[SCUFL2-121] EmptyStackException when writing workflow bundle Created: 2012-04-05  Updated: 2013-04-23  Resolved: 2012-07-09

Status: Resolved
Project: Scufl 2
Component/s: None
Affects Version/s: 0.9.2
Fix Version/s: 0.11.0

Type: Bug Priority: Critical
Reporter: David Withers (Inactive) Assignee: Stian Soiland-Reyes
Resolution: Fixed Votes: 0
Labels: profile, rdfxml, scufl2tools, workflowBundle
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Attachments: File rest.t2flow    
Issue Links:
Depends
has dependent SCAPE-3 OSGi Tavern 3 command-line - multiple... In Progress

 Description   

Getting an EmptyStackException when writing a workflow bundle. Using WorkflowBundleIO to read a t2flow and write it out as a workflow bundle.

WorkflowBundle bundle = workflowBundleIO.readBundle(t2FlowWorkflow, null);
workflowBundleIO.writeBundle(bundle, workflowFile, RDFXMLReader.APPLICATION_VND_TAVERNA_SCUFL2_WORKFLOW_BUNDLE);

The stack trace is

java.util.EmptyStackException
	at java.util.Stack.peek(Stack.java:85)
	at java.util.Stack.pop(Stack.java:67)
	at uk.org.taverna.scufl2.rdfxml.PropertyResourceSerialiser.visitLeave(PropertyResourceSerialiser.java:192)
	at uk.org.taverna.scufl2.api.common.Visitor$VisitorWithPath.visitLeave(Visitor.java:177)
	at uk.org.taverna.scufl2.api.property.PropertyResource.accept(PropertyResource.java:231)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLSerializer$ProfileSerialisationVisitor.configuration(RDFXMLSerializer.java:111)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLSerializer$ProfileSerialisationVisitor.visit(RDFXMLSerializer.java:249)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLSerializer$ProfileSerialisationVisitor.visitEnter(RDFXMLSerializer.java:259)
	at uk.org.taverna.scufl2.api.configurations.Configuration.accept(Configuration.java:68)
	at uk.org.taverna.scufl2.api.profiles.Profile.accept(Profile.java:64)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLSerializer.makeProfile(RDFXMLSerializer.java:639)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLSerializer.profileDoc(RDFXMLSerializer.java:727)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLWriter.makeUCFPackage(RDFXMLWriter.java:82)
	at uk.org.taverna.scufl2.rdfxml.RDFXMLWriter.writeBundle(RDFXMLWriter.java:49)
	at uk.org.taverna.scufl2.api.io.WorkflowBundleIO.writeBundle(WorkflowBundleIO.java:323)
	at uk.org.taverna.commandline.TavernaCommandLineTest.getScufl2Workflow(TavernaCommandLineTest.java:142)


 Comments   
Comment by David Withers (Inactive) [ 2012-04-05 ]

Attached the t2flow file that caused error when writing as a scufl2 bundle

Comment by Stian Soiland-Reyes [ 2012-07-09 ]

Fixed by avoiding the extra pop when inside a PropertyList

Comment by Jenkins Automated build [ 2012-07-09 ]

Integrated in scufl2 #3467
Test reproducing SCUFL2-121 (Revision 5d0810fc30ee28783f81bc6f2afa78d23c343c1e)
SCUFL2-121 fixed emptystackexception (Revision 0d28856999f2b786c789989508859112f390a553)

Result = SUCCESS
stian : 5d0810fc30ee28783f81bc6f2afa78d23c343c1e
Files :

  • scufl2-t2flow/src/test/resources/rest.t2flow
  • scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/EmptyStackTest.java

stian : 0d28856999f2b786c789989508859112f390a553
Files :

  • scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/PropertyResourceSerialiser.java
Comment by Jenkins Automated build [ 2012-07-09 ]

Integrated in scufl2 #3468
Test reproducing SCUFL2-121 (Revision 5d0810fc30ee28783f81bc6f2afa78d23c343c1e)
SCUFL2-121 fixed emptystackexception (Revision 0d28856999f2b786c789989508859112f390a553)

Result = SUCCESS
stian : 5d0810fc30ee28783f81bc6f2afa78d23c343c1e
Files :

  • scufl2-t2flow/src/test/resources/rest.t2flow
  • scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/EmptyStackTest.java

stian : 0d28856999f2b786c789989508859112f390a553
Files :

  • scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/PropertyResourceSerialiser.java
Comment by Jenkins Automated build [ 2012-10-05 ]

Integrated in scufl2 #3488
Test reproducing SCUFL2-121 (Revision 024af89d41d36fca8325ffac95453b9ccc01e69e)
SCUFL2-121 fixed emptystackexception (Revision 208b0c3a02d6d6bd2f667c400b1e5239bc2f86ef)

Result = SUCCESS
stian@mygrid.org.uk : 024af89d41d36fca8325ffac95453b9ccc01e69e
Files :

  • scufl2-t2flow/src/test/resources/rest.t2flow
  • scufl2-t2flow/src/test/java/uk/org/taverna/scufl2/translator/t2flow/EmptyStackTest.java

stian@mygrid.org.uk : 208b0c3a02d6d6bd2f667c400b1e5239bc2f86ef
Files :

  • scufl2-rdfxml/src/main/java/uk/org/taverna/scufl2/rdfxml/PropertyResourceSerialiser.java
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