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Incident #9044

closed

File Delete operation is not working with the Workspace

Added by Gianpaolo Coro almost 8 years ago. Updated almost 8 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Valentina Marioli
Category:
High-Throughput-Computing
Target version:
Data Processing
Start date:
Jun 26, 2017
Due date:
% Done:

100%

Estimated time:
Infrastructure:
Production

Description

The Delete operation returns OK but the file is not really deleted. I'm using the statistical.manager user on the /Home/statistical.manager/Workspace/DataMinerAlgorithms folder, which is shared among several users.

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 #1

Updated by Roberto Cirillo almost 8 years ago

I see the following exception in catalina.out of workspace-repository node:

26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Get Inpustream: 0
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - No multipart boundary was found
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Called Rest Servlet Upload with parameters:
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Session Id: session-workspacerep.imarine-854068
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - name: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - description: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - parentPath: /Home/statistical.manager/Workspace/DataMinerAlgorithms/
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - mimetype: null
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - size: null
26.06.2017 16:22:50.794 [ajp-bio-8009-exec-9] *INFO*  HomeManageFactory - getHomeManagerFactory
26.06.2017 16:22:50.804 [ajp-bio-8009-exec-9] *ERROR*  org.gcube.common.homelibrary.jcr.repository.JCRRepository - Error retrieving Root Node null
26.06.2017 16:22:50.807 [ajp-bio-8009-exec-9] *ERROR*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Error saving inpustream for file: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:118) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:148) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:175) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload.doPost(Upload.java:156) ~[Upload.class:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650) [servlet-api.jar:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:95) [common-smartgears-2.1.1-SNAPSHOT.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.67]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.67]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423) [catalina.jar:7.0.67]
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.67]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) [tomcat-coyote.jar:7.0.67]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) [tomcat-coyote.jar:7.0.67]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.67]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
Caused by: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:82) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.home.JCRHome.<init>(JCRHome.java:38) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:116) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 28 common frames omitted
Caused by: org.gcube.common.homelibrary.model.exceptions.RepositoryException: null
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.init(JCRRepository.java:352) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:80) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 30 common frames omitted
26.06.2017 16:22:50.808 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - **** parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar save in storage and jackrabbit in 21 millis
26.06.2017 16:22:50.840 [ajp-bio-8009-exec-9] *INFO*  HomeManageFactory - getHomeManagerFactory
26.06.2017 16:22:50.850 [ajp-bio-8009-exec-9] *ERROR*  org.gcube.common.homelibrary.jcr.repository.JCRRepository - Error retrieving Root Node null
26.06.2017 16:22:50.850 [ajp-bio-8009-exec-9] *ERROR*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Delete - Error deleting item: /Home/statistical.manager/Workspace/DataMinerAlgorithms/parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:118) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:148) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:175) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Delete.doPost(Delete.java:104) [Delete.class:na]
    at org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Delete.doGet(Delete.java:36) [Delete.class:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:624) [servlet-api.jar:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:95) [common-smartgears-2.1.1-SNAPSHOT.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.67]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.67]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423) [catalina.jar:7.0.67]
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.67]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) [tomcat-coyote.jar:7.0.67]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) [tomcat-coyote.jar:7.0.67]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.67]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
Caused by: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:82) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.home.JCRHome.<init>(JCRHome.java:38) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:116) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 29 common frames omitted
Caused by: org.gcube.common.homelibrary.model.exceptions.RepositoryException: null
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.init(JCRRepository.java:352) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:80) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 31 common frames omitted
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Get Inpustream: 0
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - No multipart boundary was found
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Called Rest Servlet Upload with parameters:
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Session Id: session-workspacerep.imarine-854070
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - name: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - description: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - parentPath: /Home/statistical.manager/Workspace/DataMinerAlgorithms/
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - mimetype: null
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - size: null
26.06.2017 16:22:50.864 [ajp-bio-8009-exec-9] *INFO*  HomeManageFactory - getHomeManagerFactory
26.06.2017 16:22:50.874 [ajp-bio-8009-exec-9] *ERROR*  org.gcube.common.homelibrary.jcr.repository.JCRRepository - Error retrieving Root Node null
26.06.2017 16:22:50.877 [ajp-bio-8009-exec-9] *ERROR*  org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload - Error saving inpustream for file: parallelized_STEP1_VPA_ICCAT_BFT_E_Retros.jar
org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:118) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:148) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:175) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.apache.jackrabbit.j2ee.workspacemanager.servlets.rest.Upload.doPost(Upload.java:156) ~[Upload.class:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650) [servlet-api.jar:na]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:95) [common-smartgears-2.1.1-SNAPSHOT.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.67]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.67]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.67]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) [catalina.jar:7.0.67]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.67]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423) [catalina.jar:7.0.67]
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.67]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) [tomcat-coyote.jar:7.0.67]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316) [tomcat-coyote.jar:7.0.67]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_131]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_131]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.67]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_131]
Caused by: org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.model.exceptions.RepositoryException
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:82) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.home.JCRHome.<init>(JCRHome.java:38) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.JCRHomeManager.getHome(JCRHomeManager.java:116) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 28 common frames omitted
Caused by: org.gcube.common.homelibrary.model.exceptions.RepositoryException: null
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.init(JCRRepository.java:352) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    at org.gcube.common.homelibrary.jcr.repository.JCRRepository.<init>(JCRRepository.java:80) ~[home-library-jcr-2.9.0-4.5.0-149341.jar:na]
    ... 30 common frames omitted
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 #2

Updated by Valentina Marioli almost 8 years ago

  • Status changed from New to In Progress
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 #3

Updated by Valentina Marioli almost 8 years ago

  • Status changed from In Progress to Feedback
  • % Done changed from 0 to 100

Jackrabbit has been restarted and the rest APIs are now working. The issue seemed due to a problem retrieving the servlets list from the GCoreEndpoint.

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 #4

Updated by Gianpaolo Coro almost 8 years ago

  • Status changed from Feedback to Closed

It works, thanks.

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