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Missed port of an obo fix
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@ignazio1977
ignazio1977 committed Jun 13, 2015
1 parent 8c1e9d4 commit 4f025f0
Showing 1 changed file with 142 additions and 72 deletions.
214 changes: 142 additions & 72 deletions oboformat/src/main/java/org/obolibrary/macro/MacroExpansionGCIVisitor.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
package org.obolibrary.macro;

import java.util.Collections;
import java.util.HashSet;
import java.util.Set;

import org.semanticweb.owlapi.io.OWLParserException;
Expand All @@ -16,10 +18,17 @@ public class MacroExpansionGCIVisitor {
private final OWLOntologyManager outputManager;
private final OWLOntology outputOntology;
protected final ManchesterSyntaxTool manchesterSyntaxTool;
private final GCIVisitor visitor;
private final boolean shouldAddExpansionMarker;
protected boolean preserveAnnotationsWhenExpanding = false;

/**
* @param inputOntology
* input ontology
* @param outputManager
* manager for output ontology
* @param preserveAnnotationsWhenExpanding
* annotations should be preserved
*/
public MacroExpansionGCIVisitor(OWLOntology inputOntology, OWLOntologyManager outputManager,
boolean preserveAnnotationsWhenExpanding) {
this(outputManager, inputOntology, false);
Expand All @@ -31,12 +40,13 @@ public MacroExpansionGCIVisitor(OWLOntology inputOntology, OWLOntologyManager ou
* inputOntology
* @param outputManager
* outputManager
* @param shouldAddExpansionMarker
* expansion marker should be added
*/
public MacroExpansionGCIVisitor(OWLOntologyManager outputManager, OWLOntology inputOntology,
boolean shouldAddExpansionMarker) {
this.inputOntology = inputOntology;
this.shouldAddExpansionMarker = shouldAddExpansionMarker;
visitor = new GCIVisitor(inputOntology);
manchesterSyntaxTool = new ManchesterSyntaxTool(inputOntology);
this.outputManager = outputManager;
try {
Expand Down Expand Up @@ -64,99 +74,159 @@ protected void output(OWLAxiom axiom) {
* @return ontology for gci
*/
public OWLOntology createGCIOntology() {
for (OWLAxiom ax : inputOntology.getAxioms()) {
if (ax instanceof OWLSubClassOfAxiom) {
visitor.visit((OWLSubClassOfAxiom) ax);
} else if (ax instanceof OWLEquivalentClassesAxiom) {
visitor.visit((OWLEquivalentClassesAxiom) ax);
} else if (ax instanceof OWLClassAssertionAxiom) {
visitor.visit((OWLClassAssertionAxiom) ax);
} else if (ax instanceof OWLAnnotationAssertionAxiom) {
expand((OWLAnnotationAssertionAxiom) ax);
}
}
MacroExpansions expansions = new MacroExpansions();
outputManager.addAxioms(outputOntology, expansions.getNewAxioms());
outputManager.removeAxioms(outputOntology, expansions.getRmAxioms());
return outputOntology;
}

private void expand(OWLAnnotationAssertionAxiom ax) {
OWLAnnotationProperty prop = ax.getProperty();
String expandTo = visitor.expandAssertionToMap.get(prop.getIRI());
if (expandTo != null) {
LOG.info("Template to Expand {}", expandTo);
expandTo = expandTo.replaceAll("\\?X", manchesterSyntaxTool.getId((IRI) ax.getSubject()));
expandTo = expandTo.replaceAll("\\?Y", manchesterSyntaxTool.getId((IRI) ax.getValue()));
LOG.info("Expanding {}", expandTo);
try {
Set<OntologyAxiomPair> setAxp = manchesterSyntaxTool.parseManchesterExpressionFrames(expandTo);
for (OntologyAxiomPair axp : setAxp) {
output(axp.getAxiom());
private class MacroExpansions {

private Set<OWLAxiom> newAxioms = new HashSet<>();
private Set<OWLAxiom> rmAxioms = new HashSet<>();
GCIVisitor visitor = new GCIVisitor(inputOntology);

public MacroExpansions() {
for (OWLSubClassOfAxiom axiom : inputOntology.getAxioms(AxiomType.SUBCLASS_OF)) {
OWLAxiom newAxiom = visitor.visit(axiom);
// System.out.println("not adding " + newAxiom);
}
for (OWLEquivalentClassesAxiom axiom : inputOntology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
OWLAxiom newAxiom = visitor.visit(axiom);
// System.out.println("not adding " + newAxiom);
}
for (OWLClassAssertionAxiom axiom : inputOntology.getAxioms(AxiomType.CLASS_ASSERTION)) {
OWLAxiom newAxiom = visitor.visit(axiom);
// System.out.println("not adding " + newAxiom);
}
for (OWLAnnotationAssertionAxiom axiom : inputOntology.getAxioms(AxiomType.ANNOTATION_ASSERTION)) {
if (expand(axiom)) {
// System.out.println("not removing " + axiom);
}
} catch (Exception ex) {
LOG.error(ex.getMessage(), ex);
}
}
}

private class GCIVisitor extends AbstractMacroExpansionVisitor {

GCIVisitor(OWLOntology inputOntology) {
super(inputOntology);
private void replaceIfDifferent(OWLAxiom ax, OWLAxiom exAx) {
if (!ax.equals(exAx)) {
newAxioms.add(exAx);
rmAxioms.add(ax);
}
}

@Override
protected OWLClassExpression expandOWLObjSomeVal(OWLClassExpression filler, OWLObjectPropertyExpression p) {
OWLClassExpression gciRHS = expandObject(filler, p);
if (gciRHS != null) {
OWLClassExpression gciLHS = dataFactory.getOWLObjectSomeValuesFrom(p, filler);
OWLEquivalentClassesAxiom ax = dataFactory.getOWLEquivalentClassesAxiom(gciLHS, gciRHS);
output(ax);
}
return gciRHS;
public Set<OWLAxiom> getNewAxioms() {
return newAxioms;
}

@Override
protected OWLClassExpression expandOWLObjHasVal(OWLObjectHasValue desc, OWLIndividual filler,
OWLObjectPropertyExpression p) {
OWLClassExpression gciRHS = expandObject(filler, p);
if (gciRHS != null) {
OWLClassExpression gciLHS = dataFactory.getOWLObjectHasValue(p, filler);
OWLEquivalentClassesAxiom ax = dataFactory.getOWLEquivalentClassesAxiom(gciLHS, gciRHS);
output(ax);
}
return gciRHS;
public Set<OWLAxiom> getRmAxioms() {
return rmAxioms;
}

private OWLClassExpression expandObject(Object filler, OWLObjectPropertyExpression p) {
OWLClassExpression result = null;
IRI iri = ((OWLObjectProperty) p).getIRI();
IRI templateVal = null;
if (expandExpressionMap.containsKey(iri)) {
if (filler instanceof OWLObjectOneOf) {
Set<OWLIndividual> inds = ((OWLObjectOneOf) filler).getIndividuals();
if (inds.size() == 1) {
OWLIndividual ind = inds.iterator().next();
if (ind instanceof OWLNamedIndividual) {
templateVal = ((OWLNamedObject) ind).getIRI();
private boolean expand(OWLAnnotationAssertionAxiom ax) {
OWLAnnotationProperty prop = ax.getProperty();
boolean didExpansion = false;
String expandTo = visitor.expandAssertionToMap.get(prop.getIRI());
if (expandTo != null) {
LOG.info("Template to Expand {}", expandTo);
expandTo = expandTo.replaceAll("\\?X", manchesterSyntaxTool.getId((IRI) ax.getSubject()));
expandTo = expandTo.replaceAll("\\?Y", manchesterSyntaxTool.getId((IRI) ax.getValue()));
LOG.info("Expanding {}", expandTo);
try {
Set<OntologyAxiomPair> setAxp = manchesterSyntaxTool.parseManchesterExpressionFrames(expandTo);
for (OntologyAxiomPair axp : setAxp) {
OWLAxiom axiom = axp.getAxiom();
if (shouldPreserveAnnotationsWhenExpanding()) {
Set<OWLAnnotation> annotationsWithOptionalExpansionMarker = visitor
.getAnnotationsWithOptionalExpansionMarker(ax);
axiom = axiom.getAnnotatedAxiom(annotationsWithOptionalExpansionMarker);
}
newAxioms.add(axiom);
didExpansion = true;
}
} catch (Exception ex) {
LOG.error(ex.getMessage(), ex);
}
}
return didExpansion;
}

private class GCIVisitor extends AbstractMacroExpansionVisitor {

final Set<OWLAnnotation> expansionMarkingAnnotations;

GCIVisitor(OWLOntology inputOntology) {
super(inputOntology, shouldAddExpansionMarker);
if (shouldAddExpansionMarker) {
expansionMarkingAnnotations = Collections.singleton(expansionMarkerAnnotation);
} else {
expansionMarkingAnnotations = EMPTY_ANNOTATIONS;
}
}

@Override
protected OWLClassExpression expandOWLObjSomeVal(OWLClassExpression filler, OWLObjectPropertyExpression p) {
OWLClassExpression gciRHS = expandObject(filler, p);
if (gciRHS != null) {
OWLClassExpression gciLHS = dataFactory.getOWLObjectSomeValuesFrom(p, filler);
OWLEquivalentClassesAxiom ax = dataFactory.getOWLEquivalentClassesAxiom(gciLHS, gciRHS,
expansionMarkingAnnotations);
newAxioms.add(ax);
}
if (filler instanceof OWLNamedObject) {
templateVal = ((OWLNamedObject) filler).getIRI();
return gciRHS;
}

@Override
protected OWLClassExpression expandOWLObjHasVal(OWLObjectHasValue desc, OWLIndividual filler,
OWLObjectPropertyExpression p) {
OWLClassExpression gciRHS = expandObject(filler, p);
if (gciRHS != null) {
OWLClassExpression gciLHS = dataFactory.getOWLObjectHasValue(p, filler);
OWLEquivalentClassesAxiom ax = dataFactory.getOWLEquivalentClassesAxiom(gciLHS, gciRHS,
expansionMarkingAnnotations);
newAxioms.add(ax);
}
if (templateVal != null) {
String tStr = expandExpressionMap.get(iri);
String exStr = tStr.replaceAll("\\?Y", manchesterSyntaxTool.getId(templateVal));
try {
result = manchesterSyntaxTool.parseManchesterExpression(exStr);
} catch (OWLParserException e) {
LOG.error(e.getMessage(), e);
return gciRHS;
}

private OWLClassExpression expandObject(Object filler, OWLObjectPropertyExpression p) {
OWLClassExpression result = null;
IRI iri = ((OWLObjectProperty) p).getIRI();
IRI templateVal = null;
if (expandExpressionMap.containsKey(iri)) {
if (filler instanceof OWLObjectOneOf) {
Set<OWLIndividual> inds = ((OWLObjectOneOf) filler).getIndividuals();
if (inds.size() == 1) {
OWLIndividual ind = inds.iterator().next();
if (ind instanceof OWLNamedIndividual) {
templateVal = ((OWLNamedObject) ind).getIRI();
}
}
}
if (filler instanceof OWLNamedObject) {
templateVal = ((OWLNamedObject) filler).getIRI();
}
if (templateVal != null) {
String tStr = expandExpressionMap.get(iri);
String exStr = tStr.replaceAll("\\?Y", manchesterSyntaxTool.getId(templateVal));
try {
result = manchesterSyntaxTool.parseManchesterExpression(exStr);
} catch (OWLParserException e) {
LOG.error(e.getMessage(), e);
}
}
}
return result;
}
return result;
}
}

public boolean shouldPreserveAnnotationsWhenExpanding() {
return preserveAnnotationsWhenExpanding;
}

public void setPreserveAnnotationsWhenExpanding(boolean preserveAnnotationsWhenExpanding) {
this.preserveAnnotationsWhenExpanding = preserveAnnotationsWhenExpanding;
}

/** Call this method to clear internal references. */
public void dispose() {
manchesterSyntaxTool.dispose();
Expand Down

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