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Impossible to create properties with a characteristic set to '' #716

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bjonnh opened this issue Jul 31, 2020 · 1 comment · Fixed by #719
Closed

Impossible to create properties with a characteristic set to '' #716

bjonnh opened this issue Jul 31, 2020 · 1 comment · Fixed by #719
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@beckyjackson

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@bjonnh
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bjonnh commented Jul 31, 2020

**Robot version ** 1.7.0

** Problem ** When trying to create properties from a template, I get a index out of bound error
It seems to work without the CHARACTERISTIC column. When playing around I had another error message that said that the characteristic '' was not valid, but I couldn't find how I got that one.

It works if they are both set to transitive, so it seems that the empty characteristic should be handled?

** Source file **

id,type,Label,comment,characteristic
ID,TYPE,A rdfs:label,A rdfs:comment,CHARACTERISTIC SPLIT=|
nav:x,owl:ObjectProperty,x,x,
nav:y,owl:ObjectProperty,y,y,transitive

**Output with -vvv **

        --ontology-iri "https://onto.nprod.net/nav.owl" \
        --prefix "ero:http://purl.obolibrary.org/obo/ERO_" --prefix "nav:https://onto.nprod.net/NAV_" \
        --output tables/current/properties.owl
2020-07-31 17:24:33,903 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
2020-07-31 17:24:33,905 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
2020-07-31 17:24:33,906 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
2020-07-31 17:24:33,906 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyManager
2020-07-31 17:24:33,943 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
2020-07-31 17:24:33,944 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
2020-07-31 17:24:33,944 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
2020-07-31 17:24:33,945 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLDataFactory
2020-07-31 17:24:34,278 DEBUG org.semanticweb.owlapi.utilities.Injector - Injecting object uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl@544820b7
2020-07-31 17:24:34,293 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
2020-07-31 17:24:34,294 DEBUG org.semanticweb.owlapi.utilities.Injector - No files found for META-INF/services/org.semanticweb.owlapi.model.OWLOntologyIRIMapper
2020-07-31 17:24:34,297 DEBUG org.semanticweb.owlapi.utilities.Injector - Injecting values [[]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setIRIMappers(java.util.Set).
2020-07-31 17:24:34,299 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
2020-07-31 17:24:34,300 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
2020-07-31 17:24:34,300 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
2020-07-31 17:24:34,300 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLOntologyFactory
2020-07-31 17:24:34,305 DEBUG org.semanticweb.owlapi.utilities.Injector - Injecting values [[uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl@b7838a9]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyFactories(java.util.Set).
2020-07-31 17:24:34,306 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
2020-07-31 17:24:34,307 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
2020-07-31 17:24:34,307 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
2020-07-31 17:24:34,307 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.io.OWLParserFactory
2020-07-31 17:24:34,336 DEBUG org.semanticweb.owlapi.utilities.Injector - Injecting values [[org.semanticweb.owlapi.rio.RioTrigParserFactory@3a3e4aff, org.semanticweb.owlapi.rio.RioJsonLDParserFactory@1522d8a0, org.semanticweb.owlapi.rio.RioRDFaParserFactory@1c6804cd, org.semanticweb.owlapi.krss2.parser.KRSS2OWLParserFactory@58fe0499, org.semanticweb.owlapi.rio.RioTrixParserFactory@7e22550a, org.semanticweb.owlapi.rio.RioNQuadsParserFactory@b6b1987, org.semanticweb.owlapi.rio.RioN3ParserFactory@774698ab, org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParserFactory@1cbf6e72, org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParserFactory@6035b93b, org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParserFactory@5c00384f, org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParserFactory@62163b39, org.semanticweb.owlapi.rio.RioRDFXMLParserFactory@39ad977d, org.semanticweb.owlapi.rio.RioBinaryRdfParserFactory@4bc28c33, org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParserFactory@674658f7, org.semanticweb.owlapi.rio.RioNTriplesParserFactory@698122b2, org.semanticweb.owlapi.rio.RioTurtleParserFactory@7516e4e5, org.semanticweb.owlapi.owlxml.parser.OWLXMLParserFactory@fb9c7aa, org.semanticweb.owlapi.rio.RioJsonParserFactory@6bea52d4]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyParsers(java.util.Set).
2020-07-31 17:24:34,337 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading file META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
2020-07-31 17:24:34,338 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
2020-07-31 17:24:34,338 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
2020-07-31 17:24:34,338 DEBUG org.semanticweb.owlapi.utilities.Injector - Loading URL for service jar:file:XXX/2020-newnavigator/local/robot.jar!/META-INF/services/org.semanticweb.owlapi.model.OWLStorerFactory
2020-07-31 17:24:34,350 DEBUG org.semanticweb.owlapi.utilities.Injector - Injecting values [[org.semanticweb.owlapi.rio.RioTrigStorerFactory@19ae6bb, org.semanticweb.owlapi.rio.RioNQuadsStorerFactory@42f48531, org.semanticweb.owlapi.rio.RioRDFXMLStorerFactory@505a9d7c, org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxHTMLStorerFactory@4fbda97b, org.semanticweb.owlapi.oboformat.OBOFormatStorerFactory@1080b026, org.semanticweb.owlapi.rio.RioTrixStorerFactory@72cf2de5, org.semanticweb.owlapi.owlxml.renderer.OWLXMLStorerFactory@75d0911a, org.semanticweb.owlapi.rio.RioNTriplesStorerFactory@1f2f9244, org.semanticweb.owlapi.krss2.renderer.KRSS2OWLSyntaxStorerFactory@7c2b6087, org.semanticweb.owlapi.manchestersyntax.renderer.ManchesterSyntaxStorerFactory@4b672daa, org.semanticweb.owlapi.rio.RioBinaryRdfStorerFactory@25e2a451, org.semanticweb.owlapi.functional.renderer.FunctionalSyntaxStorerFactory@22b53226, org.semanticweb.owlapi.rio.RioJsonLDStorerFactory@201b6b6f, org.semanticweb.owlapi.latex.renderer.LatexStorerFactory@27305e6, org.semanticweb.owlapi.rdf.rdfxml.renderer.RDFXMLStorerFactory@422c3c7a, org.semanticweb.owlapi.rio.RioTurtleStorerFactory@45c8d09f, org.semanticweb.owlapi.rio.RioJsonStorerFactory@3e5499cc, org.semanticweb.owlapi.rdf.turtle.renderer.TurtleStorerFactory@3b77a04f, org.semanticweb.owlapi.rio.RioN3StorerFactory@2a3c96e3, org.semanticweb.owlapi.dlsyntax.renderer.DLSyntaxStorerFactory@354fc8f0]] on method public void uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.setOntologyStorers(java.util.Set).
2020-07-31 17:24:34,388 DEBUG org.obolibrary.robot.ExceptionHelper - Missing exception ID: Index 4 out of bounds for length 4
Index 4 out of bounds for length 4
java.lang.IndexOutOfBoundsException: Index 4 out of bounds for length 4
        at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
        at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
        at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:248)
        at java.base/java.util.Objects.checkIndex(Objects.java:372)
        at java.base/java.util.ArrayList.get(ArrayList.java:459)
        at org.obolibrary.robot.Template.getCharacteristics(Template.java:2188)
        at org.obolibrary.robot.Template.addObjectPropertyAxioms(Template.java:1002)
        at org.obolibrary.robot.Template.processRow(Template.java:721)
        at org.obolibrary.robot.Template.generateOutputOntology(Template.java:361)
        at org.obolibrary.robot.TemplateOperation.template(TemplateOperation.java:181)
        at org.obolibrary.robot.TemplateCommand.execute(TemplateCommand.java:147)
        at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:248)
        at org.obolibrary.robot.CommandManager.execute(CommandManager.java:192)
        at org.obolibrary.robot.CommandManager.main(CommandManager.java:139)
        at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:59)
@bjonnh
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bjonnh commented Jul 31, 2020

If I put the CHARACTERISTICS SPLIT=| column before another column, then I get:

java.lang.Exception: template#UNKNOWN CHARACTERISTIC ERROR property 'NAV_x' has unknown characteristic '' at line 3, column 3 in table "tables/current/properties.csv".
        at org.obolibrary.robot.Template.addObjectPropertyAxioms(Template.java:1034)
        at org.obolibrary.robot.Template.processRow(Template.java:721)
        at org.obolibrary.robot.Template.generateOutputOntology(Template.java:361)
        at org.obolibrary.robot.TemplateOperation.template(TemplateOperation.java:181)
        at org.obolibrary.robot.TemplateCommand.execute(TemplateCommand.java:147)
        at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:248)
        at org.obolibrary.robot.CommandManager.execute(CommandManager.java:192)
        at org.obolibrary.robot.CommandManager.main(CommandManager.java:139)
        at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:59)

bjonnh added a commit to bjonnh/robot that referenced this issue Jul 31, 2020
@bjonnh
Solve issue ontodev#716: empty characteristics for properties
c89bcc2 
This handle the two cases raised by this issue:
- we need to allow empty characteristics
- in the case of characteristics being the last	column,
  the list of elements in the row is one element short
  when the characteristic is empty, handling that case
bjonnh added a commit to bjonnh/robot that referenced this issue Jul 31, 2020
@bjonnh
Solve issue ontodev#716: empty characteristics for properties
26fbf33 
This handle the two cases raised by this issue:
- we need to allow empty characteristics
- in the case of characteristics being the last	column,
  the list of elements in the row is one element short
  when the characteristic is empty, handling that case
@bjonnh bjonnh mentioned this issue Jul 31, 2020
Closed
1 task
@beckyjackson beckyjackson mentioned this issue Aug 3, 2020
Merged
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Handle empty property charactersitics ontodev/robot
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@bjonnh @beckyjackson