Deprecated API

Contents

• Fields
• Methods
• Constructors

Fields

Field	Description
org.obolibrary.robot.checks.Report.error
org.obolibrary.robot.checks.Report.info
org.obolibrary.robot.checks.Report.warn

Methods

Method	Description
org.obolibrary.robot.checks.Report.addViolations(String, String, List<Violation>)	violations should be added to their appropriate ReportQuery object
org.obolibrary.robot.checks.Report.toCSV()
org.obolibrary.robot.checks.Report.toTSV()
org.obolibrary.robot.checks.Violation.addStatement(String, String)	String properties are no longer recommended; create an OWLEntity for the property instead
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.DiffOperation.getAxiomStrings(OWLOntology)	This functionality is no longer used within DiffOperation.
org.obolibrary.robot.IOHelper.addPrefixesAndSave(OWLOntology, File, List<String>)	replaced by IOHelper.saveOntology(OWLOntology, OWLDocumentFormat, IRI, Map, boolean)
org.obolibrary.robot.IOHelper.createIRI(String, boolean)	replaced by IOHelper.createIRI(String)
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.MireotOperation.getDescendants(OWLOntology, Set<IRI>, Set<OWLAnnotationProperty>, boolean, Map<IRI, IRI>)	replaced by MireotOperation.getDescendants(OWLOntology, Set, Set, Map, Map)
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(Map<File, Tuple<ResultSetRewindable, OutputStream>>)	previously used as test method.
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.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.RelatedObjectsHelper.getAxioms(OWLOntology, Set<OWLObject>, Set<Class<? extends OWLAxiom>>, boolean, boolean)	replaced by RelatedObjectsHelper.filterAxiomsByAxiomType(Set, Set, Set, boolean, boolean)
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.TemplateHelper.getAnnotationProperty(QuotedEntityChecker, String)
org.obolibrary.robot.TemplateHelper.getCellContent(List<List<String>>, int, Integer)	TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateHelper.getEntity(QuotedEntityChecker, IRI, String, String)	TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateHelper.getIRIAnnotation(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.TemplateHelper.getStringAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.getStringAnnotations(QuotedEntityChecker, String, String, String)
org.obolibrary.robot.TemplateHelper.getTypedAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateHelper.processSplit(String, String, List<String>)	TemplateOperation replaced with Template class
org.obolibrary.robot.TemplateOperation.getAnnotationProperty(QuotedEntityChecker, String)
org.obolibrary.robot.TemplateOperation.getDatatype(QuotedEntityChecker, String)
org.obolibrary.robot.TemplateOperation.getEntity(QuotedEntityChecker, IRI, String, String)
org.obolibrary.robot.TemplateOperation.getIRIAnnotation(QuotedEntityChecker, String, IRI)
org.obolibrary.robot.TemplateOperation.getIRIs(Map<String, List<List<String>>>, IOHelper)
org.obolibrary.robot.TemplateOperation.getLanguageAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateOperation.getStringAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateOperation.getTypedAnnotation(QuotedEntityChecker, String, String)
org.obolibrary.robot.TemplateOperation.template(Map<String, List<List<String>>>)
org.obolibrary.robot.TemplateOperation.validateTemplateString(String)

Constructors

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