INCATools / INCATools/dosdp-tools
Unclear manchester syntax error reporting
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- Dominant language
- Scala
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- 33
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Description
```
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
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the command using examples/obi/X_X_information_content_entity_is_about_X.yaml and examples/obi/_input.ttl. Start with expressionFor in ExpandedDOSDP.scala and trace the error through SPARQL.scala and cli/Query.scala; done means the Manchester syntax failure identifies the problematic generated expression or declared label clearly.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- scala
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100