Uses of Class
org.obolibrary.robot.IOHelper

Packages that use IOHelper

Package	Description
org.obolibrary.robot
org.obolibrary.robot.checks

Uses of IOHelper in org.obolibrary.robot

Methods in org.obolibrary.robot that return IOHelper

Modifier and Type	Method	Description
IOHelper	QuotedEntityChecker.getIOHelper()	Get the configured IOHelper.

Methods in org.obolibrary.robot with parameters of type IOHelper

Modifier and Type	Method	Description
static String	DiffOperation.addLabels(IOHelper ioHelper, Map<org.semanticweb.owlapi.model.IRI,String> labels, String axiom)	Deprecated. This functionality is now provided by the owl-diff library and no longer used to format results in DiffOperation.
static boolean	DiffOperation.compare(org.semanticweb.owlapi.model.OWLOntology ontology1, org.semanticweb.owlapi.model.OWLOntology ontology2, IOHelper ioHelper, Writer writer, Map<String,String> options)	Given two ontologies, a Writer, and a set of diff options, get their differences and write then to the writer.
static org.semanticweb.owlapi.model.OWLOntology	QueryOperation.convertModel(org.apache.jena.rdf.model.Model model, IOHelper ioHelper, String catalogPath)	Given a Model, an IOHelper, and a path to an XML catalog, convert the model to an OWLOntology object.
static Table	ExportOperation.createExportTable(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, List<String> columnNames, Map<String,String> options)	Given an ontology, an ioHelper, a list of columns, an output export file, and a map of options, export details about the entities in the ontology to the export file.
static org.semanticweb.owlapi.model.OWLAnnotation	TemplateHelper.getAnnotation(String tableName, QuotedEntityChecker checker, IOHelper ioHelper, String template, String value)	Deprecated.
static org.semanticweb.owlapi.model.OWLAnnotation	TemplateHelper.getAnnotation(QuotedEntityChecker checker, IOHelper ioHelper, String template, String value)	Deprecated.
protected static Set<org.semanticweb.owlapi.model.OWLAnnotation>	RelatedObjectsHelper.getAnnotations(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String annotation)	Given an IOHelper and an annotation as CURIE=..., return the OWLAnnotation object(s).
static List<org.semanticweb.owlapi.model.IRI>	TemplateHelper.getIRIs(String tableName, List<List<String>> rows, IOHelper ioHelper)	Get a list of the IRIs defined in a template table.
static List<org.semanticweb.owlapi.model.IRI>	TemplateHelper.getIRIs(Map<String,List<List<String>>> tables, IOHelper ioHelper)	Get a list of the IRIs defined in a set of template tables.
static List<org.semanticweb.owlapi.model.IRI>	TemplateOperation.getIRIs(String tableName, List<List<String>> rows, IOHelper ioHelper)	Deprecated.
static List<org.semanticweb.owlapi.model.IRI>	TemplateOperation.getIRIs(Map<String,List<List<String>>> tables, IOHelper ioHelper)	Deprecated.
static Report	ReportOperation.getReport(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options)	Given an ontology, an IOHelper, and a map of options, create a Report object and run the report queries specified in a profile (from options, or default).
static Report	ReportOperation.getTDBReport(IOHelper ioHelper, org.apache.jena.query.Dataset dataset, Map<String,String> options)	Given a dataset and a map of options, create a Report object and run (on TDB dataset) the report queries specified in a profile (from options, or default).
static void	RenameOperation.renameFull(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> mappings)	Given an ontology, an IOHelper, and a map of old IRIs to new IRIs, rename each old IRI with the new IRI.
static void	RenameOperation.renameFull(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> mappings, boolean allowMissingEntities)	Given an ontology, an IOHelper, and a map of old IRIs to new IRIs, rename each old IRI with the new IRI.
static void	RenameOperation.renamePrefixes(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> mappings)	Given an ontology, an IOHelper, and a map of old IRI bases to new IRI bases, rename each IRI with the 'old base' as a prefix, replacing it with the 'new base'.
static void	RepairOperation.repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper)	Repairs ontology
static void	RepairOperation.repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, boolean mergeAxiomAnnotations)	Repairs ontology
static void	RepairOperation.repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, boolean mergeAxiomAnnotations, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)	Repairs ontology
static void	RepairOperation.repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options)	Repairs ontology
static void	RepairOperation.repair(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options, boolean mergeAxiomAnnotations)	Repairs ontology
static void	RepairOperation.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	RepairOperation.repairInvalidReferences(IOHelper iohelper, org.semanticweb.owlapi.model.OWLOntology ontology, Set<InvalidReferenceViolation> violations)	Repairs invalid references
static void	RepairOperation.repairInvalidReferences(IOHelper iohelper, org.semanticweb.owlapi.model.OWLOntology ontology, Set<InvalidReferenceViolation> violations, Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> migrateAnnotations)	Repairs invalid references
static void	ReportOperation.report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper)	Report on the ontology using the rules within the profile and print results.
static boolean	ReportOperation.report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String profilePath, String outputPath, String format, String failOn)	Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), and a level to fail on, report on the ontology using the rules within the profile and write results to the output path.
static boolean	ReportOperation.report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String profilePath, String outputPath, String format, String failOn, boolean useLabels)	Given an ontology, an IOHelper, a profile path (or null), an output path (or null), a report format (or null), a level to fail on, and a boolean indicating to use labels, report on the ontology using the rules within the profile and write results to the output path.
static boolean	ReportOperation.report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, String outputPath, Map<String,String> options)	Given an ontology, an IOHelper, an output path (or null), and a map of options (or null), report on the ontology using the rules within the profile specified by the options and write results to the output path.
static void	ReportOperation.report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Map<String,String> options)	Report on the ontology using the rules within the profile and print results.
static Set<org.semanticweb.owlapi.model.OWLObject>	RelatedObjectsHelper.select(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String selector)	Given an ontology, a set of objects, and a selector, return the related objects related to the set of OWL objects based on the selector.
static Set<org.semanticweb.owlapi.model.OWLObject>	RelatedObjectsHelper.select(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, List<String> selectors)	Given an ontology, a set of objects, and a list of selector strings, return the objects related to the set of OWLObjects based on the set of selectors.
static Set<org.semanticweb.owlapi.model.OWLObject>	RelatedObjectsHelper.selectCURIE(IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String selector)	Given an IOHelper, a set of objects, and a selector string for CURIE pattern, return a set of objects matching that CURIE pattern.
static Set<org.semanticweb.owlapi.model.OWLObject>	RelatedObjectsHelper.selectGroups(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, List<List<String>> selectorGroups)	Given an ontology, a set of objects, and a list of select groups (as lists), return the objects related to the set of OWLObjects based on each set of selectors.
static Set<org.semanticweb.owlapi.model.OWLObject>	RelatedObjectsHelper.selectPattern(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, Set<org.semanticweb.owlapi.model.OWLObject> objects, String annotationPattern)	Given an ontology, a set of objects, and a pattern to match annotations to, return a set of objects that are annotated with the matching annotation.
void	QuotedEntityChecker.setIOHelper(IOHelper ioHelper)	Add an IOHelper for resolving names to IRIs.
static org.semanticweb.owlapi.model.OWLOntology	TemplateOperation.template(Map<String,List<List<String>>> tables, org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper)	Deprecated.
static org.semanticweb.owlapi.model.OWLOntology	TemplateOperation.template(Map<String,List<List<String>>> tables, org.semanticweb.owlapi.model.OWLOntology inputOntology, QuotedEntityChecker checker, IOHelper ioHelper)	Deprecated.
static org.semanticweb.owlapi.model.OWLOntology	TemplateOperation.template(org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper, String tableName, List<List<String>> table)	Given an OWLOntology, an IOHelper, a table name, and the table contents, use the table as the template to generate an output OWLOntology.
static org.semanticweb.owlapi.model.OWLOntology	TemplateOperation.template(org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper, String tableName, List<List<String>> table, Map<String,String> options)	Given an OWLOntology, an IOHelper, a table name, the table contents, and a map of template options, use the table as the template to generate an output OWLOntology.
static org.semanticweb.owlapi.model.OWLOntology	TemplateOperation.template(org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper, Map<String,List<List<String>>> tables, Map<String,String> options)	Given an OWLOntology, an IOHelper, a map of table names to table contents, and a map of template options, use the tables as templates to generate a merged output ontology.
static void	ReasonerHelper.validate(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, String unsatisfiableModulePath, IOHelper ioHelper)	Validates ontology, writes unsatisfiable module.

Constructors in org.obolibrary.robot with parameters of type IOHelper

Constructor	Description
Template(String name, List<List<String>> rows, IOHelper ioHelper)	Given a template name, a list of rows, and an IOHelper, create a template object with a new QuotedEntityChecker.
Template(String name, List<List<String>> rows, org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper)	Given a template name, a list of rows, an input ontology, and an IOHelper, create a template object with a new QuotedEntityChecker with the IOHelper populated by the input ontology.
Template(String name, List<List<String>> rows, org.semanticweb.owlapi.model.OWLOntology inputOntology, IOHelper ioHelper, QuotedEntityChecker checker)	Given a template name, a list of rows, an IOHelper, and a QuotedEntityChecker, create a template object.

Uses of IOHelper in org.obolibrary.robot.checks

Constructors in org.obolibrary.robot.checks with parameters of type IOHelper

Constructor	Description
Report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper)	Deprecated. Report will not do anything with the ontology when not using labels.
Report(org.semanticweb.owlapi.model.OWLOntology ontology, IOHelper ioHelper, boolean useLabels)	Create a new report object with an ontology to (maybe) get labels from and a defined IOHelper.