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  • #842

Closed
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Opened Jun 13, 2019 by Piotr Gawron@piotr.gawron
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retrieving autocomplete list sometimes take a lot of time

the reason is this stacktrace:

2019-06-13 09:04:01,244 ERROR [http-bio-8080-exec-59] (BaseController.java:47) - lcsb.mapviewer.annotation.services.DrugSearchException: lcsb.mapviewer.annotation.services.annotators.UniprotSearchException: Problem with accessing uniprot webpage
lcsb.mapviewer.annotation.services.DrugSearchException: lcsb.mapviewer.annotation.services.annotators.UniprotSearchException: Problem with accessing uniprot webpage
	at lcsb.mapviewer.annotation.services.ChEMBLParser.targetComponentToMiriamData(ChEMBLParser.java:263)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.getTargetFromId(ChEMBLParser.java:212)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.getTargetsByDrugId(ChEMBLParser.java:300)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.parseDrug(ChEMBLParser.java:421)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.getDrugById(ChEMBLParser.java:524)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.getDrugsByChemblTarget(ChEMBLParser.java:642)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.getDrugListByTarget(ChEMBLParser.java:595)
	at lcsb.mapviewer.annotation.services.DrugAnnotation.getDrugListByTargets(DrugAnnotation.java:173)
	at lcsb.mapviewer.annotation.services.DrugAnnotation.getSuggestedQueryListWithoutCache(DrugAnnotation.java:324)
	at lcsb.mapviewer.annotation.services.DrugAnnotation.getSuggestedQueryList(DrugAnnotation.java:267)
	at lcsb.mapviewer.services.search.drug.DrugService.getSuggestedQueryList(DrugService.java:375)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	at com.sun.proxy.$Proxy90.getSuggestedQueryList(Unknown Source)
	at lcsb.mapviewer.api.projects.drugs.DrugRestImpl.getSuggestedQueryList(DrugRestImpl.java:209)
	at lcsb.mapviewer.api.projects.drugs.DrugRestImpl$$FastClassBySpringCGLIB$$9a4d0be7.invoke(<generated>)
	at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
	at lcsb.mapviewer.api.projects.drugs.DrugRestImpl$$EnhancerBySpringCGLIB$$2a610177.getSuggestedQueryList(<generated>)
	at lcsb.mapviewer.api.projects.drugs.DrugController.getSuggestedQueryList(DrugController.java:54)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
	at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
	at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:849)
	at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:760)
	at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
	at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
	at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
	at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
	at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:624)
	at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at lcsb.mapviewer.web.bean.utils.ApiAccessControlFilter.doFilter(ApiAccessControlFilter.java:42)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at lcsb.mapviewer.web.bean.utils.JsfAjaxAccessControlAllowFilter.doFilter(JsfAjaxAccessControlAllowFilter.java:37)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at lcsb.mapviewer.web.bean.utils.XFrameAccessControlFilter.doFilter(XFrameAccessControlFilter.java:54)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:221)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:436)
	at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1078)
	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
	at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:748)
Caused by: lcsb.mapviewer.annotation.services.annotators.UniprotSearchException: Problem with accessing uniprot webpage
	at lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator.uniProtToHgnc(UniprotAnnotator.java:249)
	at lcsb.mapviewer.annotation.services.ChEMBLParser.targetComponentToMiriamData(ChEMBLParser.java:260)
	... 81 more
Caused by: lcsb.mapviewer.annotation.services.WrongResponseCodeIOException: java.io.FileNotFoundException: https://www.uniprot.org/uniprot/.txt
	at lcsb.mapviewer.annotation.cache.WebPageDownloader$1Task.call(WebPageDownloader.java:147)
	at lcsb.mapviewer.annotation.cache.WebPageDownloader$1Task.call(WebPageDownloader.java:98)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.io.FileNotFoundException: https://www.uniprot.org/uniprot/.txt
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1944)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1939)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1938)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1508)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)
	at lcsb.mapviewer.annotation.cache.WebPageDownloader$1Task.call(WebPageDownloader.java:143)
	... 5 more
Caused by: java.io.FileNotFoundException: https://www.uniprot.org/uniprot/.txt
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:347)
	at lcsb.mapviewer.annotation.cache.WebPageDownloader$1Task.call(WebPageDownloader.java:123)
	... 5 more

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Reference: minerva/core#842