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OHDSI / WebAPI

OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
Apache License 2.0
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Illegal Annotation Exception #2362

Closed nzurawski closed 2 months ago

nzurawski commented 2 months ago

Expected behavior

WebAPI to load Atlas

Actual behavior

When Atlas first loads and attempts to connect to WebAPI the WebAPI is unable to initalize and the developer tools console throws generic CORS errors. Meanwhile the log file from Apache shows Illegal Annotation Exceptions as seen below 2024-04-18 18:44:23.005 ERROR http-nio-8080-exec-30 org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator - [] - Failed to generate the schema for the JAX-B elements com.sun.xml.bind.v2.runtime.IllegalAnnotationsException: 2 counts of IllegalAnnotationExceptions at com.sun.xml.bind.v2.runtime.IllegalAnnotationsException$Builder.check(IllegalAnnotationsException.java:106) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getTypeInfoSet(JAXBContextImpl.java:471) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:303) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:139) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1156) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:165) ~[jaxb-runtime-2.3.1.jar:2.3.1] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_401] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.find(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.JAXBContext.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.JAXBContext.newInstance(Unknown Source) ~[?:1.8.0_401] at org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator.buildModelAndSchemas(WadlGeneratorJAXBGrammarGenerator.java:365) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator.createExternalGrammar(WadlGeneratorJAXBGrammarGenerator.java:314) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlBuilder.generate(WadlBuilder.java:124) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlApplicationContextImpl.getApplication(WadlApplicationContextImpl.java:157) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlApplicationContextImpl.getApplication(WadlApplicationContextImpl.java:175) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.processor.WadlModelProcessor$OptionsHandler.apply(WadlModelProcessor.java:143) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.processor.WadlModelProcessor$OptionsHandler.apply(WadlModelProcessor.java:125) [jersey-server-2.25.1.jar:?] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_401] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_401] at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:315) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:297) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:267) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228) [jersey-container-servlet-core-2.25.1.jar:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:212) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) [tomcat-websocket.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.ohdsi.webapi.shiro.filters.CacheFilter.doFilter(CacheFilter.java:35) [classes/:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.ohdsi.webapi.shiro.filters.ExceptionHandlerFilter.doFilter(ExceptionHandlerFilter.java:28) [classes/:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:93) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:128) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter.access$000(ErrorPageFilter.java:66) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter$1.doFilterInternal(ErrorPageFilter.java:103) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:121) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) [catalina.jar:8.5.100] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) [catalina.jar:8.5.100] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) [catalina.jar:8.5.100] at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:679) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) [catalina.jar:8.5.100] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:346) [catalina.jar:8.5.100] at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:617) [tomcat-coyote.jar:8.5.100] at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) [tomcat-coyote.jar:8.5.100] at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:934) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1690) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) [tomcat-util.jar:8.5.100] at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-util.jar:8.5.100] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63) [tomcat-util.jar:8.5.100] at java.lang.Thread.run(Unknown Source) [?:1.8.0_401] 2024-04-18 18:45:23.241 ERROR http-nio-8080-exec-27 org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator - [] - Failed to generate the schema for the JAX-B elements com.sun.xml.bind.v2.runtime.IllegalAnnotationsException: 2 counts of IllegalAnnotationExceptions at com.sun.xml.bind.v2.runtime.IllegalAnnotationsException$Builder.check(IllegalAnnotationsException.java:106) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.getTypeInfoSet(JAXBContextImpl.java:471) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:303) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl.<init>(JAXBContextImpl.java:139) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1156) ~[jaxb-runtime-2.3.1.jar:2.3.1] at com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:165) ~[jaxb-runtime-2.3.1.jar:2.3.1] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_401] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.ContextFinder.find(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.JAXBContext.newInstance(Unknown Source) ~[?:1.8.0_401] at javax.xml.bind.JAXBContext.newInstance(Unknown Source) ~[?:1.8.0_401] at org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator.buildModelAndSchemas(WadlGeneratorJAXBGrammarGenerator.java:365) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.generators.WadlGeneratorJAXBGrammarGenerator.createExternalGrammar(WadlGeneratorJAXBGrammarGenerator.java:314) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlBuilder.generate(WadlBuilder.java:124) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlApplicationContextImpl.getApplication(WadlApplicationContextImpl.java:157) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.internal.WadlApplicationContextImpl.getApplication(WadlApplicationContextImpl.java:175) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.processor.WadlModelProcessor$OptionsHandler.apply(WadlModelProcessor.java:143) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.wadl.processor.WadlModelProcessor$OptionsHandler.apply(WadlModelProcessor.java:125) [jersey-server-2.25.1.jar:?] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_401] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[?:1.8.0_401] at java.lang.reflect.Method.invoke(Unknown Source) ~[?:1.8.0_401] at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:315) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:297) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.internal.Errors.process(Errors.java:267) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317) [jersey-common-2.25.1.jar:?] at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154) [jersey-server-2.25.1.jar:?] at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341) [jersey-container-servlet-core-2.25.1.jar:?] at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228) [jersey-container-servlet-core-2.25.1.jar:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:212) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51) [tomcat-websocket.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:458) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:373) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387) [shiro-core-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:370) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137) [shiro-web-1.12.0.jar:1.12.0] at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:154) [shiro-web-1.12.0.jar:1.12.0] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.ohdsi.webapi.shiro.filters.CacheFilter.doFilter(CacheFilter.java:35) [classes/:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.ohdsi.webapi.shiro.filters.ExceptionHandlerFilter.doFilter(ExceptionHandlerFilter.java:28) [classes/:?] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:93) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:197) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:128) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter.access$000(ErrorPageFilter.java:66) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter$1.doFilterInternal(ErrorPageFilter.java:103) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.3.25.RELEASE.jar:4.3.25.RELEASE] at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:121) [spring-boot-1.5.22.RELEASE.jar:1.5.22.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:181) [catalina.jar:8.5.100] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:156) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:168) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:90) [catalina.jar:8.5.100] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:483) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:130) [catalina.jar:8.5.100] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:93) [catalina.jar:8.5.100] at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:679) [catalina.jar:8.5.100] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) [catalina.jar:8.5.100] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:346) [catalina.jar:8.5.100] at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:617) [tomcat-coyote.jar:8.5.100] at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:63) [tomcat-coyote.jar:8.5.100] at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:934) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1690) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:52) [tomcat-coyote.jar:8.5.100] at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191) [tomcat-util.jar:8.5.100] at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659) [tomcat-util.jar:8.5.100] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:63) [tomcat-util.jar:8.5.100] at java.lang.Thread.run(Unknown Source) [?:1.8.0_401]

Steps to reproduce behavior

I am using WebAPI and Atlas version 2.14. I tried to use the source code from the latest release of Atlas (2.14.1) but every time I've run the NPM run build command on that directory I somehow end up with DEV 2.15 version so I decided to just use 2.14

I did notice in the issues history a virtually identical issue opened years ago (https://github.com/OHDSI/WebAPI/issues/1887) however that issue was closed without resolution. Is there something obvious I'm doing wrong here?

nzurawski commented 2 months ago

Hi. Updating this post to add that I was able update to Atlas 2.14.1 but the issue persists as above with no changes.

chrisknoll commented 2 months ago

Was it something like this? https://stackoverflow.com/questions/30362637/failed-to-generate-the-schema-for-the-jax-b-only-happens-during-cors-call-to-re

Also, which version of JDK are you using? Is Security enabled? Does your atlas configuration for security enabled match your webAPI security enabled setting? Which WebAPI request was this failing on?

nzurawski commented 2 months ago

Thanks for the reply Chris. It is indeed like that link with the same errors being thrown in the developer tools console in Chrome.

I'm using the 1.8 version of both JDK and JRE. Security is not enabled at the moment. This is a new install and so I'm trying to get it working without security first.

This error happens as soon as I load Atlas, before I have a chance to do literally anything. If there's any additional information I can look up in the logs for you please let me know though.

Also worth noting that WebAPI starts just fine from the Tomcat Manager console. It's only when Atlas reaches out to it that I get this error. FWIW, I'm including a PW scrubbed version of the WebAPI settings file as well as the full text of our config-local file for Atlas below with organization redacted.

`define([], function () { var configLocal = {};

configLocal.api = {
    name: 'ORG REDACTED',
    url: 'http://localhost:8080/WebAPI/'
};

return configLocal;

}); settings.txt `

chrisknoll commented 2 months ago

When Atlas first starts up, it does contact WebAPI for some server information, so even before you do anything, it is making WebAPI calls.

I don't see any issues with your config settings, I run like that in my local environment. Things i was looking for was <security.origin>*</security.origin> (the stack overflow posts mentioned something about CORS), I specificially have 

    configLocal.userAuthenticationEnabled = false;

in my config-local.js, but i think security is disabled by default, so I just have that param there to toggle between on and off.

I think it has something to do with how your browser is invoking the WebAPI endpoints. The articles indicated it was soemthing with CORS, but we're setting all the header attributes on the Java side, so there should be nothing to change related to the suggestions in that article.

We have an atlas-demo site set up at https://atlas-demo.ohdsi.org if you could try to open that, maybe it would test if it is a browser thing. But I'm unable to reproduce this, so will have to wait for others to experience this problem to get more information about what could be the cause (like reverse proxies or something like that).

nzurawski commented 2 months ago

Closing this with the comment that I was running the Maven script wrong. At one point I had tried to add an offline tag to the script and forgot to remove it.