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https://issues.apache.org/jira/browse/CTAKES-558?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649939#comment-17649939
]
Sean Finan commented on CTAKES-558:
-----------------------------------
The lack of drug-related information is not a bug. To produce them you should
try adding DrugMentionAnnotator from the ctakes-drug-ner module to your
pipeline. There are different ways to accomplish this.
I think that Ritika is on the right track regarding your sql problem.
> StrengthAnnotation,DrugchangeStatus
> Annotation,StrengthAnnotation,FractionStrengthAnnotation,FrequencyUnitAnnotation
> not coming in the ctakes-web-rest web app
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Key: CTAKES-558
> URL: https://issues.apache.org/jira/browse/CTAKES-558
> Project: cTAKES
> Issue Type: Bug
> Reporter: Chainthanya
> Priority: Major
>
> I am trying Ctakes-web-rest project. I got the output in that API Response.
> But for me StrengthAnnotation,DrugchangeStatus
> Annotation,StrengthAnnotation,FractionStrengthAnnotation,FrequencyUnitAnnotation
> is not there in that API Response. How to enable this annotation. I need to
> add anything in that code. And one more thing I tried your github link code
> also for that I got Text analysed successful message with empty response
> json. I want to fix this issue. Please advice. Awaiting your reply.
>
>
>
> Please find the error response below:
>
>
> 28-Mar-2022 21:14:20.453 INFO [localhost-startStop-1]
> org.apache.catalina.core.ApplicationContext.log No Spring
> WebApplicationInitializer types detected on classpath
> 28-Mar-2022 21:14:20.765 INFO [localhost-startStop-1]
> org.apache.catalina.core.ApplicationContext.log Initializing Spring
> FrameworkServlet 'ctakes-rest-service'
> 28-Mar-2022 21:14:32.259 SEVERE [localhost-startStop-1]
> org.apache.catalina.core.ApplicationContext.log Servlet.init() for servlet
> [ctakes-rest-service] threw exception
> 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:1173)
> at
> org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1118)
> at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1011)
> at
> org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4952)
> at
> org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5266)
> at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
> at
> org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:753)
> at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:727)
> at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:695)
> at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1016)
> at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1903)
> at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> at java.lang.Thread.run(Thread.java:748)
> 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$PipelineRunner.<init>(CtakesRestController.java:105)
> at
> org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:92)
> at
> org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:59)
> 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)
> ... 34 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:274)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:172)
> 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:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:435)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:379)
> at
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:192)
> 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:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
> at
> org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:101)
> Caused by: org.apache.uima.resource.ResourceInitializationException: MESSAGE
> LOCALIZATION FAILED: Can't find resource for bundle
> java.util.PropertyResourceBundle, key Could not construct
> org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
> at
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:139)
> 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:267)
> Caused by:
> org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE
> LOCALIZATION FAILED: Can't find resource for bundle
> java.util.PropertyResourceBundle, key Could not construct
> org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:198)
> 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:137)
> ... 60 more
> Caused by: java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195)
> ... 63 more
> Caused by: com.mysql.cj.jdbc.exceptions.CommunicationsException:
> Communications link failure
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