Package org.obolibrary.robot.checks

Class InvalidReferenceChecker

java.lang.Object

org.obolibrary.robot.checks.InvalidReferenceChecker

public class InvalidReferenceChecker
extends Object

Checks to determine if axioms contain invalid references: to dangling classes or deprecated classes.

This is a structural check. To determine the *logical* validity of an axiom reference, robot uses OWL reasoning.

See: https://github.com/ontodev/robot/issues/1

Author:

cjm

Constructor Summary

Constructors

Constructor	Description
InvalidReferenceChecker()

Method Summary

Modifier and Type	Method	Description
static Set<InvalidReferenceViolation>	checkImportModule(org.semanticweb.owlapi.model.OWLOntology importModule, org.semanticweb.owlapi.model.OWLOntology baseOntology)	Checks an import module.
static Set<InvalidReferenceViolation>	getInvalidReferenceViolations(org.semanticweb.owlapi.model.OWLOntology ontology, boolean ignoreDangling)
static Set<InvalidReferenceViolation>	getInvalidReferenceViolations(org.semanticweb.owlapi.model.OWLOntology ontology, Set<org.semanticweb.owlapi.model.OWLAxiom> axioms, boolean ignoreDangling)	Finds axioms that reference a deprecated or dangling entity.
static boolean	isDangling(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity)	Checks if entity is dangling.
static boolean	isDeprecated(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLEntity entity)	Checks if entity is deprecated.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

InvalidReferenceChecker

public InvalidReferenceChecker()

Method Detail

isDangling

public static boolean isDangling(org.semanticweb.owlapi.model.OWLOntology ontology,
                                 org.semanticweb.owlapi.model.OWLEntity entity)

Checks if entity is dangling.

Parameters:

ontology - the OWLOntology to check

entity - the OWLEntity to check

Returns:

true if owlClass has no logical or non-logical axioms

isDeprecated

public static boolean isDeprecated(org.semanticweb.owlapi.model.OWLOntology ontology,
                                   org.semanticweb.owlapi.model.OWLEntity entity)

Checks if entity is deprecated.

Parameters:

ontology - the OWLOntology to check

entity - the OWLEntity to check

Returns:

true if entity is deprecated

getInvalidReferenceViolations

public static Set<InvalidReferenceViolation> getInvalidReferenceViolations(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                           Set<org.semanticweb.owlapi.model.OWLAxiom> axioms,
                                                                           boolean ignoreDangling)

Finds axioms that reference a deprecated or dangling entity.

Declaration axioms that reference a deprecated class do not count.

Note that this does not count the value field of an annotation assertion, since these reference IRIs and not entities

Parameters:

ontology - the OWLOntology to check

axioms - set of OWLAxioms to check

ignoreDangling - if true, ignore dangling entities

Returns:

all violations

getInvalidReferenceViolations

public static Set<InvalidReferenceViolation> getInvalidReferenceViolations(org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                           boolean ignoreDangling)

Parameters:

ontology - the OWLOntology to check

ignoreDangling - boolean to ignore dangling classes

Returns:

all violations in ontology

checkImportModule

public static Set<InvalidReferenceViolation> checkImportModule(org.semanticweb.owlapi.model.OWLOntology importModule,
                                                               org.semanticweb.owlapi.model.OWLOntology baseOntology)

Checks an import module. If the base ontology refers to deprecated entities in the import module this constitutes a violation

Parameters:

importModule - the OWLOntology import to check

baseOntology - the base OWLOntology to check

Returns:

all deprecation-reference violations in baseOntology with respect to import module