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Cyclic imports and missing declarations cause parsing error #798

Open daltontc opened 5 years ago

daltontc commented 5 years ago

If I have 2 ontologies that import each other and one of them has AnnotationAxioms, the ontology with AnnotationAxioms will not resolve properly due to how the ontologies are compared for equivalency. The first time an ontology is evaluated to see if it is equivalent, the object used is without the AnnotationAxioms. After it passes and is renamed, it is added to the list of ontologies in the closure. Then, after the fact, the AnnotationAxioms are added back into that ontology in the list. When the ontology is evaluated again later, it fails because the ontologies aren't equal because the object passed in doesn't have AnnotationAxiom whilst the one in the list of ontologies does.

Is this the intended design? Not processing AnnotationAxioms in the config is not an option for me either.

ignazio1977 commented 5 years ago

Do you have an example to share? There are recent bug fixes in the area which have not been released yet.

daltontc commented 5 years ago

ImportsHasAnnotationAxiom.txt HasAnnotationAxiom.txt

Github wouldn't let me upload .ttl files so I changed the extension to.txt.

When I try to process HasAnnotationAxiom with a config of private final OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);, I get a stacktrace of:


Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI(<https://mobi.com/ontologies/10/2018/HasAnnotationAxiom>) VersionIRI(<null>))
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:734) ~[?:?]
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:593) ~[?:?]
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actuallyApply(OWLOntologyManagerImpl.java:641) ~[?:?]
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChangesAndGetDetails(OWLOntologyManagerImpl.java:610) ~[?:?]
    at org.semanticweb.owlapi.model.HasApplyChanges.applyChanges(HasApplyChanges.java:37) ~[?:?]
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:689) ~[?:?]
    at org.semanticweb.owlapi.model.OWLOntology.applyChange(OWLOntology.java:92) ~[?:?]
    at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.applyChange(ConcurrentOWLOntologyImpl.java:2489) ~[?:?]
    at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.chooseAndSetOntologyIRI(OWLRDFConsumer.java:1491) ~[?:?]
    at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1409) ~[?:?]
    at org.semanticweb.owlapi.rio.RioOWLRDFConsumerAdapter.endRDF(RioOWLRDFConsumerAdapter.java:80) ~[?:?]
    at org.semanticweb.owlapi.rio.RioParserImpl$RioParserRDFHandler.endRDF(RioParserImpl.java:278) ~[?:?]
    at org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:123) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntology.createOntologyFromSesameModel(SimpleOntology.java:303) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntology.<init>(SimpleOntology.java:207) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.createOntology(SimpleOntologyManager.java:213) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.createOntologyFromCommit(SimpleOntologyManager.java:518) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.getOntology(SimpleOntologyManager.java:498) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.lambda$retrieveOntology$1(SimpleOntologyManager.java:281) ~[?:?]
    at java.util.Optional.flatMap(Optional.java:241) ~[?:?]
    at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.retrieveOntology(SimpleOntologyManager.java:281) ~[?:?]
    at com.mobi.ontology.rest.impl.OntologyRestImpl.getOntology(OntologyRestImpl.java:1152) ~[?:?]
    at com.mobi.ontology.rest.impl.OntologyRestImpl.getOntology(OntologyRestImpl.java:227) ~[?:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]```
ignazio1977 commented 5 years ago

788 exhibited a similar stack trace and #791 fixed issues related to the order in which ontology annotations are parsed. With the latest version5 code, I do not get the exception any more, so I assume these bug fixes sorted this issue as well.

The fix will be included in 5.1.8 once it is released.

daltontc commented 5 years ago

bao_core.owl.txt bao_complete.owl.txt

This issue is still happening with the circular dependency between bao_core and bao_complete from Bioassay

daltontc commented 5 years ago

I am using 5.1.9

daltontc commented 5 years ago

@ignazio1977 Can I use this issue still or should I create a new issue?

ignazio1977 commented 5 years ago

This one is fine

daltontc commented 5 years ago

Has there been any updates on this? Have you been able to replicate the issue with the provided ontologies?

ignazio1977 commented 5 years ago

I've tried to replicate this but failed again.

I've added some debug calls and, at the point where the stack trace above, the ontologies being compared have the same annotation axioms:

import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat;
import org.semanticweb.owlapi.io.IRIDocumentSource;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.util.VersionInfo;

public class bao {
public static void main(String[] args) throws OWLOntologyCreationException {
    System.out.println("bao.main() " + VersionInfo.getVersionInfo());
    OWLManager.createOWLOntologyManager()
        .loadOntologyFromOntologyDocument(new IRIDocumentSource(
            IRI.create("http://www.bioassayontology.org/bao/bao_core.owl"),
            new RDFXMLDocumentFormat(), null));
}
}

bao.main() The OWL API (version 5.1.10-SNAPSHOT)
HasAxiomsByType.equalAxioms() 
Ontology(OntologyID(Anonymous-2)) [Axioms: 876 Logical Axioms: 467] First 20 axioms: {...}
Ontology(OntologyID(OntologyIRI(<http://www.bioassayontology.org/bao/bao_core.owl>) VersionIRI(<http://www.bioassayontology.org/bao/bao_core.owl>))) [Axioms: 876 Logical Axioms: 467] First 20 axioms: {...}

Would you mind running the code above in your setup, just to confirm there is only one OWLAPI version in your path?

ignazio1977 commented 5 years ago

Looking at the stack trace line numbers, I believe your first error came from OWLAPI 5.1.7. I've tried running my code with that version, but still cannot replicate the problem.

At the bottom of the stack trace, the classes involved appear to use a Sesame model as source for the ontology. Maybe the translation causes the order in which triples are seen to be different, and that's what's triggering the exception. Can you share that code?

daltontc commented 5 years ago

The first error was from OWLAPI 5.1.7. The newer error with BAO is definitely 5.1.9. It looks like the error stems from the VersionIRI matching the OntologyIRI in bao_complete.owl.

Caused by: org.semanticweb.owlapi.model.OWLOntologyRenameException: Could not rename ontology. An ontology with this ID already exists: OntologyID(OntologyIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>) VersionIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>))
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.checkForOntologyIDChange(OWLOntologyManagerImpl.java:736) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.enactChangeApplication(OWLOntologyManagerImpl.java:595) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actuallyApply(OWLOntologyManagerImpl.java:643) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChangesAndGetDetails(OWLOntologyManagerImpl.java:612) ~[?:?]
        at org.semanticweb.owlapi.model.HasApplyChanges.applyChanges(HasApplyChanges.java:37) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.applyChange(OWLOntologyManagerImpl.java:691) ~[?:?]
        at org.semanticweb.owlapi.model.OWLOntology.applyChange(OWLOntology.java:92) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.lambda$applyChange$174(ConcurrentOWLOntologyImpl.java:1516) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.withWriteLock(ConcurrentOWLOntologyImpl.java:161) ~[?:?]
        at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.applyChange(ConcurrentOWLOntologyImpl.java:1516) ~[?:?]
        at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.chooseAndSetOntologyIRI(OWLRDFConsumer.java:1490) ~[?:?]
        at org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.endModel(OWLRDFConsumer.java:1406) ~[?:?]
        at org.semanticweb.owlapi.rio.RioOWLRDFConsumerAdapter.endRDF(RioOWLRDFConsumerAdapter.java:80) ~[?:?]
        at org.semanticweb.owlapi.rio.RioParserImpl$RioParserRDFHandler.endRDF(RioParserImpl.java:279) ~[?:?]
        at org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:123) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntology.createOntologyFromSesameModel(SimpleOntology.java:303) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntology.<init>(SimpleOntology.java:207) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.createOntology(SimpleOntologyManager.java:227) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.createOntologyFromCommit(SimpleOntologyManager.java:556) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.getOntology(SimpleOntologyManager.java:536) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.lambda$retrieveOntology$1(SimpleOntologyManager.java:297) ~[?:?]
        at java.util.Optional.flatMap(Optional.java:241) ~[?:?]
        at com.mobi.ontology.core.impl.owlapi.SimpleOntologyManager.retrieveOntology(SimpleOntologyManager.java:297) ~[?:?]
        at com.mobi.ontology.rest.impl.OntologyRestImpl.getOntology(OntologyRestImpl.java:1157) ~[?:?]
        at com.mobi.ontology.rest.impl.OntologyRestImpl.getOntology(OntologyRestImpl.java:228) ~[?:?]
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:?]
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:?]
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:?]
        at java.lang.reflect.Method.invoke(Method.java:498) ~[?:?]
        at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:315) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:297) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.internal.Errors.process(Errors.java:267) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:471) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:425) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:383) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:336) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:223) ~[15:com.eclipsesource.jaxrs.jersey-min:2.22.1]
        at com.eclipsesource.jaxrs.publisher.internal.ServletContainerBridge.service(ServletContainerBridge.java:76) ~[?:?]
        at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:841) ~[?:?]
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1650) ~[?:?]
        at org.eclipse.jetty.websocket.server.WebSocketUpgradeFilter.doFilter(WebSocketUpgradeFilter.java:206) ~[?:?]
        at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1637) ~[?:?]
        at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:533) ~[?:?]
        at org.ops4j.pax.web.service.jetty.internal.HttpServiceServletHandler.doHandle(HttpServiceServletHandler.java:71) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) ~[?:?]
        at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:548) ~[?:?]
        at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:190) ~[?:?]
        at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:1595) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.nextHandle(ScopedHandler.java:188) ~[?:?]
        at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1253) ~[?:?]
        at org.ops4j.pax.web.service.jetty.internal.HttpServiceContext.doHandle(HttpServiceContext.java:293) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:168) ~[?:?]
        at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:473) ~[?:?]
        at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1564) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.nextScope(ScopedHandler.java:166) ~[?:?]
        at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1155) ~[?:?]
        at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) ~[?:?]
        at org.ops4j.pax.web.service.jetty.internal.JettyServerHandlerCollection.handle(JettyServerHandlerCollection.java:80) ~[?:?]
        ... 17 more
daltontc commented 5 years ago 
First Pass
change = {SetOntologyID@15974} "SetOntologyID(OntologyID(OntologyIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>) VersionIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>)) OntologyID(OntologyID(Anonymous-108)))"
o = {ConcurrentOWLOntologyImpl@15957} "Ontology(OntologyID(Anonymous-108)) [Axioms: 11349 Logical Axioms: 364] First 20 axioms: {Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_33281>)) Declaration(Class(<http://purl.obolibrary.org/obo/GO_0030334>)) Declaration(Class(<http://purl.obolibrary.org/obo/GO_0000302>)) Declaration(Class(<http://purl.obolibrary.org/obo/GO_0016301>)) Declaration(Class(<http://purl.obolibrary.org/obo/CLO_0000001>)) Declaration(Class(<http://purl.obolibrary.org/obo/GO_0060964>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0003052>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0000862>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0002925>)) Declaration(Class(<http://purl.obolibrary.org/obo/GO_0001591>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0000916>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0001216>)) Declaration(Class(<http://www.bioassayontology.org/bao#BAO_0003075>)) Declaration(Class(<http://purl.obolibrar"… View

Second
change = {SetOntologyID@16112} "SetOntologyID(OntologyID(OntologyIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>) VersionIRI(<http://www.bioassayontology.org/bao/bao_complete.owl>)) OntologyID(OntologyID(Anonymous-82)))"
o = {ConcurrentOWLOntologyImpl@16110} "Ontology(OntologyID(Anonymous-82)) [Axioms: 11345 Logical Axioms: 364] First 20 axioms: {EquivalentClasses(<http://www.bioassayontology.org/bao#BAO_0000021> ObjectSomeValuesFrom(<http://www.bioassayontology.org/bao#BAO_0000135> <http://purl.obolibrary.org/obo/GO_0005764>) ) EquivalentClasses(<http://www.bioassayontology.org/bao#BAO_0003014> ObjectIntersectionOf(<http://www.bioassayontology.org/bao#BAO_0003006> ObjectSomeValuesFrom(<http://www.bioassayontology.org/bao#BAO_0000212> <http://www.bioassayontology.org/bao#BAO_0000151>) ObjectSomeValuesFrom(<http://www.bioassayontology.org/bao#BAO_0002009> ObjectUnionOf(<http://purl.obolibrary.org/obo/GO_0006355> <http://www.bioassayontology.org/bao#BAO_0002890>))) ) EquivalentClasses(<http://www.bioassayontology.org/bao#BAO_0002594> ObjectIntersectionOf(<http://www.bioassayontology.org/bao#BAO_0002593> ObjectSomeValuesFrom(<http://www.bioassayontology.org/bao#BAO_0000207> <http://www.bioassayontology.org/bao#BAO_0000045>) ObjectSomeValuesFro"… View

It seems like there are 4 axioms different when comparing ontologies?

daltontc commented 5 years ago

Sorry if I didn't communicate this well before. The issue is with http://www.bioassayontology.org/bao/bao_complete.owl. I ran the code you provided and that is fine, but when I switch the IRI to bao_complete, then the issue reveals itself.

I believe that bao_complete imports bao_core which imports bao_complete. The circular import is where the issue is.

ignazio1977 commented 5 years ago

The issue is with http://www.bioassayontology.org/bao/bao_complete.owl. I ran the code you provided and that is fine, but when I switch the IRI to bao_complete, then the issue reveals itself.

Thanks, that finally allowed me to replicate the failure. I'm also seeing another issue - I get random errors stating the XML is not well formed, always at different lines. This disappears if I open the connection, read all content into a local buffer and then parse from the buffer, making me wonder if the issue is related to timeouts happening while the parsing is ongoing.

ignazio1977 commented 5 years ago

Switching on logging at the error level, turns out there are four axioms that cannot be parsed properly on the first pass, this causes them to be parsed with #ErrorX IRIs - this ultimately causes the mismatch.

My guess at this point is that there are properties declared in the import closure but the circular dependency gets in the way of proper resolution.

2019-02-28 19:52:11:457 +0000 [main] ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? #Error1 for type Class
2019-02-28 19:52:11:485 +0000 [main] ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? #Error2 for type Class
2019-02-28 19:52:11:486 +0000 [main] ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? #Error3 for type Class
2019-02-28 19:52:11:488 +0000 [main] ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples in input? #Error4 for type Class
2019-02-28 19:52:18:926 +0000 [main] ERROR uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl - OWLOntologyManagerImpl.checkForOntologyIDChange() only in existing:[
EquivalentClasses(<bao#BAO_0000178> ObjectIntersectionOf(ObjectAllValuesFrom(<bao#BAO_0090004> <bao#BAO_0000015>) <#Error3>) )
EquivalentClasses(<bao#BAO_0002114> ObjectIntersectionOf(<#Error4> <bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0002668> <obo/UO_0000003>) ObjectAllValuesFrom(<bao#BAO_0002668> <obo/UO_0000003>)) ), 
EquivalentClasses(<bao#BAO_0000180> ObjectIntersectionOf(<#Error2> <bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0000183> <obo/UO_0000051>) ObjectAllValuesFrom(<bao#BAO_0000183> <obo/UO_0000051>)) ), 
EquivalentClasses(<bao#BAO_0000585> ObjectIntersectionOf(<#Error1> <bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0000097> <obo/UO_0000005>) ObjectAllValuesFrom(<bao#BAO_0000097> <obo/UO_0000005>)) ), 
]

2019-02-28 19:52:18:929 +0000 [main] ERROR uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl - OWLOntologyManagerImpl.checkForOntologyIDChange() only in new:[
EquivalentClasses(<bao#BAO_0000178> ObjectIntersectionOf(ObjectAllValuesFrom(<bao#BAO_0090004> <bao#BAO_0000015>) ObjectMinCardinality(1 <bao#BAO_0090004> <bao#BAO_0000015>)) ), 
EquivalentClasses(<bao#BAO_0000585> ObjectIntersectionOf(<bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0000097> <obo/UO_0000005>) ObjectAllValuesFrom(<bao#BAO_0000097> <obo/UO_0000005>) DataExactCardinality(1 <bao#BAO_0000109> xsd:float)) ), 
EquivalentClasses(<bao#BAO_0000180> ObjectIntersectionOf(<bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0000183> <obo/UO_0000051>) ObjectAllValuesFrom(<bao#BAO_0000183> <obo/UO_0000051>) DataExactCardinality(1 <bao#BAO_0002666> xsd:float)) ), 
EquivalentClasses(<bao#BAO_0002114> ObjectIntersectionOf(<bao#BAO_0000179> ObjectSomeValuesFrom(<bao#BAO_0002668> <obo/UO_0000003>) ObjectAllValuesFrom(<bao#BAO_0002668> <obo/UO_0000003>) DataExactCardinality(1 <bao#BAO_0002669> xsd:float)) )
]
ignazio1977 commented 5 years ago

It is difficult to design a general solution: with non cyclic imports, it is sufficient to parse the imported ontologies before the current ontology, recursively, to guarantee that all relevant declarations have been seen. But with a cyclic import, it is necessary to parse all ontologies to make sure all entity declarations have been seen, before all axioms can be successfully parsed. The current strategy fails because the declarations are in the ontologies standing between the two occurrences of bao_complete.owl. These ontologies have not been parsed yet when the second instance of bao_complete is parsed, so the entities declared only there are unknown - but become known when parsing the first occurrence, which is why the existing ontology has Error1, 2, 3, 4 and the new ontology does not.

It's a pretty big refactor of all the parsers to allow axiom parsing to be delayed until all ontologies have been parsed, so I'm not sure how long it is going to take to address.

In the meantime, a workaround would be to add the missing declarations to the ontology - duplicate declarations in the import closure do not cause errors, not until there are changes to be made, anyway. Another workaround would be to remove the cycle - is it correct for bao_core to import bao_complete? From the names, I'd think bao_core would be a subset of bao.

daltontc commented 5 years ago

Unfortunately I do not manage bao_complete.owl and someone wants to upload it into our tool. Would you perhaps be able to give a rough estimate how long the refactor would take?

ignazio1977 commented 5 years ago

Unfortunately I do not manage bao_complete.owl and someone wants to upload it into our tool.

If your tool works via the load*(IRI) methods, this fix will allow it to load the ontology correctly. I can't guess at how long it will take to do the complete fix.

ignazio1977 commented 5 years ago

This fix is in release 5.1.10, which should now be on maven central.

daltontc commented 5 years ago

We actually use the RioParser to parse a sesame model where this is breaking so I don't believe this fix will help us just yet :(

ignazio1977 commented 5 years ago

Uhm...

Loading any ontology included in the cycle yields the same imports closure, so what happens if instead of trying to upload bao_complete you try to upload bao_core? Bao_complete should be pulled in as an imports closure member, and saving the ontology by default adds missing declarations, so after the first load and save things might work all right.

Similarly, loading manually with code like mine and saving a local copy should create a corrected file, which could then be uploaded to your tool, or modified as needed.

giacomoronconiobda commented 1 year ago

I have the same problem with the Ontopia ontology.

ontopia.zip

I cannot understand how is it possible that the ontology is imported correctly in Protege. However it seems that the Ontology IRIs are parsed in a wrong way. 199458516-e5632946-cb7a-440f-a343-96c9872357b3

199522457-58b18b7f-0f35-44a4-a1e2-ff13e7c30ed9

vChavezB commented 10 months ago

I have the same problem with the Ontopia ontology.

ontopia.zip

I cannot understand how is it possible that the ontology is imported correctly in Protege. However it seems that the Ontology IRIs are parsed in a wrong way. 199458516-e5632946-cb7a-440f-a343-96c9872357b3

199522457-58b18b7f-0f35-44a4-a1e2-ff13e7c30ed9

I have made a PR to try to solve this. Please check https://github.com/owlcs/owlapi/pull/1117 and https://github.com/protegeproject/protege/issues/1181#issuecomment-1826466039

giacomoronconiobda commented 10 months ago

Thanks but actually I use the owlapi directly from java. I reimplemented the import mechanism by myself...

vChavezB commented 10 months ago

Thanks but actually I use the owlapi directly from java. I reimplemented the import mechanism by myself...

Ah ok. Yes the PR is actually to fix this in the owl api which in turn I use in protege.

Edit: Ok i just saw your PR https://github.com/owlcs/owlapi/pull/1060 Good to know!

Regards

vChavezB commented 3 months ago

issue should be solved, with https://github.com/owlcs/owlapi/commit/fff131933dfc8c7f932e14554eec6c53ceb68502