INCATools / INCATools/dosdp-tools

Unclear manchester syntax error reporting

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Dominant language
Scala
Stars
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Forks
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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

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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