Package org.obolibrary.robot

Class Template

java.lang.Object

org.obolibrary.robot.Template

public class Template
extends Object

Author:

Becky Tauber

Constructor Summary

Constructors

Constructor	Description
Template(String name, List<List<String>> rows)	Given a template name and a list of rows, create a template object with a new IOHelper and QuotedEntityChecker.
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)	Given a template name, a list of rows, and an input ontology, create a template object with a new IOHelper and QuotedEntityChecker populated by the input ontology.
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.

Method Summary

Modifier and Type	Method	Description
org.semanticweb.owlapi.model.OWLOntology	generateOutputOntology()	Generate an OWLOntology based on the rows of the template.
org.semanticweb.owlapi.model.OWLOntology	generateOutputOntology(String outputIRI, boolean force)	Generate an OWLOntology based on the rows of the template.
org.semanticweb.owlapi.model.OWLOntology	generateOutputOntology(String outputIRI, boolean force, String errorsPath)	Generate an OWLOntology with given IRI based on the rows of the template.
QuotedEntityChecker	getChecker()	Return the QuotedEntityChecker.

Methods inherited from class java.lang.Object

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

Constructor Detail

Template

public Template(@Nonnull
                String name,
                @Nonnull
                List<List<String>> rows)
         throws Exception

Given a template name and a list of rows, create a template object with a new IOHelper and QuotedEntityChecker. The rows are added to the object, new labels from the rows are added to the checker, and a Manchester Syntax parser is created.

Parameters:

name - template name

rows - list of rows (lists)

Throws:

Exception - on issue creating IOHelper or adding table to template object

Template

public Template(@Nonnull
                String name,
                @Nonnull
                List<List<String>> rows,
                IOHelper ioHelper)
         throws Exception

Given a template name, a list of rows, and an IOHelper, create a template object with a new QuotedEntityChecker. The rows are added to the object, new labels from the rows are added to the checker, and a Manchester Syntax parser is created.

Parameters:

name - template name

rows - list of rows (lists)

ioHelper - IOHelper to resolve prefixes

Throws:

Exception - on issue adding table to template object

Template

public Template(@Nonnull
                String name,
                @Nonnull
                List<List<String>> rows,
                org.semanticweb.owlapi.model.OWLOntology inputOntology)
         throws Exception

Given a template name, a list of rows, and an input ontology, create a template object with a new IOHelper and QuotedEntityChecker populated by the input ontology. The rows are added to the object, new labels from the rows are added to the checker, and a Manchester Syntax parser is created.

Parameters:

name - template name

rows - list of rows (lists)

inputOntology - OWLOntology to get labels of entities for QuotedEntityChecker

Throws:

Exception - on issue creating IOHelper or adding table to template object

Template

public Template(@Nonnull
                String name,
                @Nonnull
                List<List<String>> rows,
                org.semanticweb.owlapi.model.OWLOntology inputOntology,
                IOHelper ioHelper)
         throws Exception

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. The rows are added to the object, new labels from the rows are added to the checker, and a Manchester Syntax parser is created.

Parameters:

name - template name

rows - list of rows (lists)

inputOntology - OWLOntology to get labels of entities for QuotedEntityChecker

ioHelper - IOHelper to resolve prefixes

Throws:

Exception - on issue adding table to template object

Template

public Template(@Nonnull
                String name,
                @Nonnull
                List<List<String>> rows,
                org.semanticweb.owlapi.model.OWLOntology inputOntology,
                IOHelper ioHelper,
                QuotedEntityChecker checker)
         throws Exception

Given a template name, a list of rows, an IOHelper, and a QuotedEntityChecker, create a template object. The rows are added to the object, new labels from the rows are added to the checker, and a Manchester Syntax parser is created.

Parameters:

name - template name

rows - list of rows (lists)

inputOntology - OWLOntology to get labels of entities for QuotedEntityChecker

ioHelper - IOHelper to resolve prefixes

checker - QuotedEntityChecker to get entities by label

Throws:

Exception - on issue adding table to template object

Method Detail

getChecker

public QuotedEntityChecker getChecker()

Return the QuotedEntityChecker.

Returns:

QuotedEntityChecker

generateOutputOntology

public org.semanticweb.owlapi.model.OWLOntology generateOutputOntology()
                                                                throws Exception

Generate an OWLOntology based on the rows of the template.

Returns:

new OWLOntology

Throws:

Exception - on issue parsing rows to axioms or creating new ontology

generateOutputOntology

public org.semanticweb.owlapi.model.OWLOntology generateOutputOntology(String outputIRI,
                                                                       boolean force)
                                                                throws Exception

Generate an OWLOntology based on the rows of the template.

Parameters:

outputIRI - IRI for final ontology

force - if true, do not exit on errors

Returns:

new OWLOntology

Throws:

Exception - on issue parsing rows to axioms or creating new ontology

generateOutputOntology

public org.semanticweb.owlapi.model.OWLOntology generateOutputOntology(String outputIRI,
                                                                       boolean force,
                                                                       String errorsPath)
                                                                throws Exception

Generate an OWLOntology with given IRI based on the rows of the template.

Parameters:

outputIRI - IRI for final ontology

force - if true, do not exit on errors

errorsPath - path to errors table when force=true

Returns:

new OWLOntology

Throws:

Exception - on issue parsing rows to axioms or creating new ontology