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Posted to dev@ctakes.apache.org by Harpreet Khanduja <hs...@rit.edu> on 2014/07/02 01:03:41 UTC
sectionSegmentAnnotator
Hello,
I would really appreciate if anyone could help me on this.
I am trying to use SectionSegmentAnnotator in developer version of ctakes
inside eclipse.
I have included
<delegateAnalysisEngine key="SectionSegmentAnnotator">
<import location="SectionSegmentAnnotator.xml"/>
</delegateAnalysisEngine>
and
<node>SectionSegmentAnnotator</node>
in the file aggregateplaintextMLSprocessor.xml.
I am getting the following error.
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed. (Descriptor:
file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at
org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
Caused by: org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 25 more
Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
Source)
at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
Source)
at
sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
Source)
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
... 26 more
Thank you so much!
Harpreet
Re: sectionSegmentAnnotator
Posted by Harpreet Khanduja <hs...@rit.edu>.
Hello,
Thank you so much for getting back, it works but
I am trying to access the features (like segmentid, preferredText, begin
and end ) of a segment object but I am not
able to access these.
I am using
AnnotationFS curAnnot = (AnnotationFS) aIterator.get(); which is inside a
method the method is recursive.
and aIteraor is object of FSIterator.
Thank you so much.
Harpreet
On Wed, Jul 2, 2014 at 11:10 AM, Chen, Pei <Pe...@childrens.harvard.edu>
wrote:
> One can try the CDASegmentAnnotator. Both are rules/regex based but it's
> much simpler and doesn't require the find struct 3rd party lib.
>
> Sent from my iPhone
>
> > On Jul 1, 2014, at 10:19 PM, "Harpreet Khanduja" <hs...@rit.edu>
> wrote:
> >
> > Hello,p
> > Thanks for getting back.
> > I tried again and this is the error.
> >
> > Exception in thread "main" java.lang.NoSuchMethodError:
> > org.jdom.Element.addContent(Lorg/jdom/Element;)Lorg/jdom/Element;
> > at findstruct.StructModel$SM.process(StructModel.java:234)
> > at findstruct.StructModel.process(StructModel.java:43)
> > at findstruct.StructFinder.execute(StructFinder.java:53)
> > at
> >
> org.apache.ctakes.core.ae.SectionSegmentAnnotator.process(SectionSegmentAnnotator.java:90)
> > at
> >
> org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> > at
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
> > at
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> > at
> >
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
> > at
> org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:80)
> > at
> >
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
> >
> > Thank you so much,
> >
> > Harpreet
> >
> >
> > On Tue, Jul 1, 2014 at 9:51 PM, Masanz, James J. <Ma...@mayo.edu>
> > wrote:
> >
> >> Was the system you were trying to run cTAKES on connected to the
> internet
> >> at the time?
> >>
> >> In among all those messages is this line:
> >>
> >> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
> >>
> >> Or perhaps it was just a temporary glitch in your connection?
> >>
> >> -- James
> >>
> >> -----Original Message-----
> >> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> >> Sent: Tuesday, July 01, 2014 6:04 PM
> >> To: dev@ctakes.apache.org
> >> Subject: sectionSegmentAnnotator
> >>
> >> Hello,
> >>
> >> I would really appreciate if anyone could help me on this.
> >>
> >> I am trying to use SectionSegmentAnnotator in developer version of
> ctakes
> >> inside eclipse.
> >>
> >> I have included
> >> <delegateAnalysisEngine key="SectionSegmentAnnotator">
> >> <import location="SectionSegmentAnnotator.xml"/>
> >> </delegateAnalysisEngine>
> >>
> >> and
> >>
> >> <node>SectionSegmentAnnotator</node>
> >>
> >> in the file aggregateplaintextMLSprocessor.xml.
> >>
> >> I am getting the following error.
> >>
> >> Exception in thread "main"
> >> org.apache.uima.resource.ResourceInitializationException:
> Initialization of
> >> annotator class
> >> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> >> failed. (Descriptor:
> >>
> >>
> file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> >> at
> >>
> >>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> >> at
> >>
> >>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> >> at
> >>
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> >> at
> >>
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> >> at
> >>
> >>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> >> at
> >>
> >>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> >> at
> >>
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> >> at
> >>
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> >> at
> >>
> >>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> >> at
> >>
> >>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
> >> at
> >>
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> >> at
> >>
> >>
> org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
> >> at
> org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
> >> at
> >>
> >>
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
> >> Caused by: org.apache.uima.resource.ResourceInitializationException
> >> at
> >>
> >>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
> >> at
> >>
> >>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> >> ... 25 more
> >> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
> >> at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
> >> at java.net.PlainSocketImpl.connect(Unknown Source)
> >> at java.net.SocksSocketImpl.connect(Unknown Source)
> >> at java.net.Socket.connect(Unknown Source)
> >> at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
> >> at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
> >> at sun.net.NetworkClient.doConnect(Unknown Source)
> >> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> >> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> >> at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
> >> at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
> >> at
> >>
> >>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
> >> Source)
> >> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown
> Source)
> >> at
> >>
> >>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
> >> Source)
> >> at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
> >> Source)
> >> at
> >>
> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
> >> Source)
> >> at
> >>
> >>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
> >> at
> >>
> >>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
> >> ... 26 more
> >>
> >>
> >> Thank you so much!
> >>
> >> Harpreet
> >>
>
Re: sectionSegmentAnnotator
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
One can try the CDASegmentAnnotator. Both are rules/regex based but it's much simpler and doesn't require the find struct 3rd party lib.
Sent from my iPhone
> On Jul 1, 2014, at 10:19 PM, "Harpreet Khanduja" <hs...@rit.edu> wrote:
>
> Hello,p
> Thanks for getting back.
> I tried again and this is the error.
>
> Exception in thread "main" java.lang.NoSuchMethodError:
> org.jdom.Element.addContent(Lorg/jdom/Element;)Lorg/jdom/Element;
> at findstruct.StructModel$SM.process(StructModel.java:234)
> at findstruct.StructModel.process(StructModel.java:43)
> at findstruct.StructFinder.execute(StructFinder.java:53)
> at
> org.apache.ctakes.core.ae.SectionSegmentAnnotator.process(SectionSegmentAnnotator.java:90)
> at
> org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
> at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
> at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:80)
> at
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
>
> Thank you so much,
>
> Harpreet
>
>
> On Tue, Jul 1, 2014 at 9:51 PM, Masanz, James J. <Ma...@mayo.edu>
> wrote:
>
>> Was the system you were trying to run cTAKES on connected to the internet
>> at the time?
>>
>> In among all those messages is this line:
>>
>> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
>>
>> Or perhaps it was just a temporary glitch in your connection?
>>
>> -- James
>>
>> -----Original Message-----
>> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
>> Sent: Tuesday, July 01, 2014 6:04 PM
>> To: dev@ctakes.apache.org
>> Subject: sectionSegmentAnnotator
>>
>> Hello,
>>
>> I would really appreciate if anyone could help me on this.
>>
>> I am trying to use SectionSegmentAnnotator in developer version of ctakes
>> inside eclipse.
>>
>> I have included
>> <delegateAnalysisEngine key="SectionSegmentAnnotator">
>> <import location="SectionSegmentAnnotator.xml"/>
>> </delegateAnalysisEngine>
>>
>> and
>>
>> <node>SectionSegmentAnnotator</node>
>>
>> in the file aggregateplaintextMLSprocessor.xml.
>>
>> I am getting the following error.
>>
>> Exception in thread "main"
>> org.apache.uima.resource.ResourceInitializationException: Initialization of
>> annotator class
>> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
>> failed. (Descriptor:
>>
>> file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
>> at
>>
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>> at
>>
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>> at
>>
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>> at
>>
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>> at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>> at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>> at
>>
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>> at
>>
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>> at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>> at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>> at
>>
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>> at
>>
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>> at
>>
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
>> at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
>> at
>>
>> org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
>> at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
>> at
>>
>> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
>> Caused by: org.apache.uima.resource.ResourceInitializationException
>> at
>>
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
>> at
>>
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>> ... 25 more
>> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
>> at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
>> at java.net.PlainSocketImpl.connect(Unknown Source)
>> at java.net.SocksSocketImpl.connect(Unknown Source)
>> at java.net.Socket.connect(Unknown Source)
>> at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
>> at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
>> at sun.net.NetworkClient.doConnect(Unknown Source)
>> at sun.net.www.http.HttpClient.openServer(Unknown Source)
>> at sun.net.www.http.HttpClient.openServer(Unknown Source)
>> at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
>> at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
>> at
>>
>> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
>> Source)
>> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
>> at
>>
>> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
>> Source)
>> at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
>> Source)
>> at
>> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
>> Source)
>> at
>>
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
>> at
>>
>> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
>> ... 26 more
>>
>>
>> Thank you so much!
>>
>> Harpreet
>>
Re: sectionSegmentAnnotator
Posted by Harpreet Khanduja <hs...@rit.edu>.
Hello,
Thanks for getting back.
I tried again and this is the error.
Exception in thread "main" java.lang.NoSuchMethodError:
org.jdom.Element.addContent(Lorg/jdom/Element;)Lorg/jdom/Element;
at findstruct.StructModel$SM.process(StructModel.java:234)
at findstruct.StructModel.process(StructModel.java:43)
at findstruct.StructFinder.execute(StructFinder.java:53)
at
org.apache.ctakes.core.ae.SectionSegmentAnnotator.process(SectionSegmentAnnotator.java:90)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:80)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
Thank you so much,
Harpreet
On Tue, Jul 1, 2014 at 9:51 PM, Masanz, James J. <Ma...@mayo.edu>
wrote:
> Was the system you were trying to run cTAKES on connected to the internet
> at the time?
>
> In among all those messages is this line:
>
> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
>
> Or perhaps it was just a temporary glitch in your connection?
>
> -- James
>
> -----Original Message-----
> From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
> Sent: Tuesday, July 01, 2014 6:04 PM
> To: dev@ctakes.apache.org
> Subject: sectionSegmentAnnotator
>
> Hello,
>
> I would really appreciate if anyone could help me on this.
>
> I am trying to use SectionSegmentAnnotator in developer version of ctakes
> inside eclipse.
>
> I have included
> <delegateAnalysisEngine key="SectionSegmentAnnotator">
> <import location="SectionSegmentAnnotator.xml"/>
> </delegateAnalysisEngine>
>
> and
>
> <node>SectionSegmentAnnotator</node>
>
> in the file aggregateplaintextMLSprocessor.xml.
>
> I am getting the following error.
>
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> annotator class
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> failed. (Descriptor:
>
> file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> at
>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
> at
>
> org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
> at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
> at
>
> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
> Caused by: org.apache.uima.resource.ResourceInitializationException
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 25 more
> Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
> at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
> at java.net.PlainSocketImpl.connect(Unknown Source)
> at java.net.SocksSocketImpl.connect(Unknown Source)
> at java.net.Socket.connect(Unknown Source)
> at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
> at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
> at sun.net.NetworkClient.doConnect(Unknown Source)
> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> at sun.net.www.http.HttpClient.openServer(Unknown Source)
> at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
> at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
> at
>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
> Source)
> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
> at
>
> sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
> Source)
> at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
> Source)
> at
> sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
> Source)
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
> at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
> ... 26 more
>
>
> Thank you so much!
>
> Harpreet
>
RE: sectionSegmentAnnotator
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Was the system you were trying to run cTAKES on connected to the internet at the time?
In among all those messages is this line:
Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
Or perhaps it was just a temporary glitch in your connection?
-- James
-----Original Message-----
From: Harpreet Khanduja [mailto:hsk5004@rit.edu]
Sent: Tuesday, July 01, 2014 6:04 PM
To: dev@ctakes.apache.org
Subject: sectionSegmentAnnotator
Hello,
I would really appreciate if anyone could help me on this.
I am trying to use SectionSegmentAnnotator in developer version of ctakes
inside eclipse.
I have included
<delegateAnalysisEngine key="SectionSegmentAnnotator">
<import location="SectionSegmentAnnotator.xml"/>
</delegateAnalysisEngine>
and
<node>SectionSegmentAnnotator</node>
in the file aggregateplaintextMLSprocessor.xml.
I am getting the following error.
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
failed. (Descriptor:
file:/D:/workspaces/workspacectakes/ctakes/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at
org.uimafit.factory.AnalysisEngineFactory.createAggregate(AnalysisEngineFactory.java:424)
at org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:71)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:91)
Caused by: org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:85)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 25 more
Caused by: java.net.UnknownHostException: uts-ws.nlm.nih.gov
at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown
Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at
sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown
Source)
at sun.net.www.protocol.http.HttpURLConnection.getOutputStream(Unknown
Source)
at
sun.net.www.protocol.https.HttpsURLConnectionImpl.getOutputStream(Unknown
Source)
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:99)
at
org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:76)
... 26 more
Thank you so much!
Harpreet