Package org.obolibrary.robot

Class RepairOperation

java.lang.Object

org.obolibrary.robot.RepairOperation

public class RepairOperation
extends Object

Repair an ontology

Constructor Summary

Constructors

Constructor	Description
RepairOperation()

Method Summary

Modifier and Type	Method	Description
static Map<String,String>	getDefaultOptions()	Return a map from option name to default option value, for all the available repair options.
static void	mergeAxiomAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology)	Given an ontology, merge the annotations of duplicate axioms to create one axiom with all annotations.
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper)	Repairs ontology
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, boolean mergeAxiomAnnotations)	Repairs ontology
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, boolean mergeAxiomAnnotations, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)	Repairs ontology
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options)	Repairs ontology
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options, boolean mergeAxiomAnnotations)	Repairs ontology
static void	repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options, boolean mergeAxiomAnnotations, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)	Repairs ontology
static void	repairInvalidReferences(IOHelper iohelper, org.semanticweb.owlapi.model.OWLOntology ontology, Set<InvalidReferenceViolation> violations)	Repairs invalid references
static void	repairInvalidReferences(IOHelper iohelper, org.semanticweb.owlapi.model.OWLOntology ontology, Set<InvalidReferenceViolation> violations, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)	Repairs invalid references

Methods inherited from class java.lang.Object

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

Constructor Detail

RepairOperation

public RepairOperation()

Method Detail

getDefaultOptions

public static Map<String,String> getDefaultOptions()

Return a map from option name to default option value, for all the available repair options.

Returns:

a map with default values for all available options

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          boolean mergeAxiomAnnotations)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

mergeAxiomAnnotations - if true, merge annotations on duplicate axioms

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          boolean mergeAxiomAnnotations,
                          Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

mergeAxiomAnnotations - if true, merge annotations on duplicate axioms

migrateAnnotations - set of annotation properties for which to migrate values

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          Map<String,String> options)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

options - map of repair options

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          Map<String,String> options,
                          boolean mergeAxiomAnnotations)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

options - map of repair options

mergeAxiomAnnotations - if true, merge annotations on duplicate axioms

repair

public static void repair(org.semanticweb.owlapi.model.OWLOntology ontology,
                          IOHelper ioHelper,
                          Map<String,String> options,
                          boolean mergeAxiomAnnotations,
                          Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)

Repairs ontology

Parameters:

ontology - the OWLOntology to repair

ioHelper - IOHelper to work with the ontology

options - map of repair options

mergeAxiomAnnotations - if true, merge annotations on duplicate axioms

migrateAnnotations - set of annotation properties for which to migrate values

mergeAxiomAnnotations

public static void mergeAxiomAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology)

Given an ontology, merge the annotations of duplicate axioms to create one axiom with all annotations.

Parameters:

ontology - the OWLOntology to repair

repairInvalidReferences

public static void repairInvalidReferences(IOHelper iohelper,
                                           org.semanticweb.owlapi.model.OWLOntology ontology,
                                           Set<InvalidReferenceViolation> violations)

Repairs invalid references

Currently only able to repair references to deprecated classes.

Assumes OBO vocabulary

Parameters:

iohelper - IOHelper to work with the ontology

ontology - the OWLOntology to repair

violations - set of references violations

repairInvalidReferences

public static void repairInvalidReferences(IOHelper iohelper,
                                           org.semanticweb.owlapi.model.OWLOntology ontology,
                                           Set<InvalidReferenceViolation> violations,
                                           Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)

Repairs invalid references

Currently only able to repair references to deprecated classes.

Assumes OBO vocabulary

Parameters:

iohelper - IOHelper to work with the ontology

ontology - the OWLOntology to repair

violations - set of references violations

migrateAnnotations - set of annotation properties for which to migrate values