Thanks :-) Peter
Am 06.02.2014 22:20, schrieb Marshall Schor: > This is a true bug. I've reported it in Jira: > https://issues.apache.org/jira/browse/UIMA-3603 > > I've added a fix and implemented some new tests for edge cases, including this > one which was failing. Will check it in shortly. > > > -Marshall > > On 2/6/2014 2:16 PM, Marshall Schor wrote: >> I can reproduce this with a simple bit of top level code; the failure seems >> to >> depend on an unusual order of making Feature Structures, and setting up the >> DocumentAnnotation instance. >> >> I'll take a look. >> >> -Marshall >> >> On 2/6/2014 7:38 AM, Peter Klügl wrote: >>> I can fix the xmiCAS if I change the address of the DocumentAnnotation >>> to be lower than the Year... >>> >>> Peter >>> >>> Am 06.02.2014 13:23, schrieb Peter Klügl: >>>> Hi, >>>> >>>> if I open the following xmiCAS in the CAS Editor, remove the Year >>>> annotation and try to save the file, then I get the same exception. The >>>> other annotations are removable... >>>> >>>> <?xml version="1.0" encoding="UTF-8"?> >>>> <xmi:XMI xmlns:Title="http:///uima/ruta/example/Title.ecore"; >>>> xmlns:cas="http:///uima/cas.ecore"; >>>> xmlns:type="http:///org/apache/uima/ruta/type.ecore"; >>>> xmlns:xmi="http://www.omg.org/XMI"; >>>> xmlns:Author="http:///uima/ruta/example/Author.ecore"; >>>> xmlns:tcas="http:///uima/tcas.ecore"; >>>> xmlns:example="http:///uima/ruta/example.ecore"; xmi:version="2.0"> >>>> <cas:NULL xmi:id="0"/> >>>> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" >>>> mimeType="text" sofaString="Ogren, P.V., Wetzler, P.G., Bethard, S.: >>>> ClearTK: A UIMA Toolkit for Statistical Natural Language Processing. In: >>>> UIMA for NLP workshop at LREC 08. (2008) "/> >>>> <example:Year xmi:id="8" sofa="1" begin="148" end="154"/> >>>> <example:Author xmi:id="12" sofa="1" begin="0" end="40"/> >>>> <example:Title xmi:id="16" sofa="1" begin="41" end="109"/> >>>> <tcas:DocumentAnnotation xmi:id="20" sofa="1" begin="0" end="156" >>>> language="x-unspecified"/> >>>> <cas:View sofa="1" members="8 12 16 20"/> >>>> </xmi:XMI> >>>> >>>> >>>> Peter >>>> >>>> Am 06.02.2014 12:56, schrieb Peter Klügl: >>>>> Hi, >>>>> >>>>> has anyone seen the following exception. I have no idea what can cause >>>>> this problem. (the typeCode is 0 or something causing the feats int >>>>> array to be null). I added the method that causes the problem below. It >>>>> just removes some annotations dependent of its type. >>>>> >>>>> I was thinking that the problem is caused by removing annotations that >>>>> are indexed and are the value of the feature of another indexed >>>>> annotation. However, that works for almost all types. I would assume >>>>> that this functionality would not depend on the actual type or the order >>>>> in the type system, right? >>>>> >>>>> Any ideas is greatly appreciated. >>>>> >>>>> java.lang.NullPointerException >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.enqueueFeatures(XmiCasSerializer.java:593) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.enqueueFeaturesOfIndexed(XmiCasSerializer.java:521) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.serialize(XmiCasSerializer.java:241) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.access$700(XmiCasSerializer.java:108) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer.serialize(XmiCasSerializer.java:1551) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer.serialize(XmiCasSerializer.java:1616) >>>>> at >>>>> org.apache.uima.cas.impl.XmiCasSerializer.serialize(XmiCasSerializer.java:1567) >>>>> at >>>>> org.apache.uima.ruta.testing.ui.handlers.RerunActionHandler.writeXmi(RerunActionHandler.java:652) >>>>> at >>>>> org.apache.uima.ruta.testing.ui.handlers.RerunActionHandler.access$0(RerunActionHandler.java:647) >>>>> at >>>>> org.apache.uima.ruta.testing.ui.handlers.RerunActionHandler$RerunHandlerJob.writeCleanInputFiles(RerunActionHandler.java:378) >>>>> at >>>>> org.apache.uima.ruta.testing.ui.handlers.RerunActionHandler$RerunHandlerJob.evalRutaWithClassPathScript(RerunActionHandler.java:196) >>>>> at >>>>> org.apache.uima.ruta.testing.ui.handlers.RerunActionHandler$RerunHandlerJob.run(RerunActionHandler.java:182) >>>>> at org.eclipse.core.internal.jobs.Worker.run(Worker.java:53) >>>>> >>>>> >>>>> private void prepareCas(CAS cas) { >>>>> if (!includedTypes.isEmpty()) { >>>>> // exclude all other types if there are some included types >>>>> excludedTypes = new ArrayList<String>(); >>>>> List<Type> types = >>>>> cas.getTypeSystem().getProperlySubsumedTypes(cas.getAnnotationType()); >>>>> for (Type type : types) { >>>>> if (!includedTypes.contains(type.getName())) { >>>>> excludedTypes.add(type.getName()); >>>>> } >>>>> } >>>>> } >>>>> if (includedTypes.isEmpty() && excludedTypes.isEmpty()) { >>>>> // remove all annotation in default settings >>>>> String documentText = cas.getDocumentText(); >>>>> cas.reset(); >>>>> cas.setDocumentText(documentText); >>>>> } else { >>>>> List<AnnotationFS> toRemove = new LinkedList<AnnotationFS>(); >>>>> AnnotationIndex<AnnotationFS> annotationIndex = >>>>> cas.getAnnotationIndex(); >>>>> for (AnnotationFS annotationFS : annotationIndex) { >>>>> Type type = annotationFS.getType(); >>>>> String typeName = type.getName(); >>>>> if (includedTypes.contains(typeName) || >>>>> !excludedTypes.contains(typeName)) { >>>>> toRemove.add(annotationFS); >>>>> } >>>>> } >>>>> for (AnnotationFS each : toRemove) { >>>>> if (!cas.getDocumentAnnotation().equals(each)) { >>>>> cas.removeFsFromIndexes(each); >>>>> } >>>>> } >>>>> } >>>>> } >>>>>
