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broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Womtool graph bug #6744

Open shengbing opened 2 years ago

shengbing commented 2 years ago

womtool graph bug: Exception in thread "main" java.util.NoSuchElementException: key not found: ScatterVariableNode(WomIdentifier(LocalName(lane),FullyQualifiedName(lane)),PlainAnonymousExpressionNode(WomIdentifier(LocalName(lane),FullyQualifiedName(lane)),WdlWomExpression(WdlExpression(<string:255:22 identifier "TWVyZ2VJbnB1dFJlYWRz">),[Scatter fqn=MAPRSEQSingleSampleMasterWF.$scatter_0, item=lane, collection=MergeInputReads]),WomMaybeEmptyArrayType(WomMaybeEmptyArrayType(WomSingleFileType)),Map(MergeInputReads -> ConnectedInputPort(MergeInputReads,WomMaybeEmptyArrayType(WomMaybeEmptyArrayType(WomSingleFileType)),GraphNodeOutputPort(MAPRSEQSingleSampleMasterWF.MergeInputReads),wom.graph.GraphNode$GraphNodeSetter$$Lambda$512/0x0000000800491040@2a9fd482))),WomMaybeEmptyArrayType(WomSingleFileType)) at scala.collection.immutable.Map$EmptyMap$.apply(Map.scala:101) at scala.collection.immutable.Map$EmptyMap$.apply(Map.scala:99) at wom.views.GraphPrint$.relevantAsUpstream$1(GraphPrint.scala:177) at wom.views.GraphPrint$.upstreamPortToRelevantNodes$1(GraphPrint.scala:187) at wom.views.GraphPrint$.$anonfun$upstreamLinks$1(GraphPrint.scala:190) at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:245) at scala.collection.immutable.Set$Set1.foreach(Set.scala:97) at scala.collection.TraversableLike.flatMap(TraversableLike.scala:245) at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:242) at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108) at wom.views.GraphPrint$.upstreamLinksforNode$1(GraphPrint.scala:190) at wom.views.GraphPrint$.relevantAsUpstream$1(GraphPrint.scala:176) at wom.views.GraphPrint$.upstreamPortToRelevantNodes$1(GraphPrint.scala:184) at wom.views.GraphPrint$.relevantAsUpstream$1(GraphPrint.scala:178) at wom.views.GraphPrint$.upstreamPortToRelevantNodes$1(GraphPrint.scala:187) at wom.views.GraphPrint$.$anonfun$upstreamLinks$1(GraphPrint.scala:190) at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:245) at scala.collection.immutable.Set$Set1.foreach(Set.scala:97) at scala.collection.TraversableLike.flatMap(TraversableLike.scala:245) at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:242) at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108) at wom.views.GraphPrint$.upstreamLinksforNode$1(GraphPrint.scala:190) at wom.views.GraphPrint$.relevantAsUpstream$1(GraphPrint.scala:176) at wom.views.GraphPrint$.upstreamPortToRelevantNodes$1(GraphPrint.scala:187) at wom.views.GraphPrint$.$anonfun$upstreamLinks$1(GraphPrint.scala:190) at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:245) at scala.collection.immutable.HashSet$HashSet1.foreach(HashSet.scala:321) at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:977) at scala.collection.TraversableLike.flatMap(TraversableLike.scala:245) at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:242) at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108) at wom.views.GraphPrint$.upstreamLinksforNode$1(GraphPrint.scala:190) at wom.views.GraphPrint$.upstreamLinks(GraphPrint.scala:191) at wom.views.GraphPrint.$anonfun$listAllGraphNodes$2(GraphPrint.scala:33) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at scala.collection.Iterator.foreach(Iterator.scala:941) at scala.collection.Iterator.foreach$(Iterator.scala:941) at scala.collection.AbstractIterator.foreach(Iterator.scala:1429) at scala.collection.TraversableOnce.foldLeft(TraversableOnce.scala:160) at scala.collection.TraversableOnce.foldLeft$(TraversableOnce.scala:158) at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1429) at cats.kernel.Monoid.combineAll(Monoid.scala:82) at cats.kernel.Monoid.combineAll$(Monoid.scala:81) at cats.derived.MkMonoidDerivation$$anon$1.combineAll(monoid.scala:45) at cats.instances.ListInstances$$anon$1.foldMap(list.scala:70) at cats.instances.ListInstances$$anon$1.foldMap(list.scala:12) at cats.Foldable$Ops.foldMap(Foldable.scala:31) at cats.Foldable$Ops.foldMap$(Foldable.scala:31) at cats.Foldable$ToFoldableOps$$anon$5.foldMap(Foldable.scala:31) at wom.views.GraphPrint.listAllGraphNodes(GraphPrint.scala:32) at wom.views.GraphPrint.handleConditional(GraphPrint.scala:87) at wom.views.GraphPrint.$anonfun$listAllGraphNodes$2(GraphPrint.scala:36) at scala.collection.Iterator$$anon$10.next(Iterator.scala:459) at scala.collection.Iterator.foreach(Iterator.scala:941) at scala.collection.Iterator.foreach$(Iterator.scala:941) at scala.collection.AbstractIterator.foreach(Iterator.scala:1429) at scala.collection.TraversableOnce.foldLeft(TraversableOnce.scala:160) at scala.collection.TraversableOnce.foldLeft$(TraversableOnce.scala:158) at scala.collection.AbstractIterator.foldLeft(Iterator.scala:1429) at cats.kernel.Monoid.combineAll(Monoid.scala:82) at cats.kernel.Monoid.combineAll$(Monoid.scala:81) at cats.derived.MkMonoidDerivation$$anon$1.combineAll(monoid.scala:45) at cats.instances.ListInstances$$anon$1.foldMap(list.scala:70) at cats.instances.ListInstances$$anon$1.foldMap(list.scala:12) at cats.Foldable$Ops.foldMap(Foldable.scala:31) at cats.Foldable$Ops.foldMap$(Foldable.scala:31) at cats.Foldable$ToFoldableOps$$anon$5.foldMap(Foldable.scala:31) at wom.views.GraphPrint.listAllGraphNodes(GraphPrint.scala:32) at wom.views.GraphPrint.dotString(GraphPrint.scala:16) at womtool.WomtoolMain$.graph(WomtoolMain.scala:132) at womtool.WomtoolMain$.dispatchCommand(WomtoolMain.scala:55) at womtool.WomtoolMain$.runWomtool(WomtoolMain.scala:157) at womtool.WomtoolMain$.delayedEndpoint$womtool$WomtoolMain$1(WomtoolMain.scala:162) at womtool.WomtoolMain$delayedInit$body.apply(WomtoolMain.scala:25) at scala.Function0.apply$mcV$sp(Function0.scala:39) at scala.Function0.apply$mcV$sp$(Function0.scala:39) at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:17) at scala.App.$anonfun$main$1$adapted(App.scala:80) at scala.collection.immutable.List.foreach(List.scala:392) at scala.App.main(App.scala:80) at scala.App.main$(App.scala:78) at womtool.WomtoolMain$.main(WomtoolMain.scala:25) at womtool.WomtoolMain.main(WomtoolMain.scala)

lxwgcool commented 5 months ago

I also encountered the same error. Could anyone make some comments?