Task #11936

DataMiner - Fix DataMiner's provisioning in development environment

Added by Giancarlo Panichi over 1 year ago. Updated over 1 year ago.

Status:ClosedStart date:Jun 12, 2018
Priority:UrgentDue date:
Assignee:Giancarlo Panichi% Done:

100%

Category:data-analysis
Sprint:zz - DataMiner - Dev enviroment support
Milestones:
Duration:

Description

After updating the DataMiner development environment the algorithms can not longer be deployed.
Fix DataMiner's provisioning in development environment.


Related issues

Related to gCube - Task #11577: Lots of files are put inside the dataminer wps webapp dir... In Progress Oct 12, 2018
Related to gCube - Task #11956: Remove slf4j-log4j12-1.7.5.jar from wps.war Closed Jun 14, 2018
Blocked by gCube - Task #11886: wps doesn't build in gCube-snapshots from 10 January 2018 Closed Jun 07, 2018

History

#1 Updated by Giancarlo Panichi over 1 year ago

  • Blocked by Task #11886: wps doesn't build in gCube-snapshots from 10 January 2018 added

#3 Updated by Roberto Cirillo over 1 year ago

  • Status changed from New to In Progress

#4 Updated by Roberto Cirillo over 1 year ago

dataminer1-d-d4s.d4science has been upgraded but the wps application is not correctly registered on the IS service. I'm going to do further analysis

#5 Updated by Roberto Cirillo over 1 year ago

the wps deploy fails with the following exception:

2018-06-12 18:12:23,527 [localhost-startStop-1] INFO  org.apache.catalina.startup.HostConfig- Deploying web application archive /home/gcube/tomcat/webapps/wps.war
2018-06-12 18:12:42,124 [localhost-startStop-1] ERROR org.apache.catalina.core.ContainerBase- ContainerBase.addChild: start: 
org.apache.catalina.LifecycleException: Failed to start component [StandardEngine[Catalina].StandardHost[localhost].StandardContext[/wps]]
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:154)
        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: LLogger;
        at java.lang.Class.getDeclaredFields0(Native Method)
        at java.lang.Class.privateGetDeclaredFields(Class.java:2583)
        at java.lang.Class.getDeclaredFields(Class.java:1916)
        at org.apache.catalina.util.Introspection.getDeclaredFields(Introspection.java:106)
        at org.apache.catalina.startup.WebAnnotationSet.loadFieldsAnnotation(WebAnnotationSet.java:261)
        at org.apache.catalina.startup.WebAnnotationSet.loadApplicationServletAnnotations(WebAnnotationSet.java:140)
        at org.apache.catalina.startup.WebAnnotationSet.loadApplicationAnnotations(WebAnnotationSet.java:65)
        at org.apache.catalina.startup.ContextConfig.applicationAnnotationsConfig(ContextConfig.java:400)
        at org.apache.catalina.startup.ContextConfig.configureStart(ContextConfig.java:876)
        at org.apache.catalina.startup.ContextConfig.lifecycleEvent(ContextConfig.java:371)
        at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
        at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:90)
        at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5392)
        at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
        ... 10 more
Caused by: java.lang.ClassNotFoundException: Logger
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1719)
        at org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1570)
        ... 24 more

we need further analysis

#6 Updated by Roberto Cirillo over 1 year ago

I've tried to replace the wps webapp with the one present on dataminer2-d-d4s and it works properly so the problem is in the wps war.
@lucio.lelii@isti.cnr.it could you try to redeploy it?

#7 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 0 to 100
  • Assignee changed from Roberto Cirillo to Giancarlo Panichi
  • Status changed from In Progress to Feedback

I've tried to re deploy the wps webapp and now it works properly. So the problem is solved. At this moment only dataminer1-d-d4s is upgraded, @g.panichi@isti.cnr.it tell me if you want to upgrade other instances otherwise close this ticket.

#8 Updated by Roberto Cirillo over 1 year ago

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

Please ignore my previous message, I was deployed the old war. I'm sorry for that. The problem is still there.

#9 Updated by Roberto Cirillo over 1 year ago

  • Assignee changed from Giancarlo Panichi to Roberto Cirillo

#10 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 0 to 100
  • Assignee changed from Roberto Cirillo to Giancarlo Panichi
  • Status changed from In Progress to Feedback

Now it really works.
After a new deploy on nexus, I've redeployed the new war on dataminer1-d-d4s.d4science.org and now it works properly. Maybe the previous war was corrupted.
At this moment only dataminer1-d-d4s is upgraded, @g.panichi@isti.cnr.it tell me if you want to upgrade other instances otherwise close this ticket.

#11 Updated by Giancarlo Panichi over 1 year ago

  • Assignee changed from Giancarlo Panichi to Roberto Cirillo
  • Status changed from Feedback to In Progress

Please @roberto.cirillo@isti.cnr.it , can you check if ICProxy is working in the devNext scope?
If there is not, can you add it?
Thanks

#12 Updated by Roberto Cirillo over 1 year ago

  • Assignee changed from Roberto Cirillo to Giancarlo Panichi
  • Status changed from In Progress to Feedback

I've added the needed scopes by ansible.
Now IC-proxy run on devNext and NextNext VRE as requested.

#13 Updated by Giancarlo Panichi over 1 year ago

  • Assignee changed from Giancarlo Panichi to Roberto Cirillo
  • Status changed from Feedback to In Progress

There is an error on the service:

2018-06-13 12:41:20,962 [catalina-exec-9] ERROR org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/wps].[wpsServlet]- Servlet.service() for servlet [wpsServlet] in context with path [/wps] threw exception
java.lang.IllegalStateException: Cannot call sendError() after the response has been committed
    at org.apache.catalina.connector.ResponseFacade.sendError(ResponseFacade.java:450)
    at org.gcube.smartgears.managers.RequestManager.handleError(RequestManager.java:227)
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:98)
    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:220)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
    at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
    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)


#14 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 100 to 50
  • Assignee changed from Roberto Cirillo to Lucio Lelii

I think it is a service problem. I've tried to execute a GetCapabilities request and I see the following exception:

javax.servlet.ServletException: Servlet execution threw an exception
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:326)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:169)
    at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:232)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:95)
    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:220)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
    at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
    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.Error: Unresolved compilation problem: 
    The method getPrivateAlgorithmsInScope(String) is undefined for the type InfrastructureDialoguer

    at org.gcube.data.analysis.wps.GetCapabilitiesBuilder.buildGetCapabilities(GetCapabilitiesBuilder.java:119)
    at org.gcube.data.analysis.wps.RequestHandler.handle(RequestHandler.java:395)
    at org.gcube.data.analysis.wps.WebProcessingService.doGet(WebProcessingService.java:283)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
    at org.gcube.data.analysis.wps.WebProcessingService.service(WebProcessingService.java:406)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    ... 23 more

Please @lucio.lelii@isti.cnr.it could you check this exception? the error is in catalina.out

#15 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 50 to 100
  • Assignee changed from Lucio Lelii to Giancarlo Panichi
  • Status changed from In Progress to Feedback

There was an old dataminer library under wps webapp. Now we have added the right library to wps and it seems to work properly.
Please @g.panichi@isti.cnr.it check it and close the ticket if it works as expected.

#16 Updated by Giancarlo Panichi over 1 year ago

  • % Done changed from 100 to 50
  • Assignee changed from Giancarlo Panichi to Roberto Cirillo
  • Status changed from Feedback to In Progress

It seems that we have taken a step forward, now the GetCapabilities works.
There is however a problem in the execution of the algorithms.

For example, we now have this problem on two algorithms:

The computation 2754035e-dd15-4f09-ba96-364c2ca5ca1f of Quickdirty has failed.
java.lang.RuntimeException: Unresolved compilation problems: HomeManagerFactory cannot be resolved to a type HomeLibrary cannot be resolved HomeManager cannot be resolved to a type User cannot be resolved to a type Home cannot be resolved to a type Workspace cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceItem cannot be resolved to a type

The computation aaa95b9c-90fc-4b54-903c-2bfd907b1ee2 of Storagehubfacility has failed.
java.lang.RuntimeException: Unresolved compilation problems: HomeManagerFactory cannot be resolved to a type HomeLibrary cannot be resolved HomeManager cannot be resolved to a type User cannot be resolved to a type Home cannot be resolved to a type Workspace cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceFolder cannot be resolved to a type WorkspaceItem cannot be resolved to a type

#17 Updated by Roberto Cirillo over 1 year ago

  • Priority changed from Normal to Urgent
  • Assignee changed from Roberto Cirillo to Lucio Lelii

This is another service problem as the previous one. The wps war deployed on gCube-Snapshot is still wrong.
I've notice that there are several libraries that aren't present in the wps war: all the HL libraries are missing. But I not exclude that there are other libraries outdated or missing. Please @lucio.lelii@isti.cnr.it check the wps's libraries and deploy the new version on nexus.

In ghn.log I see the following exception:

2018-06-14 10:03:51,366 [pool-10-thread-3] ERROR ExecuteRequest: Exception/Error while executing ExecuteRequest for org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY: java.lang.RuntimeException: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

2018-06-14 10:03:51,366 [pool-10-thread-3] INFO  ExecutionContextFactory: Context unregistered
2018-06-14 10:03:51,370 [catalina-exec-6] WARN  RequestHandler: exception while handling ExecuteRequest.
java.util.concurrent.ExecutionException: org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at org.gcube.data.analysis.wps.RequestHandler.handle(RequestHandler.java:327)
    at org.gcube.data.analysis.wps.WebProcessingService.doGet(WebProcessingService.java:283)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
    at org.gcube.data.analysis.wps.WebProcessingService.service(WebProcessingService.java:406)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:169)
    at com.thetransactioncompany.cors.CORSFilter.doFilter(CORSFilter.java:232)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
    at org.gcube.smartgears.managers.RequestManager.doFilter(RequestManager.java:95)
    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:220)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
    at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:683)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
    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: org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:639)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:67)
    at org.gcube.common.authorization.library.AuthorizedTasks$1.call(AuthorizedTasks.java:41)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    ... 3 common frames omitted
Caused by: java.lang.RuntimeException: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:96)
    at org.n52.wps.server.AbstractAnnotatedAlgorithm.run(AbstractAnnotatedAlgorithm.java:54)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:608)
    ... 6 common frames omitted
Caused by: java.lang.Error: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.writeRunningComputationData(DataspaceManager.java:421)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper$RunDataspaceManager.run(AbstractEcologicalEngineMapper.java:281)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:295)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:266)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateStatus(AbstractEcologicalEngineMapper.java:256)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.run(AbstractEcologicalEngineMapper.java:415)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY.run(QUICKDIRTY.java:24)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:89)
    ... 8 common frames omitted
2018-06-14 10:03:51,371 [catalina-exec-6] WARN  RequestHandler: ExceptionReport not null
org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:639)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:67)
    at org.gcube.common.authorization.library.AuthorizedTasks$1.call(AuthorizedTasks.java:41)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:96)
    at org.n52.wps.server.AbstractAnnotatedAlgorithm.run(AbstractAnnotatedAlgorithm.java:54)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:608)
    ... 6 common frames omitted
Caused by: java.lang.Error: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.writeRunningComputationData(DataspaceManager.java:421)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper$RunDataspaceManager.run(AbstractEcologicalEngineMapper.java:281)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:295)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:266)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateStatus(AbstractEcologicalEngineMapper.java:256)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.run(AbstractEcologicalEngineMapper.java:415)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY.run(QUICKDIRTY.java:24)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:89)
    ... 8 common frames omitted
2018-06-14 10:03:51,371 [catalina-exec-6] ERROR RequestHandler: exception handling ExecuteRequest.
org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:639)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:67)
    at org.gcube.common.authorization.library.AuthorizedTasks$1.call(AuthorizedTasks.java:41)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:96)
    at org.n52.wps.server.AbstractAnnotatedAlgorithm.run(AbstractAnnotatedAlgorithm.java:54)
    at org.gcube.data.analysis.wps.ExecuteRequest.call(ExecuteRequest.java:608)
    ... 6 common frames omitted
Caused by: java.lang.Error: Unresolved compilation problems: 
    HomeManagerFactory cannot be resolved to a type
    HomeLibrary cannot be resolved
    HomeManager cannot be resolved to a type
    User cannot be resolved to a type
    Home cannot be resolved to a type
    Workspace cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceFolder cannot be resolved to a type
    WorkspaceItem cannot be resolved to a type

    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.writeRunningComputationData(DataspaceManager.java:421)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper$RunDataspaceManager.run(AbstractEcologicalEngineMapper.java:281)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:295)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateComputationOnWS(AbstractEcologicalEngineMapper.java:266)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.updateStatus(AbstractEcologicalEngineMapper.java:256)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper.run(AbstractEcologicalEngineMapper.java:415)
    at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.QUICKDIRTY.run(QUICKDIRTY.java:24)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.n52.wps.algorithm.annotation.AnnotationBinding$ExecuteMethodBinding.execute(AnnotationBinding.java:89)
    ... 8 common frames omitted
2018-06-14 10:03:51,442 [catalina-exec-6] INFO  RequestAccounting: REQUEST SERVED ON DataMiner:WPS(Execute) CALLED FROM roberto.cirillo@146.48.85.73 IN SCOPE /gcube/devNext/NextNext FINISHED IN 589 millis

#18 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 50 to 100
  • Assignee changed from Lucio Lelii to Giancarlo Panichi
  • Status changed from In Progress to Feedback

The new wps deployed by @lucio.lelii@isti.cnr.it on snapshots contains the HL libraries. The instance dataminer1-d-d4s.d4science.org has been upgraded.
Please @g.panichi@isti.cnr.it could you check? If this instance works properly close the ticket. Thanks.

#19 Updated by Giancarlo Panichi over 1 year ago

  • Related to Task #11577: Lots of files are put inside the dataminer wps webapp directory that should be elsewhere. added

#20 Updated by Giancarlo Panichi over 1 year ago

  • Status changed from Feedback to Closed

Ok now it seems that the provisioning on dev works as expected.
The modification requested by Lucio is still necessary in order to have a provisioning that works fully.
For this I close this ticket and invite you to follow the ticket #11577

#21 Updated by Giancarlo Panichi over 1 year ago

  • Due date set to Jun 14, 2018

#22 Updated by Roberto Cirillo over 1 year ago

Giancarlo Panichi wrote:

Ok now it seems that the provisioning on dev works as expected.
The modification requested by Lucio is still necessary in order to have a provisioning that works fully.
For this I close this ticket and invite you to follow the ticket #11577

It's not clear to me what it is not fully working. In #11577 there are listed several points, these points have all the same priority?
If not, maybe it's better to indicate a priority in order to implement first the points with an higher priority.

#23 Updated by Giancarlo Panichi over 1 year ago

  • % Done changed from 100 to 50
  • Assignee changed from Giancarlo Panichi to Roberto Cirillo
  • Status changed from Closed to In Progress
  • Due date deleted (Jun 14, 2018)

I was too hasty, you're right.
I have just discovered that there is a problem between the algorithms and the Dataminer for SL4J configurations.
There are libraries present both in the webapp and in tomcat/lib.
And therefore they do not install correctly.

For example:

Adding algorithm TUNA_ATLAS_DATA_ACCESS 
With command ./addAlgorithm.sh TUNA_ATLAS_DATA_ACCESS ACCESS_TUNA_ATLAS_DATA org.gcube.dataanalysis.executor.rscripts.TunaAtlasDataAccess /gcube/devNext/NextNext transducerers Y http://data.d4science.org/K2Q1dzlSOHA2WUFncGhJR2pFRTdYQXpSVUd4ZTg1MDlHbWJQNStIS0N6Yz0 "This R code enables users to adapt a SQL query to get data from Sardara database storing global" dev/software

9 arguments to ./addAlgorithm.sh: TUNA_ATLAS_DATA_ACCESS ACCESS_TUNA_ATLAS_DATA org.gcube.dataanalysis.executor.rscripts.TunaAtlasDataAccess /gcube/devNext/NextNext transducerers Y http://data.d4science.org/K2Q1dzlSOHA2WUFncGhJR2pFRTdYQXpSVUd4ZTg1MDlHbWJQNStIS0N6Yz0 This R code enables users to adapt a SQL query to get data from Sardara database storing global dev/software
Algorithm installer v 1.2.1
DESCRIPTION This R code enables users to adapt a SQL query to get data from Sardara database storing global
Running updater 1.2
*****Parameters
*****algorithmName:TUNA_ATLAS_DATA_ACCESS
*****implementation:org.gcube.dataanalysis.executor.rscripts.TunaAtlasDataAccess
*****category:ACCESS_TUNA_ATLAS_DATA
*****configPath:../tomcat/webapps/wps/ecocfg/
*****applicationlibs:../wps_algorithms/algorithms/dev/software
*****scope:/gcube/devNext/NextNext
*****description:This R code enables users to adapt a SQL query to get data from Sardara database storing global
*****atype:transducerers
*****skipJava:true
*****url:http://data.d4science.org/K2Q1dzlSOHA2WUFncGhJR2pFRTdYQXpSVUd4ZTg1MDlHbWJQNStIS0N6Yz0
*******1 - Downloading file
*******1 - Nothing to download
*******2 - Updating files
*******Modifying transducerer file
*******Transducerer file was not modified, since it already contains the algorithm
*******Modifying user perspective file
*******Perspective file was not modified, since it already contains the algorithm
*******2 - Files updated!
*******3 - Generating classes skipped
*******4 - Compiling the Jar skipped
*******5 - Indexing on the IS
Indexing on IS in scope /gcube/devNext/NextNext
setting scope to /gcube/devNext/NextNext
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/gcube/tomcat/webapps/wps/WEB-INF/lib/slf4j-log4j12-1.7.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/gcube/tomcat/webapps/wps/WEB-INF/lib/logback-classic-1.1.11.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/gcube/tomcat/webapps/wps/WEB-INF/lib/slf4j-nop-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/gcube/tomcat/lib/logback-classic-1.1.11.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
Exception in thread "main" java.lang.StackOverflowError
    at java.util.concurrent.ConcurrentHashMap.get(ConcurrentHashMap.java:936)
    at org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:58)
    at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:270)
    at org.apache.log4j.Category.<init>(Category.java:57)
    at org.apache.log4j.Logger.<init>(Logger.java:37)
    at org.apache.log4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:43)
    at org.apache.log4j.LogManager.getLogger(LogManager.java:45)
    at org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:66)
    at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:270)
    at org.apache.log4j.Category.<init>(Category.java:57)
    at org.apache.log4j.Logger.<init>(Logger.java:37)
    at org.apache.log4j.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:43)
    at org.apache.log4j.LogManager.getLogger(LogManager.java:45)
    at org.slf4j.impl.Log4jLoggerFactory.getLogger(Log4jLoggerFactory.java:66)
    at org.slf4j.LoggerFactory.getLogger(LoggerFactory.java:270)
    at org.apache.log4j.Category.<init>(Category.java:57)
    at org.apache.log4j.Logger.<init>(Logger.java:37)

#24 Updated by Roberto Cirillo over 1 year ago

  • Assignee changed from Roberto Cirillo to Giancarlo Panichi
  • Status changed from In Progress to Feedback

This is a stackoverflow error. I've checked the libraries and I've found the "slf4j-log4j12-1.7.5.jar" under wps/WEB-INF/lib but this library is not present in the production wps war.
I've tried to remove the library above manually. If now the algorithm works, we should remove this library from wps war deployed on Snapshot.
Please @g.panichi@isti.cnr.it could you retry?

#25 Updated by Roberto Cirillo over 1 year ago

  • % Done changed from 50 to 100
  • Status changed from Feedback to Closed

The test has been passed. I'm going to open another ticket for removing the slf4j-log4j12-1.7.5.jar library from wps.

#26 Updated by Roberto Cirillo over 1 year ago

  • Related to Task #11956: Remove slf4j-log4j12-1.7.5.jar from wps.war added

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