until it finds a few more
- I ended up with a long list of UUIDs to fix before the script would complete:
```console
$ psql -d dspace -c "update bundle set primary_bitstream_id=NULL where primary_bitstream_id in ('a7ddf477-1c04-4de0-9c7a-4d3c84a875bc', '9582b661-9c2d-4c86-be22-c3b0942b646a', '210a4d5d-3af9-46f0-84cc-682dd1431762')"
```
## 2023-04-18
- Regarding the item Abenet noticed yesterday that has a blank page and a nullPointerException
- It appears OK on DSpace Test! https://dspacetest.cgiar.org/handle/10568/75611
- And according to the REST API on CGSpace the item was modified on 2023-04-11, so last week...
- According to the DSpace logs it was Francesca who edited the item last week, so I asked her for more information before I troubleshoot more
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

369
docs/2023-04/index.html
View File

@ -20,7 +20,7 @@ Start a harvest on AReS
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-04/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-04/" />
<meta property="article:published_time" content="2023-04-02T08:19:36+03:00" /> <meta property="article:published_time" content="2023-04-02T08:19:36+03:00" />
<meta property="article:modified_time" content="2023-04-02T09:16:25+03:00" /> <meta property="article:modified_time" content="2023-04-06T16:13:30+03:00" />
@ -46,9 +46,9 @@ Start a harvest on AReS
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "April, 2023", "headline": "April, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-04/", "url": "https://alanorth.github.io/cgspace-notes/2023-04/",
"wordCount": "569", "wordCount": "1556",
"datePublished": "2023-04-02T08:19:36+03:00", "datePublished": "2023-04-02T08:19:36+03:00",
"dateModified": "2023-04-02T09:16:25+03:00", "dateModified": "2023-04-06T16:13:30+03:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"
@ -221,6 +221,369 @@ Start a harvest on AReS
</ul> </ul>
</li> </li>
</ul> </ul>
<h2 id="2023-04-17">2023-04-17</h2>
<ul>
<li>Abenet noticed a weird issue with <a href="https://cgspace.cgiar.org/handle/10568/75611">this item</a>
<ul>
<li>The item has metadata, but the page is blank</li>
<li>When I try to edit the item&rsquo;s authorization policies in XMLUI I get a nullPointerException:</li>
</ul>
</li>
</ul>
<pre tabindex="0"><code>Java stacktrace: java.lang.NullPointerException
at org.dspace.app.xmlui.aspect.administrative.authorization.EditItemPolicies.addBody(EditItemPolicies.java:166)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:234)
at sun.reflect.GeneratedMethodAccessor347.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.$Proxy201.startElement(Unknown Source)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.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.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:251)
at sun.reflect.GeneratedMethodAccessor347.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy203.startElement(Unknown Source)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.components.sax.XMLTeePipe.startElement(XMLTeePipe.java:87)
at org.apache.cocoon.components.sax.AbstractXMLByteStreamInterpreter.parse(AbstractXMLByteStreamInterpreter.java:117)
at org.apache.cocoon.components.sax.XMLByteStreamInterpreter.deserialize(XMLByteStreamInterpreter.java:44)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:324)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:326)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:326)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:750)
at sun.reflect.GeneratedMethodAccessor438.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.source.impl.SitemapSource.toSAX(SitemapSource.java:362)
at org.apache.cocoon.components.source.util.SourceUtil.toSAX(SourceUtil.java:111)
at org.apache.cocoon.components.source.util.SourceUtil.parse(SourceUtil.java:294)
at org.apache.cocoon.generation.FileGenerator.generate(FileGenerator.java:136)
at sun.reflect.GeneratedMethodAccessor436.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy198.generate(Unknown Source)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.processXMLPipeline(AbstractProcessingPipeline.java:544)
at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.processXMLPipeline(AbstractCachingProcessingPipeline.java:273)
at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:439)
at sun.reflect.GeneratedMethodAccessor255.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.$Proxy191.process(Unknown Source)
at org.apache.cocoon.components.treeprocessor.sitemap.SerializeNode.invoke(SerializeNode.java:147)
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.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:117)
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:728)
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:204)
at com.sun.proxy.$Proxy186.service(Unknown Source)
at org.dspace.springmvc.CocoonView.render(CocoonView.java:113)
at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1216)
at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:1001)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:945)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:867)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:951)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:853)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:827)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:113)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:160)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:165)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
at org.apache.catalina.valves.CrawlerSessionManagerValve.invoke(CrawlerSessionManagerValve.java:235)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:1025)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:451)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1201)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:654)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:750)
</code></pre><ul>
<li>I don&rsquo;t see anything on the DSpace issue tracker or mailing list so I asked about it on the DSpace Slack&hellip;</li>
<li>Peter said CGSpace was slow and I see a lot of locks from the XMLUI
<ul>
<li>I looked and found many locks that were many hours and days old so I killed some:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql &lt; locks-age.sql | grep -E <span style="color:#e6db74">&#34;[[:digit:]] days&#34;</span> | awk -F<span style="color:#ae81ff">\|</span> <span style="color:#e6db74">&#39;{print $10}&#39;</span> | sort -u
</span></span><span style="display:flex;"><span> 1050672
</span></span><span style="display:flex;"><span> 1053773
</span></span><span style="display:flex;"><span> 1054602
</span></span><span style="display:flex;"><span> 1054702
</span></span><span style="display:flex;"><span> 1056782
</span></span><span style="display:flex;"><span> 1057629
</span></span><span style="display:flex;"><span> 1057630
</span></span><span style="display:flex;"><span>$ psql &lt; locks-age.sql | grep -E <span style="color:#e6db74">&#34;[[:digit:]] days&#34;</span> | awk -F<span style="color:#ae81ff">\|</span> <span style="color:#e6db74">&#39;{print $10}&#39;</span> | sort -u | xargs kill
</span></span></code></pre></div><ul>
<li>I&rsquo;m also running a <code>dspace cleanup -v</code>, but it doesn&rsquo;t seem to be finishing
<ul>
<li>I recall something like there being errors in the logs rather than on the command line in DSpace 6&hellip;</li>
<li>I found it in the DSpace log:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>2023-04-17 21:09:46,004 ERROR org.hibernate.engine.jdbc.spi.SqlExceptionHelper @ ERROR: update or delete on table &#34;bitstream&#34; violates foreign key constraint &#34;bundle_primary_bitstream_id_fkey&#34; on table &#34;bundle&#34;
</span></span><span style="display:flex;"><span> Detail: Key (uuid)=(a7ddf477-1c04-4de0-9c7a-4d3c84a875bc) is still referenced from table &#34;bundle&#34;.
</span></span></code></pre></div><ul>
<li>If I mark the primary bitstream as null manually the cleanup script continues until it finds a few more
<ul>
<li>I ended up with a long list of UUIDs to fix before the script would complete:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ psql -d dspace -c <span style="color:#e6db74">&#34;update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (&#39;a7ddf477-1c04-4de0-9c7a-4d3c84a875bc&#39;, &#39;9582b661-9c2d-4c86-be22-c3b0942b646a&#39;, &#39;210a4d5d-3af9-46f0-84cc-682dd1431762&#39;)&#34;</span>
</span></span></code></pre></div><h2 id="2023-04-18">2023-04-18</h2>
<ul>
<li>Regarding the item Abenet noticed yesterday that has a blank page and a nullPointerException
<ul>
<li>It appears OK on DSpace Test! <a href="https://dspacetest.cgiar.org/handle/10568/75611">https://dspacetest.cgiar.org/handle/10568/75611</a></li>
<li>And according to the REST API on CGSpace the item was modified on 2023-04-11, so last week&hellip;</li>
<li>According to the DSpace logs it was Francesca who edited the item last week, so I asked her for more information before I troubleshoot more</li>
</ul>
</li>
</ul>
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