{"action":"created","issue":{"url":"https://api.github.com/repos/TGAC/miso-lims/issues/1412","repository_url":"https://api.github.com/repos/TGAC/miso-lims","labels_url":"https://api.github.com/repos/TGAC/miso-lims/issues/1412/labels{/name}","comments_url":"https://api.github.com/repos/TGAC/miso-lims/issues/1412/comments","events_url":"https://api.github.com/repos/TGAC/miso-lims/issues/1412/events","html_url":"https://github.com/TGAC/miso-lims/issues/1412","id":316749650,"number":1412,"title":"Update 0.2.115 - ERROR: Failed to save run: $RUN_ID","user":{"login":"sklages","id":1837422,"avatar_url":"https://avatars3.githubusercontent.com/u/1837422?v=4","gravatar_id":"","url":"https://api.github.com/users/sklages","html_url":"https://github.com/sklages","followers_url":"https://api.github.com/users/sklages/followers","following_url":"https://api.github.com/users/sklages/following{/other_user}","gists_url":"https://api.github.com/users/sklages/gists{/gist_id}","starred_url":"https://api.github.com/users/sklages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sklages/subscriptions","organizations_url":"https://api.github.com/users/sklages/orgs","repos_url":"https://api.github.com/users/sklages/repos","events_url":"https://api.github.com/users/sklages/events{/privacy}","received_events_url":"https://api.github.com/users/sklages/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-04-23T10:20:04Z","updated_at":"2018-04-24T06:08:52Z","closed_at":"2018-04-24T06:08:52Z","author_association":"NONE","body":"I have updated to `0.2.115` last Friday without any issues and coming back to office I got some errors in MISO `miso_debug.log` (which I just noticed because some runs do not show up in MISO).\r\n\r\n1. `runscanner-illumina` reported errors like:\r\n```\r\nERROR   2018-04-23 10:25:17,468 [ForkJoinPool-1-worker-2] uk.ac.bbsrc.tgac.miso.runscanner.Scheduler  - Failed to process run: /project/solexadata/machine/SN106/180420_SN106_0262_A_CCAE7ANXX\r\njava.lang.IllegalStateException: java.io.FileNotFoundException: /scratch/local2/de/miso-runscanner/tomcat/webapps/runscanner/WEB-INF/lib/spring-aop-4.3.6.RELEASE.jar (Too many open files)\r\n```\r\nI thought I could fix this by increasing `ulimit -n` (strange enough) ...\r\nAfter increasing ulimits this error did not show up again ..\r\n\r\n2. MISO still does not show some runs. `miso_debug.log` states:\r\n```\r\n2018-04-23 11:02:03 ERROR: Failed to save run: 180420_SN106_0262_A_CCAE7ANXX\r\nuk.ac.bbsrc.tgac.miso.service.security.AuthorizationException: Current user does not have permission to modify this resource\r\n    at uk.ac.bbsrc.tgac.miso.service.security.DefaultAuthorizationManager.throwIfNotWritable(DefaultAuthorizationManager.java:138)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultContainerService.create(DefaultContainerService.java:94)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultContainerService$$FastClassBySpringCGLIB$$d3adecdb.invoke(<generated>)\r\n    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)\r\n    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:721)\r\n    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\r\n    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\r\n    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)\r\n    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\r\n    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\r\n    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:656)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultContainerService$$EnhancerBySpringCGLIB$$8b18f4e3.create(<generated>)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultRunService.updateContainerFromNotification(DefaultRunService.java:692)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultRunService.processNotification(DefaultRunService.java:558)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultRunService$$FastClassBySpringCGLIB$$a883b8d1.invoke(<generated>)\r\n    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)\r\n    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:721)\r\n    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)\r\n    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)\r\n    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)\r\n    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)\r\n    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)\r\n    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:656)\r\n    at uk.ac.bbsrc.tgac.miso.service.impl.DefaultRunService$$EnhancerBySpringCGLIB$$63868285.processNotification(<generated>)\r\n    at uk.ac.bbsrc.tgac.miso.webapp.service.RunScannerClient.processResults(RunScannerClient.java:92)\r\n    at uk.ac.bbsrc.tgac.miso.webapp.service.RunScannerClient.scheduler(RunScannerClient.java:125)\r\n    at sun.reflect.GeneratedMethodAccessor229.invoke(Unknown Source)\r\n    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\r\n    at java.lang.reflect.Method.invoke(Method.java:498)\r\n    at org.springframework.scheduling.support.ScheduledMethodRunnable.run(ScheduledMethodRunnable.java:65)\r\n    at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:54)\r\n    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)\r\n    at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)\r\n    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)\r\n    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)\r\n    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)\r\n    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)\r\n    at java.lang.Thread.run(Thread.java:748)\r\n```\r\n\r\nI haven't changed the config in no way, so I am a bit confused concerning the error message `AuthorizationException: Current user does not have permission to modify this resource`.\r\n\r\nAny idea what happens here?\r\nWe now have just created some sequencing containers without having the actual runs in MISO; but MISO should find the container once the run is registered in MISO ...\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/TGAC/miso-lims/issues/comments/383814621","html_url":"https://github.com/TGAC/miso-lims/issues/1412#issuecomment-383814621","issue_url":"https://api.github.com/repos/TGAC/miso-lims/issues/1412","id":383814621,"user":{"login":"sklages","id":1837422,"avatar_url":"https://avatars3.githubusercontent.com/u/1837422?v=4","gravatar_id":"","url":"https://api.github.com/users/sklages","html_url":"https://github.com/sklages","followers_url":"https://api.github.com/users/sklages/followers","following_url":"https://api.github.com/users/sklages/following{/other_user}","gists_url":"https://api.github.com/users/sklages/gists{/gist_id}","starred_url":"https://api.github.com/users/sklages/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sklages/subscriptions","organizations_url":"https://api.github.com/users/sklages/orgs","repos_url":"https://api.github.com/users/sklages/repos","events_url":"https://api.github.com/users/sklages/events{/privacy}","received_events_url":"https://api.github.com/users/sklages/received_events","type":"User","site_admin":false},"created_at":"2018-04-24T06:08:52Z","updated_at":"2018-04-24T06:08:52Z","author_association":"NONE","body":"Oops, that's a bit embarrassing, but somehow I managed to inactivate the `notification` user while updating our user page .. :confused: Thanks, \"problem\" solved."}}
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