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ontodev / robot

ROBOT is an OBO Tool
http://robot.obolibrary.org
BSD 3-Clause "New" or "Revised" License
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Impossible to convert from obographs .json #1081

Open riiswa opened 1 year ago

riiswa commented 1 year ago

With the latest robot.jar. I got this error when I try to convert a json file to owl (``robot convert -i abox.json -o test.owl -vvv ):

DEBUG Loading ontology abox.json with catalog file null
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
DEBUG Injecting object uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl@3f28bd56
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
DEBUG No files found for META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
DEBUG Injecting values [[]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setIRIMappers(java.util.Set).
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
DEBUG Injecting values [[org.semanticweb.owlapi.rio.RioNQuadsParserFactory@66629f63, org.semanticweb.owlapi.rio.RioTrigParserFactory@439a8f59, org.semanticweb.owlapi.owlxml.parser.OWLXMLParserFactory@26fb628, org.semanticweb.owlapi.rio.RioN3ParserFactory@47da3952, org.semanticweb.owlapi.rio.RioRDFXMLParserFactory@5c48c0c0, org.semanticweb.owlapi.rio.RioJsonLDParserFactory@5f3b9c57, org.semanticweb.owlapi.rio.RioRDFaParserFactory@6e521c1e, org.semanticweb.owlapi.rio.RioNTriplesParserFactory@1568159, org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParserFactory@52500920, org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParserFactory@6c67e137, org.semanticweb.owlapi.rio.RioTurtleParserFactory@71c5b236, org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory@1c98290c, org.semanticweb.owlapi.rio.RioTrixParserFactory@2f162cc0, org.semanticweb.owlapi.rio.RioJsonParserFactory@2484f433, org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParserFactory@4215838f, org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParserFactory@751d3241, org.semanticweb.owlapi.krss2.parser.KRSS2OWLParserFactory@611df6e3, org.semanticweb.owlapi.rio.RioBinaryRdfParserFactory@1d71006f]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyParsers(java.util.Set).
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
DEBUG Injecting values [[uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl@54361a9]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyFactories(java.util.Set).
DEBUG Loading file META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
DEBUG Loading URL for service jar:file:/usr/local/bin/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
DEBUG Injecting values [[org.semanticweb.owlapi.rdf.turtle.renderer.TurtleStorerFactory@7997b197, org.semanticweb.owlapi.rio.RioNQuadsStorerFactory@3bffddff, org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterSyntaxStorerFactory@6b5176f2, org.semanticweb.owlapi.oboformat.OBOFormatStorerFactory@4a067c25, org.semanticweb.owlapi.rio.RioBinaryRdfStorerFactory@a7e2d9d, org.semanticweb.owlapi.rio.RioTrigStorerFactory@114a85c2, org.semanticweb.owlapi.rdf.rdfxml.renderer.RDFXMLStorerFactory@2c177f9e, org.semanticweb.owlapi.owlxml.renderer.OWLXMLStorerFactory@f9b7332, org.semanticweb.owlapi.rio.RioNTriplesStorerFactory@142eef62, org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxHTMLStorerFactory@7bb3a9fe, org.semanticweb.owlapi.rio.RioJsonLDStorerFactory@7de0c6ae, org.semanticweb.owlapi.functional.renderer.FunctionalSyntaxStorerFactory@1bdf8190, org.semanticweb.owlapi.rio.RioN3StorerFactory@299266e2, org.semanticweb.owlapi.krss2.renderer.KRSS2OWLSyntaxStorerFactory@6e46d9f4, org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxStorerFactory@b91d8c4, org.semanticweb.owlapi.rio.RioTurtleStorerFactory@46074492, org.semanticweb.owlapi.rio.RioJsonStorerFactory@5dcbb60, org.semanticweb.owlapi.rio.RioTrixStorerFactory@37eeec90, org.semanticweb.owlapi.latex.renderer.LatexStorerFactory@1922e6d, org.semanticweb.owlapi.rio.RioRDFXMLStorerFactory@35d6ca49]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyStorers(java.util.Set).
DEBUG Converting from JSON to RDF
DEBUG Add location: LocatorFile
DEBUG Add location: ClassLoaderLocator
DEBUG Failed to find configuration: file:location-mapping.rdf;file:location-mapping.n3;file:location-mapping.ttl;file:etc/location-mapping.rdf;file:etc/location-mapping.n3;file:etc/location-mapping.ttl
DEBUG Add location: LocatorFile
DEBUG Add location: LocatorURL
DEBUG Add location: ClassLoaderLocator
DEBUG Failed to find configuration: location-mapping.ttl;location-mapping.rdf;etc/location-mapping.rdf;etc/location-mapping.ttl
DEBUG System architecture: 64 bit
ERROR [line: 1, col: 1 ] document doesn't start with a valid json element : null
DEBUG Missing exception ID: org.apache.jena.riot.RiotException: [line: 1, col: 1 ] document doesn't start with a valid json element : null
org.apache.jena.riot.RiotException: [line: 1, col: 1 ] document doesn't start with a valid json element : null
java.lang.IllegalArgumentException: org.apache.jena.riot.RiotException: [line: 1, col: 1 ] document doesn't start with a valid json element : null
    at org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
    at org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:539)
    at org.obolibrary.robot.ConvertCommand.execute(ConvertCommand.java:130)
    at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:244)
    at org.obolibrary.robot.CommandManager.execute(CommandManager.java:188)
    at org.obolibrary.robot.CommandManager.main(CommandManager.java:135)
    at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:61)
Caused by: org.apache.jena.riot.RiotException: [line: 1, col: 1 ] document doesn't start with a valid json element : null
    at org.apache.jena.riot.system.ErrorHandlerFactory$ErrorHandlerStd.error(ErrorHandlerFactory.java:146)
    at org.apache.jena.riot.lang.JsonLDReader.read(JsonLDReader.java:124)
    at org.apache.jena.riot.RDFParser.read(RDFParser.java:353)
    at org.apache.jena.riot.RDFParser.parseNotUri(RDFParser.java:343)
    at org.apache.jena.riot.RDFParser.parse(RDFParser.java:292)
    at org.apache.jena.riot.RDFParserBuilder.parse(RDFParserBuilder.java:540)
    at org.apache.jena.riot.RDFDataMgr.parseFromInputStream(RDFDataMgr.java:901)
    at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:299)
    at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:285)
    at org.apache.jena.riot.adapters.RDFReaderRIOT.read(RDFReaderRIOT.java:69)
    at org.apache.jena.rdf.model.impl.ModelCom.read(ModelCom.java:283)
    at org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:403)
    at org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:306)
    at org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:483)
    at org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:581)
    ... 6 more

I also tested with .json file that are in the obographs example/.

jamesaoverton commented 1 year ago

Thanks for the report. Could you please provide or point to a specific JSON file, so that I can try to reproduce the problem?

riiswa commented 1 year ago

I tried with this file: https://github.com/geneontology/obographs/blob/master/examples/basic.json

jamesaoverton commented 1 year ago

Ok thanks. I can reproduce the error with that file.

There are two problems here:

  1. The fundamental problem is that the Java implementation of obographs used by ROBOT does not convert obographs JSON to OWL, according to https://github.com/geneontology/obographs/issues/87. I'm not an expert on obographs, so I could be mistaken. That issue links to a Python implementation that might do what you need.

  2. While ROBOT can output obographs JSON, it is expecting to read JSON-LD. The error message is from the Jena library complaining that the obographs JSON input is not valid JSON-LD. The input handling code is here: https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/IOHelper.java#L380

I had forgotten this, and the documentation doesn't make this clear. I will add "fix the convert documentation" to my To Do list.