[#TAV-148] Synchronised storage of metadata - myGrid

Details

Type: Improvement
Status: Closed
Priority: Major
Resolution: Fixed
Affects Version/s: None
Fix Version/s: None
Component/s: Provenance
Labels:
None

Description

Make MetadataService storage methods synchronised, or at least verify there is no race condition.

Issue Links

Depends

This issue depends on:
~~TAV-151~~ notifyThread.interrupt() considered harmful

This issue has dependent:
~~TAV-128~~ Incorrect provenance when invoking a iterated nested workflow

Activity

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Daniele Turi added a comment - 2006-09-06 17:21

The problem arised when running uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ng4j.PerProcessExecutionTest.java,
where sometimes only the provenance corresponding to workflow completed event was stored. But this might actually be caused by org.embl.ebi.escience.scufl.tools.WorkflowLauncher.execute(Map)
in Taverna, because that stops the execution when either workflow completion or failed is fired.

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Daniele Turi added a comment - 2006-09-06 17:21 The problem arised when running uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ng4j.PerProcessExecutionTest.java, where sometimes only the provenance corresponding to workflow completed event was stored. But this might actually be caused by org.embl.ebi.escience.scufl.tools.WorkflowLauncher.execute(Map) in Taverna, because that stops the execution when either workflow completion or failed is fired.

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Daniele Turi added a comment - 2006-09-11 16:02

Analysis of the log shows that actually the events are fired in the right order, but when in debug mode everything is stored, while when in normal run mode the storage of workflow completion overrides the one of workflow created.

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Daniele Turi added a comment - 2006-09-11 16:02 Analysis of the log shows that actually the events are fired in the right order, but when in debug mode everything is stored, while when in normal run mode the storage of workflow completion overrides the one of workflow created.

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Daniele Turi added a comment - 2006-09-11 18:16

Further debugging shows that the invocation of toJenaModel() in uk.ac.man.cs.img.mygrid.provenance.knowledge.store.JenaMetadataService.updateRDFGraph(String, String, String) of workflow creation fails silently during

tempModel.read(tempStringReader, namespace);

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Daniele Turi added a comment - 2006-09-11 18:16 Further debugging shows that the invocation of toJenaModel() in uk.ac.man.cs.img.mygrid.provenance.knowledge.store.JenaMetadataService.updateRDFGraph(String, String, String) of workflow creation fails silently during tempModel.read(tempStringReader, namespace);

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Daniele Turi added a comment - 2006-09-12 12:50

Got to the stack trace of the model reading the rdf:

ERROR 2006-09-12 12:47:46,525 (com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler:44) - file:etc/ont-policy.rdf(line 18 column 2): {E302} Interrupt detected.
WARN 2006-09-12 12:47:46,530 (com.hp.hpl.jena.ontology.OntDocumentManager:960) - Exception while reading configuration: rethrew: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected.
com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected.
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:188)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:183)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:129)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:197)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:184)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:236)
at com.hp.hpl.jena.ontology.OntDocumentManager.findMetadata(OntDocumentManager.java:954)
at com.hp.hpl.jena.ontology.OntDocumentManager.initialiseMetadata(OntDocumentManager.java:912)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:199)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:181)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:165)
at com.hp.hpl.jena.ontology.OntDocumentManager.getInstance(OntDocumentManager.java:243)
at com.hp.hpl.jena.ontology.OntModelSpec.getDocumentManager(OntModelSpec.java:351)
at com.hp.hpl.jena.ontology.OntModelSpec.<init>(OntModelSpec.java:214)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaOntologyAdapter.<init>(JenaOntologyAdapter.java:94)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaProvenanceOntology.<init>(JenaProvenanceOntology.java:123)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.ProvenanceOntologyFactory.getInstance(ProvenanceOntologyFactory.java:100)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.PerProcessProvenanceGenerator.workflowCreated(PerProcessProvenanceGenerator.java:350)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:134)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:108)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:191)
com.hp.hpl.jena.shared.JenaException: rethrew: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected.
at com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:45)
at com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:35)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:214)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:188)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:183)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:129)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:197)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:184)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:254)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:236)
at com.hp.hpl.jena.ontology.OntDocumentManager.findMetadata(OntDocumentManager.java:954)
at com.hp.hpl.jena.ontology.OntDocumentManager.initialiseMetadata(OntDocumentManager.java:912)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:199)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:181)
at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:165)
at com.hp.hpl.jena.ontology.OntDocumentManager.getInstance(OntDocumentManager.java:243)
at com.hp.hpl.jena.ontology.OntModelSpec.getDocumentManager(OntModelSpec.java:351)
at com.hp.hpl.jena.ontology.OntModelSpec.<init>(OntModelSpec.java:214)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaOntologyAdapter.<init>(JenaOntologyAdapter.java:94)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaProvenanceOntology.<init>(JenaProvenanceOntology.java:123)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.ProvenanceOntologyFactory.getInstance(ProvenanceOntologyFactory.java:100)
at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.PerProcessProvenanceGenerator.workflowCreated(PerProcessProvenanceGenerator.java:350)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:134)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:108)
at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:191)
Caused by: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected.

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Daniele Turi added a comment - 2006-09-12 12:50 Got to the stack trace of the model reading the rdf: ERROR 2006-09-12 12:47:46,525 (com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler:44) - file:etc/ont-policy.rdf(line 18 column 2): {E302} Interrupt detected. WARN 2006-09-12 12:47:46,530 (com.hp.hpl.jena.ontology.OntDocumentManager:960) - Exception while reading configuration: rethrew: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected. com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected. at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:188) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:183) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:129) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:197) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:184) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:254) at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:236) at com.hp.hpl.jena.ontology.OntDocumentManager.findMetadata(OntDocumentManager.java:954) at com.hp.hpl.jena.ontology.OntDocumentManager.initialiseMetadata(OntDocumentManager.java:912) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:199) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:181) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:165) at com.hp.hpl.jena.ontology.OntDocumentManager.getInstance(OntDocumentManager.java:243) at com.hp.hpl.jena.ontology.OntModelSpec.getDocumentManager(OntModelSpec.java:351) at com.hp.hpl.jena.ontology.OntModelSpec.<init>(OntModelSpec.java:214) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaOntologyAdapter.<init>(JenaOntologyAdapter.java:94) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaProvenanceOntology.<init>(JenaProvenanceOntology.java:123) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.ProvenanceOntologyFactory.getInstance(ProvenanceOntologyFactory.java:100) at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.PerProcessProvenanceGenerator.workflowCreated(PerProcessProvenanceGenerator.java:350) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:134) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:108) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:191) com.hp.hpl.jena.shared.JenaException: rethrew: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected. at com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:45) at com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:35) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:214) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:188) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:183) at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:129) at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source) at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source) at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:106) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:197) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:184) at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:254) at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:236) at com.hp.hpl.jena.ontology.OntDocumentManager.findMetadata(OntDocumentManager.java:954) at com.hp.hpl.jena.ontology.OntDocumentManager.initialiseMetadata(OntDocumentManager.java:912) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:199) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:181) at com.hp.hpl.jena.ontology.OntDocumentManager.<init>(OntDocumentManager.java:165) at com.hp.hpl.jena.ontology.OntDocumentManager.getInstance(OntDocumentManager.java:243) at com.hp.hpl.jena.ontology.OntModelSpec.getDocumentManager(OntModelSpec.java:351) at com.hp.hpl.jena.ontology.OntModelSpec.<init>(OntModelSpec.java:214) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaOntologyAdapter.<init>(JenaOntologyAdapter.java:94) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.jena.JenaProvenanceOntology.<init>(JenaProvenanceOntology.java:123) at uk.ac.man.cs.img.mygrid.provenance.knowledge.ontology.ProvenanceOntologyFactory.getInstance(ProvenanceOntologyFactory.java:100) at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.PerProcessProvenanceGenerator.workflowCreated(PerProcessProvenanceGenerator.java:350) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:134) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:108) at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:191) Caused by: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1: {E302} Interrupt detected.

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Daniele Turi added a comment - 2006-09-12 15:25

Fixing ~~TAV-151~~ fixed the problem.

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Daniele Turi added a comment - 2006-09-12 15:25 Fixing ~~TAV-151~~ fixed the problem.

People

Assignee:

Daniele Turi

Reporter:

Daniele Turi

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Dates

Created:

2006-09-06 17:04

Updated:

2006-09-12 16:11

Resolved:

2006-09-12 15:25