silwalr opened a new issue, #23:
URL: https://github.com/apache/ctakes/issues/23
Hi all,
I am running into `type Annotation was not declared in the XML descriptor`
error with ctakes-6.0-SNAPSHOT when using
`org.apache.ctakes.ytex.uima.annotators.DBConsumer` in a pipeline.
ERROR trace:
```org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator
processing failed.
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:411)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:295)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:590)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:422)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:352)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:276)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:590)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:422)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:352)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:276)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:295)
at
org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:193)
at
org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:412)
at
org.apache.ctakes.core.pipeline.PiperFileRunner.run(PiperFileRunner.java:83)
at
org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:31)
Caused by: org.apache.uima.cas.CASRuntimeException: JCas type
"org.apache.uima.jcas.tcas.Annotation" used in Java code, but was not declared
in the XML type descriptor.
at
org.apache.uima.cas.impl.TypeSystemImpl.throwMissingUIMAtype(TypeSystemImpl.java:2739)
at
org.apache.uima.cas.impl.TypeSystemImpl.getJCasRegisteredType(TypeSystemImpl.java:2715)
at org.apache.uima.jcas.impl.JCasImpl.getCasType(JCasImpl.java:262)
at
org.apache.uima.jcas.impl.JCasImpl.getAnnotationIndex(JCasImpl.java:1145)
at
org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.saveAnnoBaseHib(DocumentMapperServiceImpl.java:840)
at
org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.saveAnnotationsHib(DocumentMapperServiceImpl.java:1302)
at
org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl$12.doInTransaction(DocumentMapperServiceImpl.java:1432)
at
org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl$12.doInTransaction(DocumentMapperServiceImpl.java:1423)
at
org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at
org.apache.ctakes.ytex.uima.mapper.DocumentMapperServiceImpl.saveDocument(DocumentMapperServiceImpl.java:1423)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at
java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at
org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
at
org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123)
at
org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388)
at
org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:97)
at
org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
at
org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:215)
at jdk.proxy2/jdk.proxy2.$Proxy84.saveDocument(Unknown Source)
at
org.apache.ctakes.ytex.uima.annotators.DBConsumer.process(DBConsumer.java:149)
at
org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:50)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.lambda$callProcessMethod$3(AnalysisEngineImplBase.java:669)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.withContexts(AnalysisEngineImplBase.java:698)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.callProcessMethod(AnalysisEngineImplBase.java:668)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:383)
... 14 more
```
I am using the most recent version of ctakes available in github, and
java17.
```
openjdk version "17.0.10" 2024-01-16
OpenJDK Runtime Environment Temurin-17.0.10+7 (build 17.0.10+7)
OpenJDK 64-Bit Server VM Temurin-17.0.10+7 (build 17.0.10+7, mixed mode,
sharing)
```
I tried to implement a work around by following the workarounds provided
here:
- https://github.com/ClearTK/cleartk/issues/470
-
ctakes-core/src/main/java/org/apache/ctakes/core/cr/AbstractFileTreeReader.java
But the error isn't resolved yet.
Thanks for any help you can provide.
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: dev-unsubscr...@ctakes.apache.org.apache.org
For queries about this service, please contact Infrastructure at:
us...@infra.apache.org
