String index out of range: 3

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James Holobetz

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Oct 31, 2016, 4:07:48 PM10/31/16
to dspac...@googlegroups.com
Hello,

We are building a Dspace 5.6 server for production and we are running into an issue when trying to ingest materials. We recieve ther error: String index out of range: 3.

I did some research and this has been noted in https://jira.duraspace.org/browse/DS-3142 and http://bz.apache.org/bugzilla/show_bug.cgi?id=58999 but from the initial reports in DS-3142 this effect Dspace 6.x and not 5.x but we are in fact using the noted tomcat version.


We are running (SUSE Linux Enterprise Server) SLES 12 SP1
(all packages are part of the SLES 12 SP1 system)

tomcat 8.0.32
maven 3.3.9
java 1.7.0_111 (OpenJDK)
ant 1.9.4
postgres 9.4.9



Can anybody provide any help/direction in this matter?


James Holobetz


Terry Brady

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Oct 31, 2016, 4:14:29 PM10/31/16
to James Holobetz, DSpace Technical Support
Are you encountering this issue while performing an item submission through the UI, or are you running a bulk ingest from the command line?

Could you provide some additional details from your log files?

Terry

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Terry Brady
Applications Programmer Analyst
Georgetown University Library Information Technology
425-298-5498 (Seattle, WA)

James Holobetz

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Oct 31, 2016, 4:32:04 PM10/31/16
to Terry Brady, dspac...@googlegroups.com
We are encountering this as we are using any create/edit command in the Context menu (UI). 

Here is the log output (just realized the sitemap error; any elaboration would be wonderful);


2016-10-31 14:28:07,620 ERROR cocoon.handled  - Sitemap: error calling function 'startCreateCommunity'
        at <map:call> - resource://aspects/Administrative/sitemap.xmap:261:51
        at <map:match type="request"> - resource://aspects/Administrative/sitemap.xmap:257:53
        at <map:match> - resource://aspects/Administrative/sitemap.xmap:252:43
        at <map:select type="AuthenticatedSelector"> - resource://aspects/Administrative/sitemap.xmap:128:45
        at <map:mount> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:89:72
        at <map:select type="parameter"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:79:34
        at <map:match type="AspectMatcher"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:78:36
        at <map:mount> - file:///opt/dspace/webapps/xmlui/sitemap.xmap:488:100
        at <map:match> - file:///opt/dspace/webapps/xmlui/sitemap.xmap:487:49
        at <map:serialize type="xml"> - resource://aspects/EPerson/sitemap.xmap:302:31
        at <map:transform type="Navigation"> - resource://aspects/EPerson/sitemap.xmap:107:38
        at <map:generate> - resource://aspects/EPerson/sitemap.xmap:96:19
        at <map:serialize type="xml"> - resource://aspects/Submission/sitemap.xmap:251:38
        at <map:transform type="Navigation"> - resource://aspects/Submission/sitemap.xmap:107:45
        at <map:generate> - resource://aspects/Submission/sitemap.xmap:104:26
        at <map:serialize type="xml"> - resource://aspects/Statistics/sitemap.xmap:292:36
        at <map:generate> - resource://aspects/Statistics/sitemap.xmap:37:19
        at <map:serialize type="xml"> - resource://aspects/Workflow/sitemap.xmap:139:38
        at <map:generate> - resource://aspects/Workflow/sitemap.xmap:76:26
        at <map:serialize type="xml"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:85:34
        at <map:transform type="PageNotFound"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:84:43
        at <map:generate> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:83:22
        at <map:serialize type="xhtml"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:179:46
        at <map:transform type="i18n"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:101:44
        at <map:transform> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:97:59
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:82:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:78:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:70:51
        at <map:generate type="file"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:171:67
        at <map:match> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:167:37
org.apache.cocoon.ProcessingException: Sitemap: error calling function 'startCreateCommunity'
        at <map:call> - resource://aspects/Administrative/sitemap.xmap:261:51
        at <map:match type="request"> - resource://aspects/Administrative/sitemap.xmap:257:53
        at <map:match> - resource://aspects/Administrative/sitemap.xmap:252:43
        at <map:select type="AuthenticatedSelector"> - resource://aspects/Administrative/sitemap.xmap:128:45
        at <map:mount> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:89:72
        at <map:select type="parameter"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:79:34
        at <map:match type="AspectMatcher"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:78:36
        at <map:mount> - file:///opt/dspace/webapps/xmlui/sitemap.xmap:488:100
        at <map:match> - file:///opt/dspace/webapps/xmlui/sitemap.xmap:487:49
        at <map:serialize type="xml"> - resource://aspects/EPerson/sitemap.xmap:302:31
        at <map:transform type="Navigation"> - resource://aspects/EPerson/sitemap.xmap:107:38
        at <map:generate> - resource://aspects/EPerson/sitemap.xmap:96:19
        at <map:serialize type="xml"> - resource://aspects/Submission/sitemap.xmap:251:38
        at <map:transform type="Navigation"> - resource://aspects/Submission/sitemap.xmap:107:45
        at <map:generate> - resource://aspects/Submission/sitemap.xmap:104:26
        at <map:serialize type="xml"> - resource://aspects/Statistics/sitemap.xmap:292:36
        at <map:generate> - resource://aspects/Statistics/sitemap.xmap:37:19
        at <map:serialize type="xml"> - resource://aspects/Workflow/sitemap.xmap:139:38
        at <map:generate> - resource://aspects/Workflow/sitemap.xmap:76:26
        at <map:serialize type="xml"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:85:34
        at <map:transform type="PageNotFound"> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:84:43
        at <map:generate> - file:///opt/dspace/webapps/xmlui/aspects/aspects.xmap:83:22
        at <map:serialize type="xhtml"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:179:46
        at <map:transform type="i18n"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:101:44
        at <map:transform> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:97:59
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:82:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:78:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:70:51
        at <map:generate type="file"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:171:67
        at <map:match> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:167:37
        at org.apache.cocoon.ProcessingException.throwLocated(ProcessingException.java:111)
        at org.apache.cocoon.components.treeprocessor.sitemap.CallFunctionNode.invoke(CallFunctionNode.java:111)
        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.SelectNode.invoke(SelectNode.java:82)
        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.buildPipeline(ConcreteTreeProcessor.java:186)
        at org.apache.cocoon.components.treeprocessor.TreeProcessor.buildPipeline(TreeProcessor.java:260)
        at org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:107)
        at org.apache.cocoon.components.treeprocessor.AbstractParentProcessingNode.invokeNodes(AbstractParentProcessingNode.java:78)
        at org.apache.cocoon.components.treeprocessor.sitemap.SelectNode.invoke(SelectNode.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.buildPipeline(ConcreteTreeProcessor.java:186)
        at org.apache.cocoon.components.treeprocessor.TreeProcessor.buildPipeline(TreeProcessor.java:260)
        at org.apache.cocoon.components.treeprocessor.sitemap.MountNode.invoke(MountNode.java:107)
        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.buildPipeline(ConcreteTreeProcessor.java:186)
        at org.apache.cocoon.components.treeprocessor.TreeProcessor.buildPipeline(TreeProcessor.java:260)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:277)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at org.dspace.app.xmlui.cocoon.AspectGenerator.setup(AspectGenerator.java:81)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
        at sun.reflect.GeneratedMethodAccessor117.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.prepareInternal(Unknown Source)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:292)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at org.dspace.app.xmlui.cocoon.AspectGenerator.setup(AspectGenerator.java:81)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
        at sun.reflect.GeneratedMethodAccessor117.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.prepareInternal(Unknown Source)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:292)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at org.dspace.app.xmlui.cocoon.AspectGenerator.setup(AspectGenerator.java:81)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
        at sun.reflect.GeneratedMethodAccessor117.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.prepareInternal(Unknown Source)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:292)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at org.dspace.app.xmlui.cocoon.AspectGenerator.setup(AspectGenerator.java:81)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
        at sun.reflect.GeneratedMethodAccessor117.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.prepareInternal(Unknown Source)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:292)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at org.dspace.app.xmlui.cocoon.AspectGenerator.setup(AspectGenerator.java:81)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.prepareInternal(AbstractProcessingPipeline.java:480)
        at sun.reflect.GeneratedMethodAccessor117.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.prepareInternal(Unknown Source)
        at org.apache.cocoon.components.source.impl.SitemapSource.init(SitemapSource.java:292)
        at org.apache.cocoon.components.source.impl.SitemapSource.<init>(SitemapSource.java:148)
        at org.apache.cocoon.components.source.impl.SitemapSourceFactory.getSource(SitemapSourceFactory.java:62)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:153)
        at org.apache.cocoon.components.source.CocoonSourceResolver.resolveURI(CocoonSourceResolver.java:183)
        at org.apache.cocoon.generation.FileGenerator.setup(FileGenerator.java:99)
        at sun.reflect.GeneratedMethodAccessor70.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy56.setup(Unknown Source)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.setupPipeline(AbstractProcessingPipeline.java:343)
        at org.apache.cocoon.components.pipeline.impl.AbstractCachingProcessingPipeline.setupPipeline(AbstractCachingProcessingPipeline.java:710)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.preparePipeline(AbstractProcessingPipeline.java:466)
        at org.apache.cocoon.components.pipeline.AbstractProcessingPipeline.process(AbstractProcessingPipeline.java:411)
        at sun.reflect.GeneratedMethodAccessor125.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
        at com.sun.proxy.$Proxy55.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:729)
        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$ServiceInterceptor.invoke(ServletFactoryBean.java:264)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at com.sun.proxy.$Proxy52.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)
        at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
        at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
        at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:622)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:292)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.dspace.app.xmlui.cocoon.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:111)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter.doFilter(DSpaceCocoonServletFilter.java:274)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.dspace.app.xmlui.cocoon.servlet.multipart.DSpaceMultipartFilter.doFilter(DSpaceMultipartFilter.java:119)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.dspace.utils.servlet.DSpaceWebappServletFilter.doFilter(DSpaceWebappServletFilter.java:78)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:240)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:207)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:212)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:141)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)
        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:616)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:522)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1095)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:672)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2500)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2489)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 3
        at java.lang.String.charAt(String.java:658)
        at org.apache.catalina.loader.WebappClassLoaderBase.filter(WebappClassLoaderBase.java:2780)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1253)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1142)
        at org.mozilla.javascript.Kit.classOrNull(Kit.java:88)
        at org.mozilla.javascript.NativeJavaPackage.getPkgProperty(NativeJavaPackage.java:154)
        at org.mozilla.javascript.NativeJavaPackage.get(NativeJavaPackage.java:105)
        at org.mozilla.javascript.ScriptableObject.getProperty(ScriptableObject.java:1544)
        at org.mozilla.javascript.ScriptRuntime.getObjectProp(ScriptRuntime.java:1375)
        at org.mozilla.javascript.ScriptRuntime.getObjectProp(ScriptRuntime.java:1364)
        at org.mozilla.javascript.Interpreter.interpretLoop(Interpreter.java:2965)
        at org.mozilla.javascript.Interpreter.interpret(Interpreter.java:2394)
        at org.mozilla.javascript.InterpretedFunction.call(InterpretedFunction.java:162)
        at org.mozilla.javascript.ContextFactory.doTopCall(ContextFactory.java:393)
        at org.mozilla.javascript.ScriptRuntime.doTopCall(ScriptRuntime.java:2834)
        at org.mozilla.javascript.InterpretedFunction.exec(InterpretedFunction.java:173)
        at org.apache.cocoon.components.flow.javascript.fom.FOM_JavaScriptInterpreter.setupContext(FOM_JavaScriptInterpreter.java:465)
        at org.apache.cocoon.components.flow.javascript.fom.FOM_JavaScriptInterpreter.callFunction(FOM_JavaScriptInterpreter.java:585)
        at org.apache.cocoon.components.treeprocessor.sitemap.CallFunctionNode.invoke(CallFunctionNode.java:109)
        ... 239 more
2016-10-31 14:28:07,625 INFO  org.apache.cocoon.components.treeprocessor.sitemap.HandleErrorsNode  - Processing handle-errors at <map:handle-errors> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:188:28
2016-10-31 14:28:07,642 INFO  cocoon.access  - 'admin/community' Processed by Apache Cocoon in 35 milliseconds.

James Holobetz

unread,
Oct 31, 2016, 4:46:59 PM10/31/16
to Terry Brady, dspac...@googlegroups.com
It should be noted that this error occurs with the default/unaltered Mirage theme as well (using XMLUI). All themes are derivatives of Mirage and have reverted back to Mirage to test as well.

James

Terry Brady

unread,
Oct 31, 2016, 5:20:58 PM10/31/16
to James Holobetz, DSpace Technical Support
The Cocoon errors are always a challenge to untangle.

I have a couple additional questions that might help.

Did you upgrade from a prior version of DSpace, or is this a new installation?

I saw that you have reverted to Mirage which was a good idea to try.  Looking at the error chain, it appears to be referencing something in a custom theme.

        at <map:serialize type="xhtml"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:179:46
        at <map:transform type="i18n"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:101:44
        at <map:transform> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:97:59
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:82:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:78:51
        at <map:transform type="IncludePageMeta"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:70:51
        at <map:generate type="file"> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:171:67
        at <map:match> - file:///opt/dspace/webapps/xmlui/themes/oURspace/sitemap.xmap:167:37

If you look at those lines in your custom theme directory, can you detect anything that is missing?

Terry

Tim Donohue

unread,
Oct 31, 2016, 5:27:42 PM10/31/16
to James Holobetz, dspac...@googlegroups.com

Hi James,

As noted in the Tomcat ticket you linked to (https://bz.apache.org/bugzilla/show_bug.cgi?id=58999), and the DS-3142 ticket, this is a bug in Tomcat 8.0.32.  I suspect this Tomcat bug is not just triggered in DSpace 6, but also very likely triggered in any version of DSpace that uses XMLUI (JSPUI seems to not trigger the issue in Tomcat).  Unfortunately, some OSes still ship with Tomcat 8.0.32 by default. For example, Ubuntu 16.04 still defaults to Tomcat 8.0.32, even though others are complaining about this same bug, see https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1606331

So, long story short, I don't think there's anything wrong in your DSpace site itself.  I suspect you will have to install a different version of Tomcat to fix these errors.

- Tim

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James Holobetz

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Nov 1, 2016, 1:14:50 PM11/1/16
to Tim Donohue, dspac...@googlegroups.com
Thanks Tim, we suspected as much.

As always, we appreciate your help.

James


On Oct 31, 2016 3:27 PM, "Tim Donohue" <tdon...@duraspace.org> wrote:

Hi James,

As noted in the Tomcat ticket you linked to (https://bz.apache.org/bugzilla/show_bug.cgi?id=58999), and the DS-3142 ticket, this is a bug in Tomcat 8.0.32.  I suspect this Tomcat bug is not just triggered in DSpace 6, but also very likely triggered in any version of DSpace that uses XMLUI (JSPUI seems to not trigger the issue in Tomcat).  Unfortunately, some OSes still ship with Tomcat 8.0.32 by default. For example, Ubuntu 16.04 still defaults to Tomcat 8.0.32, even though others are complaining about this same bug, see https://bugs.launchpad.net/ubuntu/+source/tomcat8/+bug/1606331

So, long story short, I don't think there's anything wrong in your DSpace site itself.  I suspect you will have to install a different version of Tomcat to fix these errors.

- Tim

On 10/31/2016 3:07 PM, James Holobetz wrote:
Hello,

We are building a Dspace 5.6 server for production and we are running into an issue when trying to ingest materials. We recieve ther error: String index out of range: 3.

I did some research and this has been noted in https://jira.duraspace.org/browse/DS-3142 and http://bz.apache.org/bugzilla/show_bug.cgi?id=58999 but from the initial reports in DS-3142 this effect Dspace 6.x and not 5.x but we are in fact using the noted tomcat version.


We are running (SUSE Linux Enterprise Server) SLES 12 SP1
(all packages are part of the SLES 12 SP1 system)

tomcat 8.0.32
maven 3.3.9
java 1.7.0_111 (OpenJDK)
ant 1.9.4
postgres 9.4.9



Can anybody provide any help/direction in this matter?


James Holobetz


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