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Posted to dev@uima.apache.org by Peter Klügl <pk...@uni-wuerzburg.de> on 2014/02/06 12:56:54 UTC
Problem: Remove annotations and then serialize CAS
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);
}
}
}
}
Re: Problem: Remove annotations and then serialize CAS
Posted by Peter Klügl <pk...@uni-wuerzburg.de>.
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);
>>>>> }
>>>>> }
>>>>> }
>>>>> }
>>>>>
Re: Problem: Remove annotations and then serialize CAS
Posted by Marshall Schor <ms...@schor.com>.
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);
>>>> }
>>>> }
>>>> }
>>>> }
>>>>
>
Re: Problem: Remove annotations and then serialize CAS
Posted by Marshall Schor <ms...@schor.com>.
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);
>>> }
>>> }
>>> }
>>> }
>>>
>
Re: Problem: Remove annotations and then serialize CAS
Posted by Peter Klügl <pk...@uni-wuerzburg.de>.
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);
>> }
>> }
>> }
>> }
>>
Re: Problem: Remove annotations and then serialize CAS
Posted by Peter Klügl <pk...@uni-wuerzburg.de>.
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);
> }
> }
> }
> }
>