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 <[email protected]> > 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 <[email protected]> > Sent: Monday, March 18, 2019 7:27 PM > To: [email protected] > 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
