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Published 20 hours ago • verified publisher icon GoTeamEpsilon

Merging in Drug NER and latest master branches

Open gsvitak opened this issue 7 years ago • 9 comments

gsvitak avatar Sep 03 '18 02:09 gsvitak

Can somebody merge this, please?

tjaffri avatar Sep 14 '18 19:09 tjaffri

Hi @gsvitak and @tjaffri,

I must apologize for my delayed response. I just updated the README to better reflect the alpha state of this software and how we are picking back up with the project.

Life/work/other projects got in the way recently and we are going to finish it off with a more simple approach (no web viewer, Docker, or MySQL integration - just the REST server and hsqldb).

Let’s hold off on this PR until we have made more progress. (THANK you for the contribution and we'll get it in.)

With this new refreshed take on the project, I hope you follow along and consider contributing. If you do want to help, just let me know here or email me at matthewvita48 at gmail dot com.

-Matthew

MatthewVita avatar Sep 19 '18 23:09 MatthewVita

Setup complete but cannot get project running as per README

Hi @MatthewVi Could you please help with it?

HTTP Status 500 – Internal Server Error

HTTP Status 500 – Internal Server Error

Type Exception Report

Message Servlet.init() for servlet ctakes-rest-service threw exception

Description The server encountered an unexpected condition that prevented it from fulfilling the request.

Exception

javax.servlet.ServletException: Servlet.init() for servlet ctakes-rest-service threw exception

org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

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>)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

javax.servlet.ServletException: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup" failed.  (Descriptor: <unknown>)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:104)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup" failed.  (Descriptor: <unknown>)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:100)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

org.apache.uima.resource.ResourceInitializationException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:140)
org.apache.ctakes.core.concurrent.ThreadSafeWrapper.initialize(ThreadSafeWrapper.java:52)
org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup.initialize(ThreadSafeFastLookup.java:38)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:100)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

org.apache.uima.analysis_engine.annotator.AnnotatorContextException: EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException: Can't find resource for bundle java.util.PropertyResourceBundle, key Could not construct org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:198)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138)
org.apache.ctakes.core.concurrent.ThreadSafeWrapper.initialize(ThreadSafeWrapper.java:52)
org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup.initialize(ThreadSafeFastLookup.java:38)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:100)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

java.lang.reflect.InvocationTargetException
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:423)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138)
org.apache.ctakes.core.concurrent.ThreadSafeWrapper.initialize(ThreadSafeWrapper.java:52)
org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup.initialize(ThreadSafeFastLookup.java:38)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:100)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Root Cause

java.sql.SQLException: Access denied for user 'root'@'localhost'
com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:545)
com.mysql.cj.jdbc.exceptions.SQLError.createSQLException(SQLError.java:513)
com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:115)
com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:1606)
com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:633)
com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:347)
com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:219)
java.sql.DriverManager.getConnection(DriverManager.java:664)
java.sql.DriverManager.getConnection(DriverManager.java:247)
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:88)
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:423)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:195)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:155)
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:127)
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:138)
org.apache.ctakes.core.concurrent.ThreadSafeWrapper.initialize(ThreadSafeWrapper.java:52)
org.apache.ctakes.dictionary.lookup2.concurrent.ThreadSafeFastLookup.initialize(ThreadSafeFastLookup.java:38)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:100)
org.apache.ctakes.rest.service.CtakesRestController$PipelineRunner.<init>(CtakesRestController.java:91)
org.apache.ctakes.rest.service.CtakesRestController.init(CtakesRestController.java:62)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:492)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:80)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:502)
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1152)
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:684)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1539)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1495)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)

Note The full stack trace of the root cause is available in the server logs.

Apache Tomcat/8.0.53

ultragen74 avatar Oct 04 '18 16:10 ultragen74

@ultragen74 Looks like a good place to start with the errors are with getting MySQL right:

> java.sql.SQLException: Access denied for user 'root'@'localhost'

You'll want to set the root password to pass (for now) or you can use custom configurations and specify them in ./ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml. Let me know if you need a hand with this.

MatthewVita avatar Oct 05 '18 03:10 MatthewVita

@gsvitak Sorry for the wait - can you rebase this branch, clean up the <<<<<<< HEAD marker issues, and provide a few steps for QA so I can test it out?

Thanks again!

MatthewVita avatar Oct 05 '18 03:10 MatthewVita

Could someone brief the intention behind this pull request? I believe lab finder is already included in full piper

gandhirajan avatar Nov 24 '18 06:11 gandhirajan

Is this pull request stale now?

devspacenine avatar Dec 07 '19 20:12 devspacenine

Hi all,

  • You need to set the root password to pass (change be changed later) this is the java.sql.SQLException: Access denied for user 'root'@'localhost' issue

Here's my notes from looking at this:

  • I'd like a better description of what this PR is doing and if it is going outside of the full pipelines. Also, it will need rebased with the <<<<<<< HEAD marker cleaned up.

  • should all of the medicationMentions be put together in ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java? This doesn't appear to be a normal convention from what I can tell.

Once these issues are addressed/discussed, I'd love to have a couple of folks QA it before merge.

MatthewVita avatar Dec 15 '19 17:12 MatthewVita

Is this pull request stale now?

Hi, cTAKES web rest module is merged to cTAKES official codebase - https://github.com/apache/ctakes/tree/trunk/ctakes-web-rest

You can raise pull request against the same for any changes as this branch was basically meant for scaffolding the web rest module. Let me know if you have any questions.

gandhirajan avatar Dec 16 '19 13:12 gandhirajan