Deprecated API

Contents

• Deprecated Methods
• Deprecated Constructors

Deprecated Methods

Method and Description
org.obolibrary.robot.DiffOperation.addLabels(IOHelper, Map<IRI, String>, String) This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
org.obolibrary.robot.DiffOperation.addLabels(Map<IRI, String>, String) This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
org.obolibrary.robot.IOHelper.addPrefixesAndSave(OWLOntology, File, List<String>) replaced by IOHelper.saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map, boolean)
org.obolibrary.robot.QueryOperation.convertModel(Model) Use QueryOperation.convertModel(Model, IOHelper, String)
org.obolibrary.robot.QueryOperation.execConstruct(DatasetGraph, String) use QueryOperation.execConstruct(Dataset, String) instead.
org.obolibrary.robot.QueryOperation.execQuery(DatasetGraph, String) use QueryOperation.execQuery(Dataset, String) instead.
org.obolibrary.robot.QueryOperation.execVerify(DatasetGraph, String, String) use QueryOperation.execVerify(Dataset, String, String) instead
org.obolibrary.robot.QueryOperation.execVerify(Map<File, Tuple<ResultSetRewindable, OutputStream>>) previously used as test method.
org.obolibrary.robot.MireotOperation.getAncestors(OWLOntology, Set<IRI>, Set<IRI>, Set<OWLAnnotationProperty>, boolean, Map<IRI, IRI>) replaced by MireotOperation.getAncestors(OWLOntology, Set, Set, Set)
org.obolibrary.robot.TemplateHelper.getAnnotation(QuotedEntityChecker, IOHelper, String, String)
org.obolibrary.robot.TemplateHelper.getAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getAnnotation(String, QuotedEntityChecker, IOHelper, String, String)
org.obolibrary.robot.TemplateHelper.getAnnotationAxioms(OWLEntity, Set<OWLAnnotation>, Map<OWLAnnotation, Map<OWLAnnotation, Set<OWLAnnotation>>>) TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateHelper.getAnnotationProperties(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateOperation.getAnnotationProperty(QuotedEntityChecker, String)
org.obolibrary.robot.TemplateHelper.getAnnotationProperty(QuotedEntityChecker, String)
org.obolibrary.robot.RelatedObjectsHelper.getAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean, boolean) replaced by RelatedObjectsHelper.filterAxiomsByAxiomType(Set, Set, Set, boolean, boolean)
org.obolibrary.robot.DiffOperation.getAxiomStrings(OWLOntology) This functionality is no longer used within DiffOperation.
org.obolibrary.robot.TemplateHelper.getCellContent(List<List<String>>, int, Integer) TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateOperation.getDatatype(QuotedEntityChecker, String)
org.obolibrary.robot.MireotOperation.getDescendants(OWLOntology, Set<IRI>, Set<OWLAnnotationProperty>, boolean, Map<IRI, IRI>) replaced by MireotOperation.getDescendants(OWLOntology, Set, Set, Map, Map)
org.obolibrary.robot.TemplateOperation.getEntity(QuotedEntityChecker, IRI, String, String)
org.obolibrary.robot.TemplateHelper.getEntity(QuotedEntityChecker, IRI, String, String) TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateOperation.getIRIAnnotation(QuotedEntityChecker, String, IRI)
org.obolibrary.robot.TemplateHelper.getIRIAnnotation(QuotedEntityChecker, String, IRI)
org.obolibrary.robot.TemplateHelper.getIRIAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.checks.Report.getIRIs()
org.obolibrary.robot.TemplateOperation.getIRIs(Map<String, List<List<String>>>, IOHelper)
org.obolibrary.robot.checks.Report.getIRIs(Map<String, List<Violation>>)
org.obolibrary.robot.TemplateOperation.getIRIs(String, List<List<String>>, IOHelper)
org.obolibrary.robot.TemplateOperation.getLanguageAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getLanguageAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getLanguageAnnotations(QuotedEntityChecker, String, String, String)
org.obolibrary.robot.TemplateHelper.getLogicalAxioms(OWLClass, String, Set<OWLClassExpression>, Map<OWLClassExpression, Set<OWLAnnotation>>) TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateOperation.getStringAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getStringAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getStringAnnotations(QuotedEntityChecker, String, String, String)
org.obolibrary.robot.TemplateOperation.getTypedAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getTypedAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.QueryOperation.loadOntology(OWLOntology) use QueryOperation.loadOntologyAsDataset(OWLOntology) instead.
org.obolibrary.robot.QueryOperation.loadTriplesAsDataset(String, String) moved to IOHelper.loadToTDBDataset(String, String)
org.obolibrary.robot.TemplateHelper.processSplit(String, String, List<String>) TemplateOperation replaced with Template class
org.obolibrary.robot.QueryOperation.runQuery(DatasetGraph, String, File, Lang) use QueryOperation.runQuery(Dataset, String, File, Lang) instead.
org.obolibrary.robot.QueryOperation.runSparqlQuery(DatasetGraph, String, String, OutputStream) use QueryOperation.runSparqlQuery(Dataset, String, String, OutputStream) instead.
org.obolibrary.robot.QueryOperation.runVerify(DatasetGraph, String, String, Path, Lang) use QueryOperation.runVerify(Dataset, String, String, Path, Lang) instead.
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>)
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>, OWLOntology)
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>, OWLOntology, IOHelper)
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>, OWLOntology, QuotedEntityChecker)
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>, OWLOntology, QuotedEntityChecker, IOHelper)
org.obolibrary.robot.checks.Report.toCSV()
org.obolibrary.robot.checks.Report.toTSV()
org.obolibrary.robot.TemplateOperation.validateTemplateString(String)

Deprecated Constructors

Constructor and Description
org.obolibrary.robot.checks.Report(OWLOntology) Report will not do anything with the ontology when not using labels. Use either Report.Report() or Report.Report(OWLOntology, boolean) or Report.Report(OWLOntology, IOHelper, boolean).
org.obolibrary.robot.checks.Report(OWLOntology, IOHelper) Report will not do anything with the ontology when not using labels. Use either Report.Report(OWLOntology, boolean) or Report.Report(OWLOntology, IOHelper, boolean).