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INCATools / dosdp-tools

Utility for working with DOSDP design patterns and OWL ontologies
MIT License
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0.14 Beta fails to read Manchester Syntax #199

Closed matentzn closed 4 years ago

matentzn commented 4 years ago

This error looks like it is caused by Manchester syntax reading, but I verified that it did not (0.13 works normally). Could it be that the 'optionality' introduced for all vars actually causes this failure, i.e. to prevent DOSDP tools from swapping in somehow the filler variable into the manchester syntax strings?

Encountered '' at line 1 column 108. Expected one of:
    Class name
    (
    {
    Self

Exception in thread "main" org.semanticweb.owlapi.manchestersyntax.renderer.ParserException: Encountered '' at line 1 column 108. Expected one of:
    Class name
    (
    {
    Self

    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl$ExceptionBuilder.build(ManchesterOWLSyntaxParserImpl.java:2562)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNestedClassExpression(ManchesterOWLSyntaxParserImpl.java:1130)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseObjectRestriction(ManchesterOWLSyntaxParserImpl.java:756)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNonNaryClassExpression(ManchesterOWLSyntaxParserImpl.java:728)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseIntersection(ManchesterOWLSyntaxParserImpl.java:611)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseUnion(ManchesterOWLSyntaxParserImpl.java:634)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNestedClassExpression(ManchesterOWLSyntaxParserImpl.java:1103)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNonNaryClassExpression(ManchesterOWLSyntaxParserImpl.java:735)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseIntersection(ManchesterOWLSyntaxParserImpl.java:611)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseUnion(ManchesterOWLSyntaxParserImpl.java:634)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNestedClassExpression(ManchesterOWLSyntaxParserImpl.java:1103)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseObjectRestriction(ManchesterOWLSyntaxParserImpl.java:756)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNonNaryClassExpression(ManchesterOWLSyntaxParserImpl.java:728)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseIntersection(ManchesterOWLSyntaxParserImpl.java:611)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseUnion(ManchesterOWLSyntaxParserImpl.java:634)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseClassExpression(ManchesterOWLSyntaxParserImpl.java:593)
    at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxClassExpressionParser.parse(ManchesterOWLSyntaxClassExpressionParser.java:61)
    at org.monarchinitiative.dosdp.ExpandedDOSDP.$anonfun$expressionFor$1(ExpandedDOSDP.scala:81)
    at scala.Option.map(Option.scala:230)
    at org.monarchinitiative.dosdp.ExpandedDOSDP.expressionFor(ExpandedDOSDP.scala:81)
    at org.monarchinitiative.dosdp.ExpandedDOSDP.$anonfun$equivalentToExpression$1(ExpandedDOSDP.scala:30)
    at scala.Option.flatMap(Option.scala:271)
    at org.monarchinitiative.dosdp.ExpandedDOSDP.equivalentToExpression(ExpandedDOSDP.scala:29)
    at org.monarchinitiative.dosdp.ExpandedDOSDP.filledLogicalAxioms(ExpandedDOSDP.scala:69)
    at org.monarchinitiative.dosdp.cli.Generate$.$anonfun$renderPattern$5(Generate.scala:135)
    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.generic.Growable.$plus$plus$eq(Growable.scala:62)
    at scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
    at scala.collection.mutable.SetBuilder.$plus$plus$eq(SetBuilder.scala:24)
    at scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
    at scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
    at scala.collection.AbstractIterator.to(Iterator.scala:1429)
    at scala.collection.TraversableOnce.toSet(TraversableOnce.scala:309)
    at scala.collection.TraversableOnce.toSet$(TraversableOnce.scala:309)
    at scala.collection.AbstractIterator.toSet(Iterator.scala:1429)
    at org.monarchinitiative.dosdp.cli.Generate$.renderPattern(Generate.scala:82)
    at org.monarchinitiative.dosdp.cli.Generate$.renderPattern(Generate.scala:73)
    at org.monarchinitiative.dosdp.cli.Prototype$.$anonfun$axiomsFor$1(Prototype.scala:42)
    at scala.Option.map(Option.scala:230)
    at org.monarchinitiative.dosdp.cli.Prototype$.axiomsFor(Prototype.scala:36)
    at org.monarchinitiative.dosdp.cli.Prototype$.$anonfun$run$5(Prototype.scala:28)
    at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:245)
    at scala.collection.immutable.Set$Set2.foreach(Set.scala:132)
    at scala.collection.TraversableLike.flatMap(TraversableLike.scala:245)
    at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:242)
    at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
    at org.monarchinitiative.dosdp.cli.Prototype$.run(Prototype.scala:27)
    at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1(Main.scala:10)
    at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1$adapted(Main.scala:10)
    at scala.Option.foreach(Option.scala:407)
    at org.monarchinitiative.dosdp.cli.Main$.delayedEndpoint$org$monarchinitiative$dosdp$cli$Main$1(Main.scala:10)
    at org.monarchinitiative.dosdp.cli.Main$delayedInit$body.apply(Main.scala:6)
    at scala.Function0.apply$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$(App.scala:78)
    at org.monarchinitiative.dosdp.cli.Main$.main(Main.scala:6)
    at org.monarchinitiative.dosdp.cli.Main.main(Main.scala)
Makefile:485: recipe for target '../patterns/pattern.owl' failed
balhoff commented 4 years ago

It looks like you're running prototype, right? Can you send me the pattern?

matentzn commented 4 years ago

you can checkout upheno and replicate the src/ontology/Makefile command for pattern_ontology; that is the command I ran! :)