Task #8895: Reinstall dataminer[1:2]-d-d4s.d4science.org with Ubuntu 14.04 - D4Science Infrastructure - D4science

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Task #8895

closed

Reinstall dataminer[1:2]-d-d4s.d4science.org with Ubuntu 14.04

Added by Andrea Dell'Amico about 8 years ago. Updated about 8 years ago.

Status:

Closed

Priority:

Normal

Assignee:

_InfraScience Systems Engineer

Category:

System Application

Target version:

Dataminer and StatMan provisioning

Start date:

Jun 09, 2017

Due date:

% Done:

100%

Estimated time:

Infrastructure:

Development

Description

And the dev version of dataminer, with the separate algorithms repository.

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Updated by Andrea Dell'Amico about 8 years ago

Status changed from New to In Progress
% Done changed from 0 to 70

@tommaso.piccioli@isti.cnr.it rebuilt the VMs.
The provisioning is running.

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Updated by Andrea Dell'Amico about 8 years ago

Status changed from In Progress to Feedback
% Done changed from 70 to 90

Configured to run on the scopes

/gcube/devNext/NextNext, /gcube/devNext, /gcube/devsec, /gcube/devsec/devVre

As requested.

data-transfer and whn-manager fail to deploy with the same exception:

javax.servlet.ServletException: cannot manage application @ /whn-manager (see cause)
        at org.gcube.smartgears.Bootstrap.onStartup(Bootstrap.java:71)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5493)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1073)
        at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1857)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.gcube.common.resources.gcore.utils.Utils
        at org.gcube.common.resources.gcore.common.AnyWrapper.<init>(AnyWrapper.java:18)
        at org.gcube.common.resources.gcore.GCoreEndpoint$Profile$SpecificData.<init>(GCoreEndpoint.java:372)
        at org.gcube.common.resources.gcore.GCoreEndpoint$Profile.<init>(GCoreEndpoint.java:92)
        at org.gcube.common.resources.gcore.GCoreEndpoint.<init>(GCoreEndpoint.java:43)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.create(ProfileManager.java:228)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.loadOrCreateProfile(ProfileManager.java:219)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.activated(ProfileManager.java:89)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.onStart(ProfileManager.java:72)
        at org.gcube.smartgears.handlers.application.ApplicationLifecycleHandler.onEvent(ApplicationLifecycleHandler.java:42)
        at org.gcube.smartgears.handlers.application.ApplicationLifecycleHandler.onEvent(ApplicationLifecycleHandler.java:18)
        at org.gcube.smartgears.handlers.Pipeline.forward(Pipeline.java:65)
        at org.gcube.smartgears.managers.ApplicationManager.start(ApplicationManager.java:273)
        at org.gcube.smartgears.managers.ApplicationManager.start(ApplicationManager.java:120)
        at org.gcube.smartgears.Bootstrap.onStartup(Bootstrap.java:61)
        ... 12 more

While wps fails to deploy with the following exception:

javax.servlet.ServletException: cannot manage application @ /wps (see cause)
        at org.gcube.smartgears.Bootstrap.onStartup(Bootstrap.java:71)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5493)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:632)
        at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:670)
        at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.NoClassDefFoundError: org/w3c/dom/ElementTraversal
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
        at org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:2966)
        at org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:1209)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1689)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1570)
        at org.apache.xerces.jaxp.DocumentBuilderImpl.newDocument(Unknown Source)
        at org.gcube.common.resources.gcore.utils.Utils.<clinit>(Utils.java:33)
        at org.gcube.common.resources.gcore.common.AnyWrapper.<init>(AnyWrapper.java:18)
        at org.gcube.common.resources.gcore.GCoreEndpoint$Profile$SpecificData.<init>(GCoreEndpoint.java:372)
        at org.gcube.common.resources.gcore.GCoreEndpoint$Profile.<init>(GCoreEndpoint.java:92)
        at org.gcube.common.resources.gcore.GCoreEndpoint.<init>(GCoreEndpoint.java:43)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.create(ProfileManager.java:228)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.loadOrCreateProfile(ProfileManager.java:219)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.activated(ProfileManager.java:89)
        at org.gcube.smartgears.handlers.application.lifecycle.ProfileManager.onStart(ProfileManager.java:72)
        at org.gcube.smartgears.handlers.application.ApplicationLifecycleHandler.onEvent(ApplicationLifecycleHandler.java:42)
        at org.gcube.smartgears.handlers.application.ApplicationLifecycleHandler.onEvent(ApplicationLifecycleHandler.java:18)
        at org.gcube.smartgears.handlers.Pipeline.forward(Pipeline.java:65)
        at org.gcube.smartgears.managers.ApplicationManager.start(ApplicationManager.java:273)
        at org.gcube.smartgears.managers.ApplicationManager.start(ApplicationManager.java:120)
        at org.gcube.smartgears.Bootstrap.onStartup(Bootstrap.java:61)
        ... 12 more
Caused by: java.lang.ClassNotFoundException: org.w3c.dom.ElementTraversal
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1719)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1570)
        ... 35 more

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Updated by Lucio Lelii about 8 years ago

this is a known problem. The wps carries a xerces version that is not compatible with the one in the jre. For now I have fixed it replacing the xerces and xml-api jars manually. I will fix it in the next days in the WPS war.

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