Hello,
I’m trying to use Achilles on Olympus and from my understanding, Olympus should run Achilles automatically and provide the necessary .json files. I’ve used Achilles before where I had it installed and ran ‘exportToJson()’ to create the .json files and manually inserted lines into datasources.json.
System:
dbms = oracle
os = Kubuntu 15.10
browser = Chromium
framework = Spring
Log:
2015-12-04 10:33:33.686 ERROR qtp1708041420-56 org.apache.velocity - - ResourceManager : unable to find resource 'templates/common/common_template.html.vm' in any resource loader.
2015-12-04 10:33:38.640 DEBUG qtp1708041420-50 org.ohdsi.olympus.controller.AchillesController - - Attempting to parse datasources.json from : /home/AchillesWeb/data/datasources.json
2015-12-04 10:33:38.692 DEBUG qtp1708041420-59 org.ohdsi.olympus.controller.AchillesController - - Attempting to parse datasources.json from : /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/dashboard.json
2015-12-04 10:33:45.940 DEBUG qtp1708041420-58 org.ohdsi.olympus.controller.AchillesController - - Attempting to parse datasources.json from : /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/achillesheel.json
2015-12-04 10:33:45.944 ERROR qtp1708041420-58 org.ohdsi.olympus.controller.AchillesController - - Error returning datasources.json
java.io.FileNotFoundException: /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/achillesheel.json (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at java.io.FileInputStream.<init>(FileInputStream.java:101)
at java.io.FileReader.<init>(FileReader.java:58)
at org.ohdsi.olympus.controller.AchillesController.datasource(AchillesController.java:49)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:777)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:706)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:943)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:877)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:857)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:842)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:800)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669)
at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:146)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:85)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
at org.eclipse.jetty.server.Server.handle(Server.java:497)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)
at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:620)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:540)
at java.lang.Thread.run(Thread.java:745)
2015-12-04 10:33:45.962 WARN qtp1708041420-58 org.eclipse.jetty.servlet.ServletHandler - -
org.springframework.web.util.NestedServletException: Request processing failed; nested exception is java.lang.RuntimeException: java.io.FileNotFoundException: /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/achillesheel.json (No such file or directory)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:978)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:857)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:842)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:800)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669)
at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.rememberme.RememberMeAuthenticationFilter.doFilter(RememberMeAuthenticationFilter.java:146)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.csrf.CsrfFilter.doFilterInternal(CsrfFilter.java:85)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652)
at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143)
at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577)
at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223)
at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1125)
at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515)
at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185)
at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1059)
at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215)
at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97)
at org.eclipse.jetty.server.Server.handle(Server.java:497)
at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310)
at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:248)
at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540)
at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:620)
at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:540)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: java.io.FileNotFoundException: /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/achillesheel.json (No such file or directory)
at org.ohdsi.olympus.controller.AchillesController.datasource(AchillesController.java:55)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:777)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:706)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:943)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:877)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966)
... 61 more
Caused by: java.io.FileNotFoundException: /home/AchillesWeb/data/Achilles-analysis-v5-09022015-t1/achillesheel.json (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at java.io.FileInputStream.<init>(FileInputStream.java:101)
at java.io.FileReader.<init>(FileReader.java:58)
at org.ohdsi.olympus.controller.AchillesController.datasource(AchillesController.java:49)
... 74 more
Question:
Does Olympus provide the necessary .json for Achilles? If not, must I run Achilles and point the datasources to the exported .json for Olympus to run Achilles?
Thank you, I appreciate the time if you looked over this post.
-Rich M