ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Raghav Nyati <rny...@foreseemed.com>
Subject Re: Getting error while running rest service [EXTERNAL]
Date Tue, 19 Mar 2019 16:14:35 GMT
Hi Sean, 

I’m using Default.piper file with TsDictionarySubPipe lookup. 

// Commands and parameters to create a default plaintext document processing pipeline with
UMLS lookup

// set the thread count
threads 3

// Load a simple token processing pipeline from another pipeline file
load pipers/TsDefaultTokenizerPipeline

// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger

// Add Chunkers
load pipers/TsChunkerSubPipe

// Dictionary lookup
load pipers/TsDictionarySubPipe

// Add Cleartk Entity Attribute annotators
load pipers/TsAttributeCleartkSubPipe

And I’ve configured xml file in TsDictionarySubPipe as:

//  Commands and parameters to create a default dictionary lookup sub-pipeline.  This is not
a full pipeline.

// path to the xml file containing information for dictionary lookup configuration.
cli LookupXml=l
// umls credentials
cli umlsUser=user
cli umlsPass=pass

// dictionary lookup
add ThreadedUmlsDictionaryLookupAnnotator LookupXml=org/apache/ctakes/dictionary/lookup/LookupDesc.xml
Not sure if this is the right configuration for piper for Lucene dictionary lookup. 

I do have running setup using Fast dictionary lookup. But I want to enable fuzzy search by
configuring Lucene index. 

Any thoughts / suggestions / help on setting up Lucene index is appreciated. 

Thanks, 
Raghav




> On Mar 19, 2019, at 7:45 AM, Finan, Sean <Sean.Finan@childrens.harvard.edu> wrote:
> 
> Hi Raghav,
> 
> I think that your dictionary is not specified.  The (deeply embedded plus i18n) error
message is:
> 
> "Missing name for Dictionary Name"  
> 
> from 
>> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION
MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle
java.util.PropertyResourceBundle, key Missing name for Dictionary Name
> 
> There should be an xml-formatted dictionary lookup configuration file that specifies
the dictionary.   My guess is that the problem lies therein.
> 
> Sean
> 
> 
> ________________________________________
> From: Raghav Nyati <rnyati@foreseemed.com>
> Sent: Monday, March 18, 2019 7:27 PM
> To: dev@ctakes.apache.org
> Subject: Getting error while running rest service [EXTERNAL]
> 
> Hi -
> 
> I’m new to CTAKES and trying to figure out the Lucene index on rest services. While
running docker file, I’m getting below error:
> 
> 18 Mar 2019 23:22:11  INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip
> 18 Mar 2019 23:22:13  INFO ContextDependentTokenizerAnnotator - Finite state machines
loaded.
> 18 Mar 2019 23:22:13  INFO AbstractJCasTermAnnotator - Using dictionary lookup window
type: org.apache.ctakes.typesystem.type.textspan.Sentence
> 18 Mar 2019 23:22:13  INFO AbstractJCasTermAnnotator - Exclusion tagset loaded: CC CD
DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN VBP VBZ WDT WP WPS WRB
> 18 Mar 2019 23:22:13  INFO AbstractJCasTermAnnotator - Using minimum term text span:
3
> 18 Mar 2019 23:22:13  INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/LookupDesc.xml
> 18 Mar 2019 23:22:13  INFO DictionaryDescriptorParser - Parsing dictionary specifications:
> 18 Mar 2019 23:22:13 ERROR CtakesRestController - Error loading pipers
> 18 Mar 2019 23:22:13  WARN XmlWebApplicationContext - Exception encountered during context
initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException:
Error creating bean with name 'ctakesRestController': Invocation of init method failed; nested
exception is javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup"
failed.  (Descriptor: <unknown>)
> 18 Mar 2019 23:22:13 ERROR DispatcherServlet - Context initialization failed
> org.springframework.beans.factory.BeanCreationException: Error creating bean with name
'ctakesRestController': Invocation of init method failed; nested exception is javax.servlet.ServletException:
org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup" failed.  (Descriptor:
<unknown>)
>        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
>        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
>        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
>        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
>        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
>        at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
>        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
>        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
>        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
>        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
>        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
>        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
>        at org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
>        at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
>        at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
>        at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
>        at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
>        at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
>        at javax.servlet.GenericServlet.init(GenericServlet.java:158)
>        at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1123)
>        at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1078)
>        at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:971)
>        at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4854)
>        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5170)
>        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
>        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:713)
>        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
>        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695)
>        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
>        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1850)
>        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
>        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
>        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
>        at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
>        at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
>        at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1577)
>        at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:309)
>        at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
>        at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:424)
>        at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:367)
>        at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:929)
>        at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:831)
>        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
>        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1377)
>        at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1367)
>        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>        at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
>        at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
>        at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:902)
>        at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
>        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
>        at org.apache.catalina.core.StandardService.startInternal(StandardService.java:423)
>        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
>        at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:928)
>        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:638)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>        at java.lang.reflect.Method.invoke(Method.java:498)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:350)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:492)
> Caused by: javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup"
failed.  (Descriptor: <unknown>)
>        at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:95)
>        at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:82)
>        at org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:57)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>        at java.lang.reflect.Method.invoke(Method.java:498)
>        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
>        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
>        at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
>        ... 62 more
> Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup" failed.
 (Descriptor: <unknown>)
>        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:354)
>        at org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
>        ... 71 more
> Caused by: org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE
LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle,
key Missing name for Dictionary Name
>        at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:140)
>        at org.apache.ctakes.core.concurrent.ThreadSafeWrapper.initialize(ThreadSafeWrapper.java:52)
>        at org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup.initialize(ThreadSafeFastLookup.java:38)
>        at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>        ... 85 more
> Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION
MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle
java.util.PropertyResourceBundle, key Missing name for Dictionary Name
>        at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.getName(DictionaryDescriptorParser.java:293)
>        at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:177)
>        at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
>        at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
>        at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138)
>        ... 88 more
> 
> Any help is greatly appreciated.
> 
> Thanks,
> 
> Raghav


Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message