org.obolibrary.obo2owl.OwlStringTools Maven / Gradle / Ivy
package org.obolibrary.obo2owl;
import static org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.util.Collection;
import java.util.Collections;
import javax.annotation.Nullable;
import org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser;
import org.semanticweb.owlapi.functional.renderer.OWLFunctionalSyntaxRenderer;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.io.OWLRendererException;
import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.UnloadableImportException;
/**
* Tools to read and write a set of owl axioms to/from a string. Used to
* preserve untranslatable axioms in an owl2obo conversion.
*/
public class OwlStringTools {
private OwlStringTools() {
}
/**
* Create a string for the given set of axioms. Return null for empty sets
* or if the set is null.
*
* @param axioms axioms
* @param translationManager translationManager
* @return string or null
* @see #translate(String, OWLOntologyManager)
*/
public static String translate(Collection axioms,
OWLOntologyManager translationManager) {
if (axioms.isEmpty()) {
return "";
}
try {
OWLOntology ontology = translationManager.createOntology();
ontology.add(axioms);
OWLFunctionalSyntaxRenderer r = new OWLFunctionalSyntaxRenderer();
Writer writer = new StringWriter();
PrintWriter w = new PrintWriter(writer);
r.render(ontology, w);
w.flush();
return writer.toString();
} catch (OWLRendererException | OWLOntologyCreationException | OWLRuntimeException e) {
throw new OwlStringException(e);
}
}
/**
* Parse the axioms from the given axiom string. Returns null for empty and
* null strings.
*
* @param axioms axioms
* @param translationManager translationManager
* @return set of axioms or null
* @see #translate(Collection, OWLOntologyManager)
*/
public static Collection translate(@Nullable String axioms,
OWLOntologyManager translationManager) {
if (axioms == null || axioms.isEmpty()) {
return Collections.emptySet();
}
try {
OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
OWLOntologyDocumentSource documentSource = new StringDocumentSource(axioms);
OWLOntology ontology = translationManager.createOntology();
p.parse(documentSource, ontology, translationManager.getOntologyLoaderConfiguration());
return asList(ontology.axioms());
} catch (UnloadableImportException | OWLOntologyCreationException | OWLParserException e) {
throw new OWLRuntimeException(e);
}
}
/**
* Exception indicating an un-recoverable error during the handling of axiom
* strings.
*/
public static class OwlStringException extends OWLRuntimeException {
/**
* @param cause cause
*/
protected OwlStringException(Throwable cause) {
super(cause);
}
}
}