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Unclear manchester syntax error reporting #140

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cmungall opened this issue Jun 24, 2019 · 0 comments
Open

Unclear manchester syntax error reporting #140

cmungall opened this issue Jun 24, 2019 · 0 comments

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@cmungall
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pattern_name: X X information content entity is about X
pattern_iri: http://purl.obolibrary.org/obo/obi/X_X_information_content_entity_is_about_X

description: >-
  This is auto-generated. Add your description here

  Examples: [biological activity assay measuring epitope specific granzyme A release by T cells](http://purl.obolibrary.org/obo/OBI_0001809), [biological activity assay measuring epitope specific perforin release by T cells](http://purl.obolibrary.org/obo/OBI_0001497), [biological activity assay measuring epitope specific granulysin release by T cells](http://purl.obolibrary.org/obo/OBI_0001810) (71 total)

classes: 
  information content entity: "http://purl.obolibrary.org/obo/IAO_0000030"
  immune epitope assay: "http://purl.obolibrary.org/obo/OBI_1110128"


relations: 
  is about: "http://purl.obolibrary.org/obo/IAO_0000136"


vars:
  v0: "'immune epitope assay'"
  v1: "'has_specified_output'"
  v2: "'biological_process'"

name:
  # Could not induce name, using default
  text: "%s %s information content entity is about %s"
  vars:
    - v0
    - v1
    - v2

def:
  # Could not induce def, using default
  text: "Any %s that %s a Any information content entity that is about a %s"
  vars:
    - v0
    - v1
    - v2

annotationProperties:
  exact_synonym: "oio:hasExactSynonym"
  related_synonym: "oio:hasRelatedSynonym"

# could not infer annotations


equivalentTo:
  text: "%s and (%s some 'information content entity' and ('is about' some %s))"
  vars:
    - v0
    - v1
    - v2

when I run:

$ dosdp-tools query --obo-prefixes --template=examples/obi/X_X_information_content_entity_is_about_X.yaml --ontology=examples/obi/_input.ttl --outfile=examples/obi/X_X_information_content_entity_is_about_X.tsv

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/cjm/repos/dosdp-scala/target/universal/stage/lib/ch.qos.logback.logback-classic-1.2.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/cjm/repos/dosdp-scala/target/universal/stage/lib/org.slf4j.slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
Encountered some at line 1 column 18. Expected one of:
        or
        and
        )

Exception in thread "main" org.semanticweb.owlapi.manchestersyntax.renderer.ParserException: Encountered some at line 1 column 18. Expected one of:
        or
        and
        )

        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl$ExceptionBuilder.build(ManchesterOWLSyntaxParserImpl.java:2521)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNestedClassExpression(ManchesterOWLSyntaxParserImpl.java:1078)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseNonNaryClassExpression(ManchesterOWLSyntaxParserImpl.java:706)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseIntersection(ManchesterOWLSyntaxParserImpl.java:606)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseUnion(ManchesterOWLSyntaxParserImpl.java:629)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseClassExpression(ManchesterOWLSyntaxParserImpl.java:588)
        at org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxClassExpressionParser.parse(ManchesterOWLSyntaxClassExpressionParser.java:61)
        at org.monarchinitiative.dosdp.ExpandedDOSDP.expressionFor(ExpandedDOSDP.scala:76)
        at org.monarchinitiative.dosdp.ExpandedDOSDP.$anonfun$equivalentToExpression$1(ExpandedDOSDP.scala:35)
        at scala.Option.map(Option.scala:146)
        at org.monarchinitiative.dosdp.ExpandedDOSDP.equivalentToExpression(ExpandedDOSDP.scala:35)
        at org.monarchinitiative.dosdp.ExpandedDOSDP.filledLogicalAxioms(ExpandedDOSDP.scala:64)
        at org.monarchinitiative.dosdp.SPARQL$.axiomVariables(SPARQL.scala:48)
        at org.monarchinitiative.dosdp.SPARQL$.selectFor(SPARQL.scala:41)
        at org.monarchinitiative.dosdp.SPARQL$.queryFor(SPARQL.scala:32)
        at org.monarchinitiative.dosdp.cli.Query$.run(Query.scala:27)
        at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1(Main.scala:33)
        at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1$adapted(Main.scala:33)
        at scala.Option.foreach(Option.scala:257)
        at org.monarchinitiative.dosdp.cli.Main$.delayedEndpoint$org$monarchinitiative$dosdp$cli$Main$1(Main.scala:33)
        at org.monarchinitiative.dosdp.cli.Main$delayedInit$body.apply(Main.scala:29)
        at scala.Function0.apply$mcV$sp(Function0.scala:34)
        at scala.Function0.apply$mcV$sp$(Function0.scala:34)
        at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
        at scala.App.$anonfun$main$1$adapted(App.scala:76)
        at scala.collection.immutable.List.foreach(List.scala:389)
        at scala.App.main(App.scala:76)
        at scala.App.main$(App.scala:74)
        at org.monarchinitiative.dosdp.cli.Main$.main(Main.scala:29)
        at org.monarchinitiative.dosdp.cli.Main.main(Main.scala)

I am guessing that line 1 col 18 is the line in the class expression, but this is a declared label so it's not clear what the problem is

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