Project

General

Profile

Actions
Copy link

Task #5737

closed

Process resubmit fails

Added by Gianpaolo Coro over 8 years ago. Updated almost 6 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Lucio Lelii
Category:
High-Throughput-Computing
Target version:
Data Processing
Start date:
Nov 11, 2016
Due date:
% Done:

100%

Estimated time:
Infrastructure:
Production

Description

On DataMiner the process re-submission fails. Please check with

https://i-marine.d4science.org/group/stockassessment/data-miner?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.CMSY_2

Actions
Copy link
 #1

Updated by Pasquale Pagano about 8 years ago

  • Tracker changed from Incident to Task

I have to change the tracker since it is really unbelievable that an incident was not considered up to now. Please update it now.

Actions
Copy link
 #2

Updated by Giancarlo Panichi about 8 years ago

  • Assignee changed from Giancarlo Panichi to Lucio Lelii

This is a communication problem between DataMiner Service and Workspace, no problem on the portlet. Please @lucio.lelii@isti.cnr.it and @gianpaolo.coro@isti.cnr.it check the service

Actions
Copy link
 #3

Updated by Gianpaolo Coro about 8 years ago

There are issues with the Workspace interaction, perhaps due to the release of December.
When I execute a computation from a VRE through the portal, the HL returns this error:

org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException: java.lang.String cannot be cast to org.gcube.common.homelibary.model.items.ItemDelegate
org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException: java.lang.String cannot be cast to org.gcube.common.homelibary.model.items.ItemDelegate

Nevertheless, the issue does not appear by calling the DataMiner directly via http, e.g.:

http://dataminer1-p-d4s.d4science.org/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token=26209520-6e2d-4850-9716-0b2bd37fd017-843339462&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.clusterers.DBSCAN&DataInputs=OccurrencePointsTable=http://data.d4science.org/a0pFQ0RuUXhpOEpmcElhcUlmQUpWc3VLd0FWM04xMnlHbWJQNStIS0N6Yz0;FeaturesColumnNames=a|b|t;OccurrencePointsClusterLabel=OccCluster_;epsilon=10;min_points=1;

The issue is not there neither when using the proxy instead of the direct service address.

The complete stack trace of the Exception is:

org.gcube.common.homelibrary.home.exceptions.InternalErrorException: org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException: java.lang.String cannot be cast to org.gcube.common.homelibary.model.items.ItemDelegate
        at org.gcube.common.homelibrary.jcr.workspace.JCRWorkspaceItem.getAbsolutePath(JCRWorkspaceItem.java:1089)
        at org.gcube.common.homelibrary.jcr.workspace.JCRAbstractWorkspaceFolder.createFolder(JCRAbstractWorkspaceFolder.java:244)
        at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.uploadComputationData(DataspaceManager.java:271)
        at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.writeProvenance(DataspaceManager.java:406)
        at org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.dataspace.DataspaceManager.run(DataspaceManager.java:78)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.gcube.common.homelibrary.home.workspace.exceptions.ItemNotFoundException: java.lang.String cannot be cast to org.gcube.common.homelibary.model.items.ItemDelegate
        at org.gcube.common.homelibrary.jcr.workspace.servlet.JCRSession.getItemById(JCRSession.java:299)
        at org.gcube.common.homelibrary.jcr.workspace.JCRWorkspaceItem.getAbsolutePath(JCRWorkspaceItem.java:1085)
        ... 5 more

I guess the HL is not updated on DataMiner, which once gave the same issue and this issue is somehow related to the VRE and authentication indicated by the portal. @roberto.cirillo@isti.cnr.it and @valentina.marioli@isti.cnr.it could you help us please?

Actions
Copy link
 #4

Updated by Roberto Cirillo about 8 years ago

I've done some tests.

When an execution is performed by portal I see an exception on HomeLibrary webapp:

2017-02-06 18:32:59.452 INFO  [http-bio-8080-exec-1196195] SaveAccountingItem.java:68 Servlet SaveAccountingItem called for entry ADD
2017-02-06 18:32:59.453 INFO  [http-bio-8080-exec-1196195] AccountingDelegateWrapper.java:57 Adding ADD to node: /Home/roberto.cirillo/Workspace/DataMiner/Output Data Sets
2017-02-06 18:32:59.532 INFO  [http-bio-8080-exec-1196162] GetItemByPath.java:64 Servlet GetItemByPath called with parameters: [path: /Home/roberto.cirillo/Workspace/DataMiner/Computations]
2017-02-06 18:32:59.554 INFO  [http-bio-8080-exec-1196044] SaveItem.java:74 Servlet SaveItem called with parameters: [itemName: DBSCAN_ID_c276622d-8e51-47f6-98a2-7488c6488e99 - by: roberto.cirillo]
2017-02-06 18:32:59.555 INFO  [http-bio-8080-exec-1196044] ItemDelegateWrapper.java:704 Create a new node
2017-02-06 18:32:59.556 INFO  [http-bio-8080-exec-1196044] ItemDelegateWrapper.java:72 Adding node DBSCAN_ID_c276622d-8e51-47f6-98a2-7488c6488e99 to parentNode /Home/roberto.cirillo/Workspace/DataMiner/Computations - type: nthl:workspaceItem
javax.jcr.ItemExistsException: This node already exists: /Home/roberto.cirillo/Workspace/DataMiner/Computations/DBSCAN_ID_c276622d-8e51-47f6-98a2-7488c6488e99
    at org.apache.jackrabbit.core.NodeImpl.addNode(NodeImpl.java:1297)
    at org.apache.jackrabbit.core.session.AddNodeOperation.perform(AddNodeOperation.java:111)
    at org.apache.jackrabbit.core.session.AddNodeOperation.perform(AddNodeOperation.java:37)
    at org.apache.jackrabbit.core.session.SessionState.perform(SessionState.java:216)
    at org.apache.jackrabbit.core.ItemImpl.perform(ItemImpl.java:91)
    at org.apache.jackrabbit.core.NodeImpl.addNodeWithUuid(NodeImpl.java:1818)
    at org.apache.jackrabbit.core.NodeImpl.addNode(NodeImpl.java:1778)
    at org.apache.jackrabbit.j2ee.workspacemanager.ItemDelegateWrapper.addNode(ItemDelegateWrapper.java:76)
    at org.apache.jackrabbit.j2ee.workspacemanager.ItemDelegateWrapper.save(ItemDelegateWrapper.java:705)
    at org.apache.jackrabbit.j2ee.workspacemanager.servlets.post.SaveItem.doPost(SaveItem.java:79)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
    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 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.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: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:423)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
    at java.lang.Thread.run(Thread.java:744)

when the same execution is perfomed by url I don't see this exception:

2017-02-06 18:35:01.547 INFO  [http-bio-8080-exec-1196212] SaveAccountingItem.java:68 Servlet SaveAccountingItem called for entry ADD
2017-02-06 18:35:01.548 INFO  [http-bio-8080-exec-1196212] AccountingDelegateWrapper.java:57 Adding ADD to node: /Home/roberto.cirillo/Workspace/DataMiner/Output Data Sets
2017-02-06 18:35:01.644 INFO  [http-bio-8080-exec-1196208] GetItemByPath.java:64 Servlet GetItemByPath called with parameters: [path: /Home/roberto.cirillo/Workspace/DataMiner/Computations]
2017-02-06 18:35:01.672 INFO  [http-bio-8080-exec-1196219] SaveItem.java:74 Servlet SaveItem called with parameters: [itemName: DBSCAN_ID_4972d6da-a941-458f-a5c6-dcce4bb414a1 - by: roberto.cirillo]
2017-02-06 18:35:01.673 INFO  [http-bio-8080-exec-1196219] ItemDelegateWrapper.java:704 Create a new node
2017-02-06 18:35:01.674 INFO  [http-bio-8080-exec-1196219] ItemDelegateWrapper.java:72 Adding node DBSCAN_ID_4972d6da-a941-458f-a5c6-dcce4bb414a1 to parentNode /Home/roberto.cirillo/Workspace/DataMiner/Computations - type: nthl:workspaceItem
2017-02-06 18:35:01.674 ERROR [http-bio-8080-exec-1196219] ItemDelegateWrapper.java:312 hl:IsSystemFolder not present

@valentina.marioli@isti.cnr.it do you think this exception could be the problem?

Actions
Copy link
 #5

Updated by Lucio Lelii almost 6 years ago

  • Status changed from New to Closed
Actions
Copy link

Also available in: Atom PDF

Add picture from clipboard (Maximum size: 8.91 MB)