NxmlReader error | No roots in graph #634

RohitChattopadhyay · 2019-07-14T16:22:14Z

I am getting this error on several nxml files downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/comm_use.A-B.xml.tar.gz

I have made a gist using 2 such files (PMC6588870 , PMC5109642 ) here.

I am using the out of box application.conf file with outputTypes = ["indexcard"]

16:21:34.400 [ForkJoinPool-1-worker-3] ERROR org.clulab.reach.ReachCLI - 
==========

¡¡¡ NxmlReader error !!!

paper: PMC6588870

error:
java.lang.RuntimeException: No roots in graph:
dep                 reln                gov                 
---                 ----                ---                 

Find where this graph was created and make sure you're adding roots.

stack trace:
edu.stanford.nlp.semgraph.SemanticGraph.getFirstRoot(SemanticGraph.java:790)
edu.stanford.nlp.semgraph.semgrex.SemgrexPattern.matcher(SemgrexPattern.java:231)

Thanks

The text was updated successfully, but these errors were encountered:

MihaiSurdeanu · 2019-07-15T05:25:03Z

Unfortunately, this error comes from the CoreNLP parser, not from our code. So, it is harder to control... But, I believe that our code robustly skips these sentences, without failing on the whole paper. To double check, can you please:

Paste the whole stack trace here.
Attach one of these Nxml files, so I can replicate the experiment?

Thanks!

RohitChattopadhyay · 2019-07-15T07:39:45Z

Thanks

File (PMC3420630) : Gist Link

Stack trace

==========

13:06:51.123 [ForkJoinPool-1-worker-7] ERROR org.clulab.reach.ReachCLI - 
==========

 ¡¡¡ NxmlReader error !!!

paper: PMC3420630

error:
java.lang.RuntimeException: No roots in graph:
dep                 reln                gov                 
---                 ----                ---                 

Find where this graph was created and make sure you're adding roots.

stack trace:
edu.stanford.nlp.semgraph.SemanticGraph.getFirstRoot(SemanticGraph.java:790)
edu.stanford.nlp.semgraph.semgrex.SemgrexPattern.matcher(SemgrexPattern.java:231)
edu.stanford.nlp.trees.UniversalEnglishGrammaticalStructure.demoteQuantificationalModifiers(UniversalEnglishGrammaticalStructure.java:1724)
edu.stanford.nlp.trees.UniversalEnglishGrammaticalStructure.addEnhancements(UniversalEnglishGrammaticalStructure.java:871)
edu.stanford.nlp.trees.GrammaticalStructure.typedDependenciesEnhancedPlusPlus(GrammaticalStructure.java:924)
edu.stanford.nlp.semgraph.SemanticGraphFactory.makeFromTree(SemanticGraphFactory.java:249)
edu.stanford.nlp.semgraph.SemanticGraphFactory.generateEnhancedPlusPlusDependencies(SemanticGraphFactory.java:129)
edu.stanford.nlp.pipeline.ParserAnnotatorUtils.fillInParseAnnotations(ParserAnnotatorUtils.java:67)
org.clulab.processors.corenlp.CoreNLPProcessor$$anonfun$parse$1.apply(CoreNLPProcessor.scala:95)
org.clulab.processors.corenlp.CoreNLPProcessor$$anonfun$parse$1.apply(CoreNLPProcessor.scala:86)
scala.collection.Iterator$class.foreach(Iterator.scala:891)
scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
scala.collection.AbstractIterable.foreach(Iterable.scala:54)
org.clulab.processors.corenlp.CoreNLPProcessor.parse(CoreNLPProcessor.scala:86)
org.clulab.processors.Processor$class.annotate(Processor.scala:93)
org.clulab.processors.shallownlp.ShallowNLPProcessor.annotate(ShallowNLPProcessor.scala:34)
org.clulab.processors.Processor$class.annotate(Processor.scala:62)
org.clulab.processors.shallownlp.ShallowNLPProcessor.annotate(ShallowNLPProcessor.scala:34)
org.clulab.reach.ReachSystem.mkDoc(ReachSystem.scala:59)
org.clulab.reach.ReachSystem.extractFrom(ReachSystem.scala:146)
org.clulab.reach.ReachSystem.extractFrom(ReachSystem.scala:72)
org.clulab.reach.PaperReader$.getMentionsFromEntry(PaperReader.scala:158)
org.clulab.reach.ReachCLI.processPaper(ReachCLI.scala:132)
org.clulab.reach.ReachCLI$$anonfun$4.apply(ReachCLI.scala:86)
org.clulab.reach.ReachCLI$$anonfun$4.apply(ReachCLI.scala:80)
scala.collection.parallel.AugmentedIterableIterator$class.map2combiner(RemainsIterator.scala:115)
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:62)
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1054)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1051)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.internal(Tasks.scala:159)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
scala.concurrent.forkjoin.ForkJoinTask.doJoin(ForkJoinTask.java:341)
scala.concurrent.forkjoin.ForkJoinTask.join(ForkJoinTask.java:673)
scala.collection.parallel.ForkJoinTasks$WrappedTask$class.sync(Tasks.scala:378)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.sync(Tasks.scala:443)
scala.collection.parallel.ForkJoinTasks$class.executeAndWaitResult(Tasks.scala:426)
scala.collection.parallel.ForkJoinTaskSupport.executeAndWaitResult(TaskSupport.scala:56)
scala.collection.parallel.ExecutionContextTasks$class.executeAndWaitResult(Tasks.scala:558)
scala.collection.parallel.ExecutionContextTaskSupport.executeAndWaitResult(TaskSupport.scala:80)
scala.collection.parallel.ParIterableLike$ResultMapping.leaf(ParIterableLike.scala:958)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
scala.collection.parallel.ParIterableLike$ResultMapping.tryLeaf(ParIterableLike.scala:953)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

==========

Thank you

MihaiSurdeanu · 2019-07-16T15:24:41Z

I can confirm that, while this is a CoreNLP issue, we are not recovering nicely from this. We'll fix this soon.

MihaiSurdeanu · 2019-07-16T16:59:55Z

This was fixed in processors master, in the sense that we recover from the CoreNLP error wo/ crashing everything. To take advantage of the fix before the new processors release, please:

Clone processors, and run sbt +publishLocal.
In reach, change procVer to 7.5.3-SNAPSHOT in main/build.sbt.

RohitChattopadhyay · 2019-07-16T19:12:24Z

This was fixed in processors master, in the sense that we recover from the CoreNLP error wo/ crashing everything. To take advantage of the fix before the new processors release, please:

Clone processors, and run sbt +publishLocal.

In reach, change procVer to 7.5.3-SNAPSHOT in main/build.sbt.

Thanks for your help, it worked. But now I am facing another issue

Link to file( PMC4379733.nxml ) : Gist

Stacktrace

==========

 ¡¡¡ NxmlReader error !!!

paper: PMC4379733

error:
java.lang.RuntimeException: ERROR: unknown event type: Gene_or_gene_product in event:
{
  "type" : "TextBoundMention",
  "id" : "T:18956156",
  "text" : "TGF-beta1",
  "labels" : [ "Gene_or_gene_product", "MacroMolecule", "Equivalable", "BioChemicalEntity", "BioEntity", "Entity", "PossibleController" ],
  "tokenInterval" : {
    "start" : 5,
    "end" : 6
  },
  "characterStartOffset" : 8345,
  "characterEndOffset" : 8354,
  "sentence" : 62,
  "document" : "-372046785",
  "keep" : true,
  "foundBy" : "ner-gene_or_gene_product-entities"
}

stack trace:
org.clulab.reach.export.JsonOutputter$.mkEventType(JsonOutputter.scala:172)
org.clulab.reach.export.indexcards.IndexCardOutput.mkRegulationIndexCard(IndexCardOutput.scala:333)
org.clulab.reach.export.indexcards.IndexCardOutput$$anonfun$mkCards$1.apply(IndexCardOutput.scala:114)
org.clulab.reach.export.indexcards.IndexCardOutput$$anonfun$mkCards$1.apply(IndexCardOutput.scala:112)
scala.collection.immutable.List.foreach(List.scala:392)
org.clulab.reach.export.indexcards.IndexCardOutput.mkCards(IndexCardOutput.scala:112)
org.clulab.reach.export.indexcards.IndexCardOutput.writeJSON(IndexCardOutput.scala:72)
org.clulab.reach.ReachCLI.outputMentions(ReachCLI.scala:200)
org.clulab.reach.ReachCLI$$anonfun$processPaper$1.apply(ReachCLI.scala:139)
org.clulab.reach.ReachCLI$$anonfun$processPaper$1.apply(ReachCLI.scala:139)
scala.collection.immutable.List.foreach(List.scala:392)
org.clulab.reach.ReachCLI.processPaper(ReachCLI.scala:139)
org.clulab.reach.ReachCLI$$anonfun$4.apply(ReachCLI.scala:86)
org.clulab.reach.ReachCLI$$anonfun$4.apply(ReachCLI.scala:80)
scala.collection.parallel.AugmentedIterableIterator$class.map2combiner(RemainsIterator.scala:115)
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:62)
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1054)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1051)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.internal(Tasks.scala:159)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.internal(Tasks.scala:443)
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:149)
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

==========

Thank You

MihaiSurdeanu mentioned this issue Jul 16, 2019

processors does not publishLocal for scala 2.11 clulab/processors#336

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NxmlReader error | No roots in graph #634

NxmlReader error | No roots in graph #634

RohitChattopadhyay commented Jul 14, 2019 •

edited

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MihaiSurdeanu commented Jul 15, 2019

RohitChattopadhyay commented Jul 15, 2019 •

edited

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MihaiSurdeanu commented Jul 16, 2019

MihaiSurdeanu commented Jul 16, 2019

RohitChattopadhyay commented Jul 16, 2019

NxmlReader error | No roots in graph #634

NxmlReader error | No roots in graph #634

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RohitChattopadhyay commented Jul 14, 2019 • edited Loading

MihaiSurdeanu commented Jul 15, 2019

RohitChattopadhyay commented Jul 15, 2019 • edited Loading

File (PMC3420630) : Gist Link

Stack trace

MihaiSurdeanu commented Jul 16, 2019

MihaiSurdeanu commented Jul 16, 2019

RohitChattopadhyay commented Jul 16, 2019

RohitChattopadhyay commented Jul 14, 2019 •

edited

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RohitChattopadhyay commented Jul 15, 2019 •

edited

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