Hi,
I am receiving the following error after the task finished and before the
output files are copied by the CopyFileHook’s. The “key” that is not found is
the path of an input file of the task (link to link in “persistent” directory
which links to the actual input file) which is also part of the task “outputs”.
Andreas
May 05, 2015 2:43:16 AM org.openmole.core.batch.refresh.JobManager $bang
FINE: Error in job refresh
com.thoughtworks.xstream.converters.ConversionException: key not found:
/vol/medic01/users/as12312/Data/Registrations/Workspace/tmp/b6a903dd-ee14-4059-8d2e-093bd51876c4/tmp/1430789762769/18ef0801-bb7e-45c3-beab-3f0caafd54f5/3ef62b8f-8b49-4d6a-9b89-df40abdffa85/.tmp/b7a0485e-ac15-411b-bddd-b4f792dd7fa1/category6a325812-131d-4224-bbe5-a26ab106acff/mni305.nii.gz
: key not found:
/vol/medic01/users/as12312/Data/Registrations/Workspace/tmp/b6a903dd-ee14-4059-8d2e-093bd51876c4/tmp/1430789762769/18ef0801-bb7e-45c3-beab-3f0caafd54f5/3ef62b8f-8b49-4d6a-9b89-df40abdffa85/.tmp/b7a0485e-ac15-411b-bddd-b4f792dd7fa1/category6a325812-131d-4224-bbe5-a26ab106acff/mni305.nii.gz
---- Debugging information ----
message : key not found:
/vol/medic01/users/as12312/Data/Registrations/Workspace/tmp/b6a903dd-ee14-4059-8d2e-093bd51876c4/tmp/1430789762769/18ef0801-bb7e-45c3-beab-3f0caafd54f5/3ef62b8f-8b49-4d6a-9b89-df40abdffa85/.tmp/b7a0485e-ac15-411b-bddd-b4f792dd7fa1/category6a325812-131d-4224-bbe5-a26ab106acff/mni305.nii.gz
cause-exception : java.util.NoSuchElementException
cause-message : key not found:
/vol/medic01/users/as12312/Data/Registrations/Workspace/tmp/b6a903dd-ee14-4059-8d2e-093bd51876c4/tmp/1430789762769/18ef0801-bb7e-45c3-beab-3f0caafd54f5/3ef62b8f-8b49-4d6a-9b89-df40abdffa85/.tmp/b7a0485e-ac15-411b-bddd-b4f792dd7fa1/category6a325812-131d-4224-bbe5-a26ab106acff/mni305.nii.gz
class : java.io.File
required-type : java.io.File
converter-type :
com.thoughtworks.xstream.converters.SingleValueConverterWrapper
wrapped-converter : org.openmole.core.serializer.file.FileConverterInjecter
path :
/org.openmole.core.batch.message.package$ContextResults/results/tree/value/value/variables/tree/right/left/value/value
line number : 72
class[1] : org.openmole.core.workflow.data.Variable$$anon$1
converter-type[1] :
com.thoughtworks.xstream.converters.reflection.ReflectionConverter
class[2] : scala.collection.immutable.RedBlackTree$BlackTree
class[3] : scala.collection.immutable.RedBlackTree$RedTree
class[4] : scala.collection.immutable.TreeMap
class[5] : org.openmole.core.workflow.data.Context$$anon$1
class[6] : scala.util.Success
class[7] : org.openmole.core.batch.message.package$ContextResults
version : not available
-------------------------------
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:79)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshallField(AbstractReflectionConverter.java:480)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.doUnmarshal(AbstractReflectionConverter.java:412)
at
com.thoughtworks.xstream.converters.reflection.AbstractReflectionConverter.unmarshal(AbstractReflectionConverter.java:263)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
at
com.thoughtworks.xstream.core.AbstractReferenceUnmarshaller.convert(AbstractReferenceUnmarshaller.java:65)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:66)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convertAnother(TreeUnmarshaller.java:50)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.start(TreeUnmarshaller.java:134)
at
com.thoughtworks.xstream.core.AbstractTreeMarshallingStrategy.unmarshal(AbstractTreeMarshallingStrategy.java:32)
at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1206)
at com.thoughtworks.xstream.XStream.unmarshal(XStream.java:1190)
at com.thoughtworks.xstream.XStream.fromXML(XStream.java:1070)
at
org.openmole.core.serializer.file.FileInjection$class.fromXML(FileInjection.scala:30)
at
org.openmole.core.serializer.SerialiserService$$anon$7$$anon$8.fromXML(SerialiserService.scala:71)
at
org.openmole.core.serializer.SerialiserService$$anonfun$deserialiseReplaceFiles$2$$anonfun$apply$3.apply(SerialiserService.scala:148)
at
org.openmole.core.serializer.SerialiserService$$anonfun$deserialiseReplaceFiles$2$$anonfun$apply$3.apply(SerialiserService.scala:146)
at
org.openmole.core.serializer.converter.Factory$class.exec(Factory.scala:56)
at
org.openmole.core.serializer.SerialiserService$$anon$7.exec(SerialiserService.scala:69)
at
org.openmole.core.serializer.SerialiserService$$anonfun$deserialiseReplaceFiles$2.apply(SerialiserService.scala:145)
at
org.openmole.tool.lock.package$ReadWriteLockDecorator.read(package.scala:48)
at
org.openmole.core.serializer.SerialiserService$.deserialiseReplaceFiles(SerialiserService.scala:145)
at
org.openmole.core.serializer.SerialiserService$$anonfun$deserialiseReplaceFiles$1.apply(SerialiserService.scala:140)
at
org.openmole.tool.lock.package$ReadWriteLockDecorator.read(package.scala:48)
at
org.openmole.core.serializer.SerialiserService$.deserialiseReplaceFiles(SerialiserService.scala:138)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$getContextResults$1$$anonfun$apply$5.apply(GetResultActor.scala:132)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$getContextResults$1$$anonfun$apply$5.apply(GetResultActor.scala:130)
at
org.openmole.core.workspace.Workspace.withTmpFile(Workspace.scala:217)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$getContextResults$1.apply(GetResultActor.scala:130)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$getContextResults$1.apply(GetResultActor.scala:123)
at
org.openmole.core.workspace.Workspace.withTmpFile(Workspace.scala:217)
at
org.openmole.core.batch.refresh.GetResultActor.getContextResults(GetResultActor.scala:123)
at
org.openmole.core.batch.refresh.GetResultActor.getResult(GetResultActor.scala:71)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$receive$1$$anonfun$apply$mcV$sp$1.apply(GetResultActor.scala:50)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$receive$1$$anonfun$apply$mcV$sp$1.apply(GetResultActor.scala:48)
at
org.openmole.core.batch.control.UsageControl$class.tryWithToken(UsageControl.scala:28)
at
org.openmole.plugin.environment.ssh.SSHPersistentStorage$$anon$2.tryWithToken(SSHPersistentStorage.scala:46)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$receive$1.apply$mcV$sp(GetResultActor.scala:48)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$receive$1.apply(GetResultActor.scala:46)
at
org.openmole.core.batch.refresh.GetResultActor$$anonfun$receive$1.apply(GetResultActor.scala:46)
at
org.openmole.core.batch.refresh.package$.withRunFinalization(package.scala:23)
at
org.openmole.core.batch.refresh.GetResultActor.receive(GetResultActor.scala:46)
at
org.openmole.core.batch.refresh.JobManager$DispatcherActor$.receive(JobManager.scala:84)
at
org.openmole.core.batch.refresh.JobManager$$anonfun$1$$anon$1.run(JobManager.scala:63)
Caused by: java.util.NoSuchElementException: key not found:
/vol/medic01/users/as12312/Data/Registrations/Workspace/tmp/b6a903dd-ee14-4059-8d2e-093bd51876c4/tmp/1430789762769/18ef0801-bb7e-45c3-beab-3f0caafd54f5/3ef62b8f-8b49-4d6a-9b89-df40abdffa85/.tmp/b7a0485e-ac15-411b-bddd-b4f792dd7fa1/category6a325812-131d-4224-bbe5-a26ab106acff/mni305.nii.gz
at scala.collection.MapLike$class.default(MapLike.scala:228)
at scala.collection.AbstractMap.default(Map.scala:59)
at scala.collection.MapLike$class.apply(MapLike.scala:141)
at scala.collection.AbstractMap.apply(Map.scala:59)
at
org.openmole.core.serializer.file.FileInjection$class.getMatchingFile(FileInjection.scala:28)
at
org.openmole.core.serializer.SerialiserService$$anon$7$$anon$8.getMatchingFile(SerialiserService.scala:71)
at
org.openmole.core.serializer.file.FileConverterInjecter.fromString(FileConverterInjecter.scala:28)
at
com.thoughtworks.xstream.converters.SingleValueConverterWrapper.fromString(SingleValueConverterWrapper.java:41)
at
com.thoughtworks.xstream.converters.SingleValueConverterWrapper.unmarshal(SingleValueConverterWrapper.java:49)
at
com.thoughtworks.xstream.core.TreeUnmarshaller.convert(TreeUnmarshaller.java:72)
... 99 more
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