org.obolibrary.obo2owl.OWLAPIOwl2Obo Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of owlapi-oboformat Show documentation
Show all versions of owlapi-oboformat Show documentation
A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This version has been slightly modified to be included directly in the OWL API.
The upstream code for this module and its authors can be found at https://code.google.com/p/oboformat/.
package org.obolibrary.obo2owl;
import static org.semanticweb.owlapi.search.EntitySearcher.getAnnotationObjects;
import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
import java.io.UnsupportedEncodingException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.obolibrary.obo2owl.Obo2OWLConstants.Obo2OWLVocabulary;
import org.obolibrary.obo2owl.OwlStringTools.OwlStringException;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.Frame.FrameType;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.model.QualifierValue;
import org.obolibrary.oboformat.model.Xref;
import org.obolibrary.oboformat.parser.OBOFormatConstants;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLAnnotationValue;
import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLDatatype;
import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
import org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom;
import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLNamedObject;
import org.semanticweb.owlapi.model.OWLNaryPropertyAxiom;
import org.semanticweb.owlapi.model.OWLObject;
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectCardinalityRestriction;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLObjectMaxCardinality;
import org.semanticweb.owlapi.model.OWLObjectMinCardinality;
import org.semanticweb.owlapi.model.OWLObjectProperty;
import org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom;
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectUnionOf;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLQuantifiedObjectRestriction;
import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
import org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
import org.semanticweb.owlapi.vocab.Namespaces;
import org.semanticweb.owlapi.vocab.OWL2Datatype;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Optional;
import com.google.common.collect.Sets;
/**
* The Class OWLAPIOwl2Obo.
*/
public class OWLAPIOwl2Obo {
private static final String MIN_CARDINALITY = "minCardinality";
private static final String MAX_CARDINALITY = "maxCardinality";
@Nonnull
private static final String TOP_BOTTOM_NONTRANSLATEABLE =
"Assertions using owl:Thing or owl:Nothing are not translateable OBO";
/**
* The log.
*/
private static final Logger LOG = LoggerFactory.getLogger(OWLAPIOwl2Obo.class);
private static final String IRI_CLASS_SYNONYMTYPEDEF =
Obo2OWLConstants.DEFAULT_IRI_PREFIX + "IAO_synonymtypedef";
private static final String IRI_CLASS_SUBSETDEF =
Obo2OWLConstants.DEFAULT_IRI_PREFIX + "IAO_subsetdef";
/**
* The absoulte url pattern.
*/
protected final Pattern absoulteURLPattern = Pattern.compile("<\\s*http.*?>");
private static final Set SKIPPED_QUALIFIERS = Sets.newHashSet("gci_relation",
"gci_filler", "cardinality", MIN_CARDINALITY, MAX_CARDINALITY, "all_some", "all_only");
/**
* The manager.
*/
@Nonnull
protected OWLOntologyManager manager;
/**
* The owl ontology.
*/
protected OWLOntology owlOntology;
/**
* The fac.
*/
protected final OWLDataFactory fac;
/**
* The obodoc.
*/
protected OBODoc obodoc;
/**
* The untranslatable axioms.
*/
protected Set untranslatableAxioms;
/**
* The id space map.
*/
protected Map idSpaceMap;
/**
* The annotation property map.
*/
@Nonnull
public static final Map ANNOTATIONPROPERTYMAP = initAnnotationPropertyMap();
/**
* The ap to declare.
*/
protected Set apToDeclare;
/**
* The ontology id.
*/
protected String ontologyId;
/**
* The strict conversion.
*/
protected boolean strictConversion;
/**
* The discard untranslatable.
*/
protected boolean discardUntranslatable = false;
/**
* mute untranslatable axiom warnings
*/
private boolean muteUntranslatableAxioms = false;
protected final void init() {
idSpaceMap = new HashMap<>();
// legacy:
idSpaceMap.put("http://www.obofoundry.org/ro/ro.owl#", "OBO_REL");
untranslatableAxioms = new HashSet<>();
apToDeclare = new HashSet<>();
}
/**
* Instantiates a new oWLAPI owl2 obo.
*
* @param translationManager the translation manager
*/
public OWLAPIOwl2Obo(@Nonnull OWLOntologyManager translationManager) {
manager = translationManager;
fac = manager.getOWLDataFactory();
init();
}
/**
* Inits the annotation property map.
*
* @return the hash map
*/
@Nonnull
protected static Map initAnnotationPropertyMap() {
Map map = new HashMap<>();
for (String key : OWLAPIObo2Owl.ANNOTATIONPROPERTYMAP.keySet()) {
IRI propIRI = OWLAPIObo2Owl.ANNOTATIONPROPERTYMAP.get(key);
map.put(propIRI.toString(), key);
}
return map;
}
/**
* Sets the strict conversion.
*
* @param b the new strict conversion
*/
public void setStrictConversion(boolean b) {
strictConversion = b;
}
/**
* Gets the strict conversion.
*
* @return the strict conversion
*/
public boolean getStrictConversion() {
return strictConversion;
}
/**
* Checks if is discard untranslatable.
*
* @return the discardUntranslatable
*/
public boolean isDiscardUntranslatable() {
return discardUntranslatable;
}
/**
* Sets the discard untranslatable.
*
* @param discardUntranslatable the discardUntranslatable to set
*/
public void setDiscardUntranslatable(boolean discardUntranslatable) {
this.discardUntranslatable = discardUntranslatable;
}
/**
* Gets the manager.
*
* @return the manager
*/
public OWLOntologyManager getManager() {
return manager;
}
/**
* Sets the manager.
*
* @param manager the new manager
*/
public void setManager(@Nonnull OWLOntologyManager manager) {
this.manager = manager;
}
/**
* Gets the obodoc.
*
* @return the obodoc
*/
@Nonnull
public OBODoc getObodoc() {
return verifyNotNull(obodoc);
}
/**
* Sets the obodoc.
*
* @param obodoc the new obodoc
*/
public void setObodoc(@Nonnull OBODoc obodoc) {
this.obodoc = obodoc;
}
/**
* Convert.
*
* @param ont the ont
* @return the oBO doc
*/
@Nonnull
public OBODoc convert(@Nonnull OWLOntology ont) {
owlOntology = ont;
ontologyId = getOntologyId(ont);
init();
return tr();
}
@Nonnull
protected OWLOntology getOWLOntology() {
return verifyNotNull(owlOntology);
}
/**
* Gets the untranslatable axioms.
*
* @return the untranslatableAxioms
*/
public Collection getUntranslatableAxioms() {
return untranslatableAxioms;
}
/**
* Tr.
*
* @return the oBO doc
*/
@Nonnull
protected OBODoc tr() {
setObodoc(new OBODoc());
preProcess();
tr(getOWLOntology());
// declarations need to be sorted - otherwise there is a risk of id being processed before
// altId, which causes spurious clauses.
List axioms =
new ArrayList<>(getOWLOntology().getAxioms(AxiomType.DECLARATION));
axioms.sort(null);
axioms.forEach(this::consume);
AxiomType.skipDeclarations().flatMap(t -> getOWLOntology().getAxioms(t).stream())
.map(x -> (OWLAxiom) x).forEach(this::consume);
if (!untranslatableAxioms.isEmpty() && !discardUntranslatable) {
try {
String axiomString = OwlStringTools.translate(untranslatableAxioms, manager);
if (axiomString != null) {
Frame headerFrame = getObodoc().getHeaderFrame();
if (headerFrame == null) {
headerFrame = new Frame(FrameType.HEADER);
getObodoc().setHeaderFrame(headerFrame);
}
headerFrame.addClause(new Clause(OboFormatTag.TAG_OWL_AXIOMS, axiomString));
}
} catch (OwlStringException e) {
throw new OWLRuntimeException(e);
}
}
return getObodoc();
}
protected void consume(OWLAxiom ax) {
if (ax instanceof OWLDeclarationAxiom) {
tr((OWLDeclarationAxiom) ax);
} else if (ax instanceof OWLSubClassOfAxiom) {
tr((OWLSubClassOfAxiom) ax);
} else if (ax instanceof OWLDisjointClassesAxiom) {
tr((OWLDisjointClassesAxiom) ax);
} else if (ax instanceof OWLEquivalentClassesAxiom) {
tr((OWLEquivalentClassesAxiom) ax);
} else if (ax instanceof OWLClassAssertionAxiom) {
tr((OWLClassAssertionAxiom) ax);
} else if (ax instanceof OWLEquivalentObjectPropertiesAxiom) {
tr((OWLEquivalentObjectPropertiesAxiom) ax);
} else if (ax instanceof OWLSubAnnotationPropertyOfAxiom) {
tr((OWLSubAnnotationPropertyOfAxiom) ax);
} else if (ax instanceof OWLSubObjectPropertyOfAxiom) {
tr((OWLSubObjectPropertyOfAxiom) ax);
} else if (ax instanceof OWLObjectPropertyRangeAxiom) {
tr((OWLObjectPropertyRangeAxiom) ax);
} else if (ax instanceof OWLFunctionalObjectPropertyAxiom) {
tr((OWLFunctionalObjectPropertyAxiom) ax);
} else if (ax instanceof OWLSymmetricObjectPropertyAxiom) {
tr((OWLSymmetricObjectPropertyAxiom) ax);
} else if (ax instanceof OWLAsymmetricObjectPropertyAxiom) {
tr((OWLAsymmetricObjectPropertyAxiom) ax);
} else if (ax instanceof OWLObjectPropertyDomainAxiom) {
tr((OWLObjectPropertyDomainAxiom) ax);
} else if (ax instanceof OWLInverseFunctionalObjectPropertyAxiom) {
tr((OWLInverseFunctionalObjectPropertyAxiom) ax);
} else if (ax instanceof OWLInverseObjectPropertiesAxiom) {
tr((OWLInverseObjectPropertiesAxiom) ax);
} else if (ax instanceof OWLDisjointObjectPropertiesAxiom) {
tr((OWLDisjointObjectPropertiesAxiom) ax);
} else if (ax instanceof OWLReflexiveObjectPropertyAxiom) {
tr((OWLReflexiveObjectPropertyAxiom) ax);
} else if (ax instanceof OWLTransitiveObjectPropertyAxiom) {
tr((OWLTransitiveObjectPropertyAxiom) ax);
} else if (ax instanceof OWLSubPropertyChainOfAxiom) {
tr((OWLSubPropertyChainOfAxiom) ax);
} else {
if (!(ax instanceof OWLAnnotationAssertionAxiom)) {
error(ax, false);
} else {
// we presume this has been processed
}
}
}
/**
* Pre process.
*/
@SuppressWarnings("null")
protected void preProcess() {
// converse of postProcess in obo2owl
String viewRel = null;
for (OWLAnnotation ann : getOWLOntology().getAnnotations()) {
if (ann.getProperty().getIRI()
.equals(Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation.getIRI())) {
OWLAnnotationValue v = ann.getValue();
if (v instanceof OWLLiteral) {
viewRel = ((OWLLiteral) v).getLiteral();
} else {
viewRel = getIdentifier((IRI) v);
}
break;
}
}
if (viewRel != null) {
// OWLObjectProperty vp = fac.getOWLObjectProperty(pIRI);
Set rmAxioms = new HashSet<>();
Set newAxioms = new HashSet<>();
for (OWLEquivalentClassesAxiom eca : getOWLOntology()
.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
int numNamed = 0;
Set xs = new HashSet<>();
for (OWLClassExpression x : eca.getClassExpressions()) {
if (x instanceof OWLClass) {
xs.add(x);
numNamed++;
continue;
} else if (x instanceof OWLObjectSomeValuesFrom) {
OWLObjectProperty p =
(OWLObjectProperty) ((OWLObjectSomeValuesFrom) x).getProperty();
if (!getIdentifier(p).equals(viewRel)) {
LOG.error("Expected: {} got: {} in {}", viewRel, p, eca);
}
xs.add(((OWLObjectSomeValuesFrom) x).getFiller());
} else {
LOG.error("Unexpected: {}", eca);
}
}
if (numNamed == 1) {
rmAxioms.add(eca);
newAxioms.add(fac.getOWLEquivalentClassesAxiom(xs));
} else {
LOG.error("ECA did not fit expected pattern: {}", eca);
}
}
getOWLOntology().getOWLOntologyManager().removeAxioms(getOWLOntology(), rmAxioms);
getOWLOntology().getOWLOntologyManager().addAxioms(getOWLOntology(), newAxioms);
}
}
protected void add(@Nullable Frame f) {
if (f != null) {
try {
getObodoc().addFrame(f);
} catch (Exception ex) {
LOG.error(ex.getMessage(), ex);
}
}
}
/**
* Tr object property.
*
* @param prop the prop
* @param tag the tag
* @param value the value
* @param annotations the annotations
* @return true, if successful
*/
@SuppressWarnings("null")
protected boolean trObjectProperty(@Nullable OWLObjectProperty prop, @Nullable String tag,
@Nullable String value, @Nonnull Set annotations) {
if (prop == null || value == null) {
return false;
}
Frame f = getTypedefFrame(prop);
Clause clause;
if (OboFormatTag.TAG_ID.getTag().equals(tag)) {
clause = f.getClause(tag);
if (tag != null) {
clause.setValue(value);
} else {
clause = new Clause(tag, value);
f.addClause(clause);
}
} else {
clause = new Clause(tag, value);
f.addClause(clause);
}
addQualifiers(clause, annotations);
return true;
}
/**
* Tr object property.
*
* @param prop the prop
* @param tag the tag
* @param value the value
* @param annotations the annotations
* @return true, if successful
*/
protected boolean trObjectProperty(@Nullable OWLObjectProperty prop, String tag,
@Nullable Boolean value, @Nonnull Set annotations) {
if (prop == null || value == null) {
return false;
}
Frame f = getTypedefFrame(prop);
Clause clause = new Clause(tag);
clause.addValue(value);
f.addClause(clause);
addQualifiers(clause, annotations);
return true;
}
/**
* Tr nary property axiom.
*
* @param ax the ax
* @param tag the tag
*/
protected void trNaryPropertyAxiom(
@Nonnull OWLNaryPropertyAxiom ax, String tag) {
Set set = ax.getProperties();
if (set.size() > 1) {
boolean first = true;
OWLObjectProperty prop = null;
String disjointFrom = null;
for (OWLObjectPropertyExpression ex : set) {
if (ex.isBottomEntity() || ex.isTopEntity()) {
error(tag + " using Top or Bottom entities are not supported in OBO.", ax,
false);
return;
}
if (first) {
first = false;
if (ex instanceof OWLObjectProperty) {
prop = (OWLObjectProperty) ex;
}
} else {
disjointFrom = getIdentifier(ex); // getIdentifier(ex);
}
}
if (trObjectProperty(prop, tag, disjointFrom, ax.getAnnotations())) {
return;
}
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLSubPropertyChainOfAxiom ax) {
OWLObjectPropertyExpression pEx = ax.getSuperProperty();
if (pEx.isAnonymous()) {
error(ax, false);
return;
}
OWLObjectProperty p = pEx.asOWLObjectProperty();
if (p.isBottomEntity() || p.isTopEntity()) {
error("Property chains using Top or Bottom entities are not supported in OBO.", ax,
false);
return;
}
List list = ax.getPropertyChain();
if (list.size() != 2) {
error(ax, false);
return;
}
OWLObjectPropertyExpression exp1 = list.get(0);
OWLObjectPropertyExpression exp2 = list.get(1);
if (exp1.isBottomEntity() || exp1.isTopEntity() || exp2.isBottomEntity()
|| exp2.isTopEntity()) {
error("Property chains using Top or Bottom entities are not supported in OBO.", ax,
false);
return;
}
String rel1 = getIdentifier(exp1);
String rel2 = getIdentifier(exp2);
if (rel1 == null || rel2 == null) {
error(ax, false);
return;
}
// set of unprocessed annotations
Set unprocessedAnnotations = new HashSet<>(ax.getAnnotations());
Frame f = getTypedefFrame(p);
Clause clause;
if (rel1.equals(f.getId())) {
clause = new Clause(OboFormatTag.TAG_TRANSITIVE_OVER, rel2);
} else {
OboFormatTag tag = OboFormatTag.TAG_HOLDS_OVER_CHAIN;
for (OWLAnnotation ann : ax.getAnnotations()) {
if (OWLAPIObo2Owl.IRI_PROP_ISREVERSIBLEPROPERTYCHAIN
.equals(ann.getProperty().getIRI().toString())) {
tag = OboFormatTag.TAG_EQUIVALENT_TO_CHAIN;
// remove annotation from unprocessed set.
unprocessedAnnotations.remove(ann);
break;
}
}
clause = new Clause(tag);
clause.addValue(rel1);
clause.addValue(rel2);
}
f.addClause(clause);
addQualifiers(clause, unprocessedAnnotations);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLEquivalentObjectPropertiesAxiom ax) {
trNaryPropertyAxiom(ax, OboFormatTag.TAG_EQUIVALENT_TO.getTag());
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLTransitiveObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_TRANSITIVE.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLDisjointObjectPropertiesAxiom ax) {
trNaryPropertyAxiom(ax, OboFormatTag.TAG_DISJOINT_FROM.getTag());
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLReflexiveObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_REFLEXIVE.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLInverseFunctionalObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_INVERSE_FUNCTIONAL.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLInverseObjectPropertiesAxiom ax) {
OWLObjectPropertyExpression prop1 = ax.getFirstProperty();
OWLObjectPropertyExpression prop2 = ax.getSecondProperty();
if (prop1 instanceof OWLObjectProperty && prop2 instanceof OWLObjectProperty
&& trObjectProperty((OWLObjectProperty) prop1, OboFormatTag.TAG_INVERSE_OF.getTag(),
getIdentifier(prop2), ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLObjectPropertyDomainAxiom ax) {
OWLObjectPropertyExpression propEx = ax.getProperty();
if (propEx.isAnonymous()) {
error(ax, true);
return;
}
OWLObjectProperty prop = propEx.asOWLObjectProperty();
OWLClassExpression domain = ax.getDomain();
if (domain.isBottomEntity() || domain.isTopEntity()) {
// at least get the type def frame
getTypedefFrame(prop);
// now throw the error
error("domains using top or bottom entities are not translatable to OBO.", ax, false);
return;
}
String range = getIdentifier(domain);
if (range != null) {
if (trObjectProperty(prop, OboFormatTag.TAG_DOMAIN.getTag(), range,
ax.getAnnotations())) {
return;
} else {
error("trObjectProperty failed for " + prop, ax, true);
}
} else {
error("no range translatable for " + ax, false);
}
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLAsymmetricObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_ASYMMETRIC.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLSymmetricObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_SYMMETRIC.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLFunctionalObjectPropertyAxiom ax) {
OWLObjectPropertyExpression prop = ax.getProperty();
if (prop instanceof OWLObjectProperty && trObjectProperty((OWLObjectProperty) prop,
OboFormatTag.TAG_IS_FUNCTIONAL.getTag(), Boolean.TRUE, ax.getAnnotations())) {
return;
}
error(ax, true);
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLObjectPropertyRangeAxiom ax) {
OWLClassExpression owlRange = ax.getRange();
OWLObjectPropertyExpression propEx = ax.getProperty();
if (propEx.isAnonymous()) {
error(ax, false);
}
OWLObjectProperty prop = propEx.asOWLObjectProperty();
if (owlRange.isBottomEntity() || owlRange.isTopEntity()) {
// at least create the property frame
getTypedefFrame(prop);
// error message
error("ranges using top or bottom entities are not translatable to OBO.", ax, false);
return;
}
String range = getIdentifier(owlRange); // getIdentifier(ax.getRange());
if (range != null && trObjectProperty(prop, OboFormatTag.TAG_RANGE.getTag(), range,
ax.getAnnotations())) {
return;
}
error(ax, false);
}
@SuppressWarnings("null")
protected void tr(@Nonnull OWLSubObjectPropertyOfAxiom ax) {
OWLObjectPropertyExpression sup = ax.getSuperProperty();
OWLObjectPropertyExpression sub = ax.getSubProperty();
if (sub.isBottomEntity() || sub.isTopEntity() || sup.isBottomEntity()
|| sup.isTopEntity()) {
error("SubProperties using Top or Bottom entites are not supported in OBO.", false);
return;
}
if (sub instanceof OWLObjectProperty && sup instanceof OWLObjectProperty) {
String supId = getIdentifier(sup);
if (supId.startsWith("owl:")) {
return;
}
Frame f = getTypedefFrame((OWLObjectProperty) sub);
Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
f.addClause(clause);
addQualifiers(clause, ax.getAnnotations());
} else {
error(ax, true);
}
}
@SuppressWarnings("null")
protected void tr(@Nonnull OWLSubAnnotationPropertyOfAxiom ax) {
OWLAnnotationProperty sup = ax.getSuperProperty();
OWLAnnotationProperty sub = ax.getSubProperty();
if (sub.isBottomEntity() || sub.isTopEntity() || sup.isBottomEntity()
|| sup.isTopEntity()) {
error("SubAnnotationProperties using Top or Bottom entites are not supported in OBO.",
false);
return;
}
String tagObject = owlObjectToTag(sup);
if (OboFormatTag.TAG_SYNONYMTYPEDEF.getTag().equals(tagObject)) {
String name = "";
String scope = null;
for (OWLAnnotationAssertionAxiom axiom : getOWLOntology()
.getAnnotationAssertionAxioms(sub.getIRI())) {
String tg = owlObjectToTag(axiom.getProperty());
if (OboFormatTag.TAG_NAME.getTag().equals(tg)) {
name = ((OWLLiteral) axiom.getValue()).getLiteral();
} else if (OboFormatTag.TAG_SCOPE.getTag().equals(tg)) {
scope = owlObjectToTag(axiom.getValue());
}
}
Frame hf = getObodoc().getHeaderFrame();
Clause clause = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF);
clause.addValue(getIdentifier(sub));
clause.addValue(name);
if (scope != null) {
clause.addValue(scope);
}
addQualifiers(clause, ax.getAnnotations());
if (!hf.getClauses().contains(clause)) {
hf.addClause(clause);
} else {
LOG.error("duplicate clause: {} in header", clause);
}
return;
} else if (OboFormatTag.TAG_SUBSETDEF.getTag().equals(tagObject)) {
String comment = "";
for (OWLAnnotationAssertionAxiom axiom : getOWLOntology()
.getAnnotationAssertionAxioms(sub.getIRI())) {
String tg = owlObjectToTag(axiom.getProperty());
if (OboFormatTag.TAG_COMMENT.getTag().equals(tg)) {
comment = ((OWLLiteral) axiom.getValue()).getLiteral();
break;
}
}
Frame hf = getObodoc().getHeaderFrame();
Clause clause = new Clause(OboFormatTag.TAG_SUBSETDEF);
clause.addValue(getIdentifier(sub));
clause.addValue(comment);
if (!hf.getClauses().contains(clause)) {
hf.addClause(clause);
} else {
LOG.error("duplicate clause: {} in header", clause);
}
addQualifiers(clause, ax.getAnnotations());
return;
}
if (sub instanceof OWLObjectProperty && sup instanceof OWLObjectProperty) {
String supId = getIdentifier(sup); // getIdentifier(sup);
if (supId.startsWith("owl:")) {
return;
}
Frame f = getTypedefFrame(sub);
Clause clause = new Clause(OboFormatTag.TAG_IS_A, supId);
f.addClause(clause);
addQualifiers(clause, ax.getAnnotations());
} else {
error(ax, true);
}
}
/**
* Tr.
*
* @param aanAx the aan ax
* @param frame the frame
*/
protected void tr(@Nonnull OWLAnnotationAssertionAxiom aanAx, @Nonnull Frame frame) {
boolean success = tr(aanAx.getProperty(), aanAx.getValue(), aanAx.getAnnotations(), frame);
if (!success) {
untranslatableAxioms.add(aanAx);
}
}
/**
* Tr.
*
* @param prop the prop
* @param annVal the ann val
* @param qualifiers the qualifiers
* @param frame the frame
* @return true, if successful
*/
@SuppressWarnings("null")
protected boolean tr(OWLAnnotationProperty prop, @Nonnull OWLAnnotationValue annVal,
@Nonnull Set qualifiers, @Nonnull Frame frame) {
String tagString = owlObjectToTag(prop);
OboFormatTag tag = null;
if (tagString != null) {
tag = OBOFormatConstants.getTag(tagString);
}
if (tag == null) {
if (annVal instanceof IRI && FrameType.TERM.equals(frame.getType())
&& isMetadataTag(prop)) {
String propId = this.getIdentifier(prop);
if (propId != null) {
Clause clause = new Clause(OboFormatTag.TAG_RELATIONSHIP);
clause.addValue(propId);
clause.addValue(getIdentifier((IRI) annVal));
addQualifiers(clause, qualifiers);
frame.addClause(clause);
return true;
}
}
// annotation property does not correspond to a mapping to a tag in
// the OBO syntax -
// use the property_value tag
return trGenericPropertyValue(prop, annVal, qualifiers, frame);
}
Object value = getValue(annVal, tagString);
String valueString = value.toString().trim();
if (!valueString.isEmpty()) {
if (tag == OboFormatTag.TAG_ID) {
if (!frame.getId().equals(value)) {
warn("Conflicting id definitions: 1) " + frame.getId() + " 2)" + value);
return false;
}
return true;
}
Clause clause = new Clause(tag);
if (tag == OboFormatTag.TAG_DATE) {
try {
clause.addValue(OBOFormatConstants.headerDateFormat().parseObject(valueString));
} catch (ParseException e) {
error("Could not parse date string: " + valueString, true);
return false;
}
} else {
clause.addValue(value);
}
Set unprocessedQualifiers = new HashSet<>(qualifiers);
if (tag == OboFormatTag.TAG_DEF) {
for (OWLAnnotation aan : qualifiers) {
String propId = owlObjectToTag(aan.getProperty());
if ("xref".equals(propId)) {
OWLAnnotationValue v = aan.getValue();
String xrefValue;
if (v instanceof IRI) {
xrefValue = v.toString();
} else {
xrefValue = ((OWLLiteral) v).getLiteral();
}
Xref xref = new Xref(xrefValue);
clause.addXref(xref);
unprocessedQualifiers.remove(aan);
}
}
} else if (tag == OboFormatTag.TAG_XREF) {
Xref xref = new Xref(valueString);
for (OWLAnnotation annotation : qualifiers) {
if (fac.getRDFSLabel().equals(annotation.getProperty())) {
OWLAnnotationValue owlAnnotationValue = annotation.getValue();
if (owlAnnotationValue instanceof OWLLiteral) {
unprocessedQualifiers.remove(annotation);
String xrefAnnotation = ((OWLLiteral) owlAnnotationValue).getLiteral();
xrefAnnotation = xrefAnnotation.trim();
if (!xrefAnnotation.isEmpty()) {
xref.setAnnotation(xrefAnnotation);
}
}
}
}
clause.setValue(xref);
} else if (tag == OboFormatTag.TAG_EXACT || tag == OboFormatTag.TAG_NARROW
|| tag == OboFormatTag.TAG_BROAD || tag == OboFormatTag.TAG_RELATED) {
handleSynonym(qualifiers, tag.getTag(), clause, unprocessedQualifiers);
} else if (tag == OboFormatTag.TAG_SYNONYM) {
// This should never happen.
// All synonyms need to be qualified with a type.
String synonymType = null;
handleSynonym(qualifiers, synonymType, clause, unprocessedQualifiers);
}
addQualifiers(clause, unprocessedQualifiers);
// before adding the clause check for redundant clauses
boolean redundant = false;
for (Clause frameClause : frame.getClauses()) {
if (clause.equals(frameClause)) {
redundant = handleDuplicateClause(frame, frameClause);
}
}
if (!redundant) {
frame.addClause(clause);
}
} else {
return false;
}
return true;
}
private boolean isMetadataTag(OWLAnnotationProperty p) {
final IRI metadataTagIRI = IRI.create(
Obo2OWLConstants.OIOVOCAB_IRI_PREFIX + OboFormatTag.TAG_IS_METADATA_TAG.getTag());
Set axioms =
owlOntology.getAnnotationAssertionAxioms(p.getIRI());
for (OWLAnnotationAssertionAxiom ax : axioms) {
if (metadataTagIRI.equals(ax.getProperty().getIRI())) {
return true;
}
}
return false;
}
/**
* Handle synonym.
*
* @param qualifiers the qualifiers
* @param scope the scope
* @param clause the clause
* @param unprocessedQualifiers the unprocessed qualifiers
*/
protected void handleSynonym(@Nonnull Set qualifiers, @Nullable String scope,
@Nonnull Clause clause, @Nonnull Set unprocessedQualifiers) {
clause.setTag(OboFormatTag.TAG_SYNONYM.getTag());
String type = null;
clause.setXrefs(new ArrayList());
for (OWLAnnotation aan : qualifiers) {
String propId = owlObjectToTag(aan.getProperty());
if (OboFormatTag.TAG_XREF.getTag().equals(propId)) {
OWLAnnotationValue v = aan.getValue();
String xrefValue;
if (v instanceof IRI) {
xrefValue = v.toString();
} else {
xrefValue = ((OWLLiteral) v).getLiteral();
}
Xref xref = new Xref(xrefValue);
clause.addXref(xref);
unprocessedQualifiers.remove(aan);
} else if (OboFormatTag.TAG_HAS_SYNONYM_TYPE.getTag().equals(propId)) {
type = getIdentifier(aan.getValue());
unprocessedQualifiers.remove(aan);
}
}
if (scope != null) {
clause.addValue(scope);
if (type != null) {
clause.addValue(type);
}
}
}
/**
* Handle a duplicate clause in a frame during translation.
*
* @param frame the frame
* @param clause the clause
* @return true if the clause is to be marked as redundant and will not be added to the
*/
protected boolean handleDuplicateClause(@Nonnull Frame frame, Clause clause) {
// default is to report it via the logger and remove it.
LOG.error("Duplicate clause '{}' generated in frame: {}", clause, frame.getId());
return true;
}
/**
* Tr generic property value.
*
* @param prop the prop
* @param annVal the ann val
* @param qualifiers the qualifiers
* @param frame the frame
* @return true, if successful
*/
@SuppressWarnings("null")
protected boolean trGenericPropertyValue(OWLAnnotationProperty prop, OWLAnnotationValue annVal,
@Nonnull Set qualifiers, @Nonnull Frame frame) {
// no built-in obo tag for this: use the generic property_value tag
Clause clause = new Clause(OboFormatTag.TAG_PROPERTY_VALUE.getTag());
String propId = getIdentifier(prop);
addQualifiers(clause, qualifiers);
if (!propId.equals("shorthand")) {
clause.addValue(propId);
if (annVal instanceof OWLLiteral) {
OWLLiteral owlLiteral = (OWLLiteral) annVal;
clause.addValue(owlLiteral.getLiteral());
OWLDatatype datatype = owlLiteral.getDatatype();
IRI dataTypeIri = datatype.getIRI();
if (!OWL2Datatype.isBuiltIn(dataTypeIri)) {
error("Untranslatable axiom due to unknown data type: " + annVal, true);
return false;
}
if (Namespaces.XSD.inNamespace(dataTypeIri)) {
clause.addValue(dataTypeIri.prefixedBy("xsd:"));
} else if (dataTypeIri.isPlainLiteral()) {
clause.addValue("xsd:string");
} else {
clause.addValue(dataTypeIri.toString());
}
} else if (annVal instanceof IRI) {
clause.addValue(getIdentifier((IRI) annVal));
}
frame.addClause(clause);
}
return true;
}
/**
* Gets the value.
*
* @param annVal the ann val
* @param tag the tag
* @return the value
*/
@SuppressWarnings("null")
@Nullable
protected Object getValue(@Nonnull OWLAnnotationValue annVal, String tag) {
Object value = annVal.toString();
if (annVal instanceof OWLLiteral) {
OWLLiteral l = (OWLLiteral) annVal;
value = l.isBoolean() ? Boolean.valueOf(l.parseBoolean()) : l.getLiteral();
} else if (annVal instanceof IRI) {
value = getIdentifier((IRI) annVal);
}
if (OboFormatTag.TAG_EXPAND_EXPRESSION_TO.getTag().equals(tag)) {
String s = value.toString();
Matcher matcher = absoulteURLPattern.matcher(s);
while (matcher.find()) {
String m = matcher.group();
m = m.replace("<", "");
m = m.replace(">", "");
int i = m.lastIndexOf('/');
m = m.substring(i + 1);
s = s.replace(matcher.group(), m);
}
value = s;
}
return value;
}
/**
* Adds the qualifiers.
*
* @param c the c
* @param qualifiers the qualifiers
*/
protected static void addQualifiers(@Nonnull Clause c, @Nonnull Set qualifiers) {
for (OWLAnnotation ann : qualifiers) {
String prop = owlObjectToTag(ann.getProperty());
if (prop == null) {
prop = ann.getProperty().getIRI().toString();
}
if (SKIPPED_QUALIFIERS.contains(prop)) {
continue;
}
String value = ann.getValue().toString();
if (ann.getValue() instanceof OWLLiteral) {
value = ((OWLLiteral) ann.getValue()).getLiteral();
} else if (ann.getValue() instanceof IRI) {
value = getIdentifier((IRI) ann.getValue());
}
assert value != null;
QualifierValue qv = new QualifierValue(prop, value);
c.addQualifierValue(qv);
}
}
/**
* E.g. http://purl.obolibrary.org/obo/go.owl to "go"
* if does not match this pattern, then retain original IRI
*
* @param ontology the ontology
* @return The OBO ID of the ontology
*/
public static String getOntologyId(OWLOntology ontology) {
Optional ontologyIRI = ontology.getOntologyID().getOntologyIRI();
if (!ontologyIRI.isPresent()) {
return "";
}
return getOntologyId(ontologyIRI.get());
}
/**
* Gets the ontology id.
*
* @param iriObj the iri obj
* @return the ontology id
*/
public static String getOntologyId(@Nonnull IRI iriObj) {
// String id = getIdentifier(ontology.getOntologyID().getOntologyIRI());
String iri = iriObj.toString();
String id;
if (iri.startsWith("http://purl.obolibrary.org/obo/")) {
id = iri.replace("http://purl.obolibrary.org/obo/", "");
if (id.endsWith(".owl")) {
id = id.replaceFirst(".owl$", "");
}
} else {
id = iri;
}
// int index = iri.lastIndexOf("/");
// id = iri.substring(index+1);
// index = id.lastIndexOf(".owl");
// if(index>0){
// id = id.substring(0, index);
// }
return id;
}
/**
* Gets the data version.
*
* @param ontology the ontology
* @return the data version
*/
@Nullable
public static String getDataVersion(@Nonnull OWLOntology ontology) {
String oid = getOntologyId(ontology);
Optional v = ontology.getOntologyID().getVersionIRI();
if (v.isPresent()) {
String vs = v.get().toString().replace("http://purl.obolibrary.org/obo/", "");
vs = vs.replaceFirst(oid + '/', "");
vs = vs.replace('/' + oid + ".owl", "");
return vs;
}
return null;
}
/**
* Tr.
*
* @param ontology the ontology
*/
protected void tr(@Nonnull OWLOntology ontology) {
Frame f = new Frame(FrameType.HEADER);
getObodoc().setHeaderFrame(f);
for (IRI iri : ontology.getDirectImportsDocuments()) {
Clause c = new Clause(OboFormatTag.TAG_IMPORT.getTag());
// c.setValue(getOntologyId(iri));
c.setValue(iri.toString());
f.addClause(c);
}
String id = getOntologyId(ontology);
Clause c = new Clause(OboFormatTag.TAG_ONTOLOGY.getTag());
c.setValue(id);
f.addClause(c);
String vid = getDataVersion(ontology);
if (vid != null) {
Clause c2 = new Clause(OboFormatTag.TAG_DATA_VERSION.getTag());
c2.setValue(vid);
f.addClause(c2);
}
for (OWLAnnotation ann : ontology.getAnnotations()) {
OWLAnnotationProperty property = ann.getProperty();
String tagString = owlObjectToTag(property);
if (OboFormatTag.TAG_COMMENT.getTag().equals(tagString)) {
property = fac.getOWLAnnotationProperty(
OWLAPIObo2Owl.trTagToIRI(OboFormatTag.TAG_REMARK.getTag()));
}
tr(property, ann.getValue(), ann.getAnnotations(), f);
}
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLEquivalentClassesAxiom ax) {
/*
* Assumption: the underlying data structure is a set The order is not guaranteed to be
* preserved.
*/
Set expressions = ax.getClassExpressions();
// handle expression list with size other than two elements as error
if (expressions.size() != 2) {
error(ax, false);
return;
}
Iterator it = expressions.iterator();
OWLClassExpression ce1 = it.next();
OWLClassExpression ce2 = it.next();
if (ce1.isBottomEntity() || ce1.isTopEntity() || ce2.isBottomEntity()
|| ce2.isTopEntity()) {
error(
"Equivalent classes axioms using Top or Bottom entities are not supported in OBO.",
ax, false);
return;
}
if (!(ce1 instanceof OWLClass)) {
// check whether ce2 is the actual OWLEntity
if (ce2 instanceof OWLClass) {
// three way exchange
OWLClassExpression temp = ce2;
ce2 = ce1;
ce1 = temp;
} else {
// this might happen for some GCI axioms, which are not
// expressible in OBO
error("GCI axioms are not expressible in OBO.", ax, false);
return;
}
}
Frame f = getTermFrame(ce1.asOWLClass());
if (f == null) {
error(ax, false);
return;
}
boolean isUntranslateable = false;
List equivalenceAxiomClauses = new ArrayList<>();
String cls2 = getIdentifier(ce2);
if (cls2 != null) {
Clause c = new Clause(OboFormatTag.TAG_EQUIVALENT_TO.getTag());
c.setValue(cls2);
f.addClause(c);
addQualifiers(c, ax.getAnnotations());
} else if (ce2 instanceof OWLObjectUnionOf) {
List list2 = ((OWLObjectUnionOf) ce2).getOperandsAsList();
for (OWLClassExpression oce : list2) {
String id = getIdentifier(oce);
if (id == null) {
isUntranslateable = true;
error(ax, true);
return;
}
Clause c = new Clause(OboFormatTag.TAG_UNION_OF.getTag());
c.setValue(id);
equivalenceAxiomClauses.add(c);
addQualifiers(c, ax.getAnnotations());
}
} else if (ce2 instanceof OWLObjectIntersectionOf) {
List list2 = ((OWLObjectIntersectionOf) ce2).getOperandsAsList();
for (OWLClassExpression ce : list2) {
String r = null;
cls2 = getIdentifier(ce);
int exact = -1; // cardinality
int min = -1; // minCardinality
int max = -1; // maxCardinality
Boolean allSome = null; // all_some
Boolean allOnly = null; // all_only
if (ce instanceof OWLObjectSomeValuesFrom) {
OWLObjectSomeValuesFrom ristriction = (OWLObjectSomeValuesFrom) ce;
r = getIdentifier(ristriction.getProperty());
cls2 = getIdentifier(ristriction.getFiller());
} else if (ce instanceof OWLObjectExactCardinality) {
OWLObjectExactCardinality card = (OWLObjectExactCardinality) ce;
r = getIdentifier(card.getProperty());
cls2 = getIdentifier(card.getFiller());
exact = card.getCardinality();
} else if (ce instanceof OWLObjectMinCardinality) {
OWLObjectMinCardinality card = (OWLObjectMinCardinality) ce;
r = getIdentifier(card.getProperty());
cls2 = getIdentifier(card.getFiller());
min = card.getCardinality();
} else if (ce instanceof OWLObjectMaxCardinality) {
OWLObjectMaxCardinality card = (OWLObjectMaxCardinality) ce;
r = getIdentifier(card.getProperty());
cls2 = getIdentifier(card.getFiller());
max = card.getCardinality();
} else if (ce instanceof OWLObjectAllValuesFrom) {
OWLObjectAllValuesFrom all = (OWLObjectAllValuesFrom) ce;
OWLClassExpression filler = all.getFiller();
if (filler instanceof OWLClass) {
r = getIdentifier(all.getProperty());
cls2 = getIdentifier(filler);
allOnly = Boolean.TRUE;
} else if (filler instanceof OWLObjectComplementOf) {
OWLObjectComplementOf restriction = (OWLObjectComplementOf) filler;
r = getIdentifier(all.getProperty());
cls2 = getIdentifier(restriction.getOperand());
exact = 0;
}
} else if (ce instanceof OWLObjectIntersectionOf) {
// either a min-max or a some-all combination
Set operands = ((OWLObjectIntersectionOf) ce).getOperands();
if (operands.size() == 2) {
for (OWLClassExpression operand : operands) {
if (operand instanceof OWLObjectMinCardinality) {
OWLObjectMinCardinality card = (OWLObjectMinCardinality) operand;
r = getIdentifier(card.getProperty());
cls2 = getIdentifier(card.getFiller());
min = card.getCardinality();
} else if (operand instanceof OWLObjectMaxCardinality) {
OWLObjectMaxCardinality card = (OWLObjectMaxCardinality) operand;
r = getIdentifier(card.getProperty());
cls2 = getIdentifier(card.getFiller());
max = card.getCardinality();
} else if (operand instanceof OWLObjectAllValuesFrom) {
OWLObjectAllValuesFrom all = (OWLObjectAllValuesFrom) operand;
r = getIdentifier(all.getProperty());
cls2 = getIdentifier(all.getFiller());
allOnly = Boolean.TRUE;
} else if (operand instanceof OWLObjectSomeValuesFrom) {
OWLObjectSomeValuesFrom all = (OWLObjectSomeValuesFrom) operand;
r = getIdentifier(all.getProperty());
cls2 = getIdentifier(all.getFiller());
allSome = Boolean.TRUE;
}
}
}
}
if (cls2 != null) {
Clause c = new Clause(OboFormatTag.TAG_INTERSECTION_OF.getTag());
if (r != null) {
c.addValue(r);
}
c.addValue(cls2);
equivalenceAxiomClauses.add(c);
if (exact > -1) {
c.addQualifierValue(
new QualifierValue("cardinality", Integer.toString(exact)));
}
if (min > -1) {
c.addQualifierValue(
new QualifierValue(MIN_CARDINALITY, Integer.toString(min)));
}
if (max > -1) {
c.addQualifierValue(
new QualifierValue(MAX_CARDINALITY, Integer.toString(max)));
}
if (allSome != null) {
String string = allSome.toString();
assert string != null;
c.addQualifierValue(new QualifierValue("all_some", string));
}
if (allOnly != null) {
String string = allOnly.toString();
assert string != null;
c.addQualifierValue(new QualifierValue("all_only", string));
}
addQualifiers(c, ax.getAnnotations());
} else if (!f.getClauses(OboFormatTag.TAG_INTERSECTION_OF).isEmpty()) {
error(
"The axiom is not translated (maximimum one IntersectionOf EquivalenceAxiom)",
ax, false);
} else {
isUntranslateable = true;
error(ax, false);
}
}
} else {
isUntranslateable = true;
error(ax, false);
}
// Only add clauses if the *entire* equivalence axiom can be translated
if (!isUntranslateable) {
for (Clause c : equivalenceAxiomClauses) {
f.addClause(c);
}
}
}
/**
* Tr.
*
* @param ax the ax
*/
protected void tr(@Nonnull OWLDisjointClassesAxiom ax) {
// use set, the OWL-API does not provide an order
Set set = ax.getClassExpressions();
if (set.size() != 2) {
error("Expected two classes in a disjoin classes axiom.", ax, false);
}
Iterator it = set.iterator();
OWLClassExpression ce1 = it.next();
OWLClassExpression ce2 = it.next();
if (ce1.isBottomEntity() || ce1.isTopEntity() || ce2.isBottomEntity()
|| ce2.isTopEntity()) {
error("Disjoint classes axiom using Top or Bottom entities are not supported.", ax,
false);
}
String cls2 = getIdentifier(ce2);
if (cls2 == null) {
error(ax, true);
return;
}
if (ce1.isAnonymous()) {
error(ax, false);
return;
}
OWLClass cls1 = ce1.asOWLClass();
Frame f = getTermFrame(cls1);
Clause c = new Clause(OboFormatTag.TAG_DISJOINT_FROM.getTag());
c.setValue(cls2);
f.addClause(c);
addQualifiers(c, ax.getAnnotations());
}
/**
* Tr.
*
* @param axiom the axiom
*/
protected void tr(@Nonnull OWLDeclarationAxiom axiom) {
OWLEntity entity = axiom.getEntity();
if (entity.isBottomEntity() || entity.isTopEntity()) {
return;
}
Set set =
owlOntology.getAnnotationAssertionAxioms(entity.getIRI());
if (set.isEmpty()) {
return;
}
boolean isClass = entity.isOWLClass();
boolean isObjectProperty = entity.isOWLObjectProperty();
// check whether the entity is an alt_id
Optional altIdOptional = checkForOboAltId(set);
if (altIdOptional.isPresent()) {
// the entity will not be translated
// instead create the appropriate alt_id in the replaced_by frame
String currentId = getIdentifier(entity.getIRI());
addAltId(altIdOptional.get().replacedBy, currentId, isClass, isObjectProperty);
// add unrelated annotations to untranslatableAxioms axioms
untranslatableAxioms.addAll(altIdOptional.get().unrelated);
return;
}
// translate
Frame f = null;
if (isClass) {
f = getTermFrame(entity.asOWLClass());
} else if (isObjectProperty) {
f = getTypedefFrame(entity.asOWLObjectProperty());
} else if (entity.isOWLAnnotationProperty()) {
for (OWLAxiom a : set) {
OWLAnnotationAssertionAxiom ax = (OWLAnnotationAssertionAxiom) a;
OWLAnnotationProperty prop = ax.getProperty();
String tag = owlObjectToTag(prop);
if (OboFormatTag.TAG_IS_METADATA_TAG.getTag().equals(tag)) {
f = getTypedefFrame(entity);
break;
}
}
}
if (f != null) {
for (OWLAnnotationAssertionAxiom a : set) {
assert a != null;
tr(a, f);
}
add(f);
}
}
private void addAltId(@Nonnull String replacedBy, @Nonnull String altId, boolean isClass,
boolean isProperty) {
Frame replacedByFrame = null;
if (isClass) {
replacedByFrame = getTermFrame(replacedBy);
} else if (isProperty) {
replacedByFrame = getTypedefFrame(replacedBy);
}
if (replacedByFrame != null) {
boolean addClause = true;
// check existing alt_ids to avoid duplicate clauses
Collection existing = replacedByFrame.getClauses(OboFormatTag.TAG_ALT_ID);
for (Clause clause : existing) {
if (altId.equals(clause.getValue(String.class))) {
addClause = false;
}
}
if (addClause) {
replacedByFrame.addClause(new Clause(OboFormatTag.TAG_ALT_ID, altId));
}
}
}
/**
* Helper class: allow to return two values for the alt id check.
*/
private static class OboAltIdCheckResult {
final String replacedBy;
final Set unrelated;
OboAltIdCheckResult(@Nonnull String replacedBy,
@Nonnull Set unrelated) {
this.replacedBy = replacedBy;
this.unrelated = unrelated;
}
}
/**
* Check the entity annotations for axioms declaring it to be an obsolete entity, with
* 'obsolescence reason' being 'term merge', and a non-empty 'replaced by' literal. This
* corresponds to an OBO alternate identifier. Track non related annotations.
*
* @param annotations set of annotations for the entity @return replaced_by if it is an alt_id
* @return optional check result
*/
@Nonnull
private static Optional checkForOboAltId(
Set annotations) {
String replacedBy = null;
boolean isMerged = false;
boolean isDeprecated = false;
final Set unrelatedAxioms = new HashSet<>();
for (OWLAnnotationAssertionAxiom axiom : annotations) {
OWLAnnotationProperty prop = axiom.getProperty();
if (prop.isDeprecated()) {
isDeprecated = true;
} else if (Obo2OWLConstants.IRI_IAO_0000231.equals(prop.getIRI())) {
OWLAnnotationValue value = axiom.getValue();
Optional asIRI = value.asIRI();
if (asIRI.isPresent()) {
isMerged = Obo2OWLConstants.IRI_IAO_0000227.equals(asIRI.get());
} else {
unrelatedAxioms.add(axiom);
}
} else if (Obo2OWLVocabulary.IRI_IAO_0100001.iri.equals(prop.getIRI())) {
OWLAnnotationValue value = axiom.getValue();
Optional asLiteral = value.asLiteral();
if (asLiteral.isPresent()) {
replacedBy = asLiteral.get().getLiteral();
} else {
// fallback: also check for an IRI
Optional asIRI = value.asIRI();
if (asIRI.isPresent()) {
// translate IRI to OBO style ID
replacedBy = getIdentifier(asIRI.get());
} else {
unrelatedAxioms.add(axiom);
}
}
} else {
unrelatedAxioms.add(axiom);
}
}
Optional result;
if (replacedBy != null && isMerged && isDeprecated) {
result = Optional.of(new OboAltIdCheckResult(replacedBy, unrelatedAxioms));
} else {
result = Optional.absent();
}
return result;
}
/**
* Gets the identifier.
*
* @param obj the obj
* @return the identifier
*/
@Nullable
public String getIdentifier(OWLObject obj) {
try {
return getIdentifierFromObject(obj, getOWLOntology());
} catch (UntranslatableAxiomException e) {
error(e.getMessage(), true);
}
return null;
}
/**
* @return true if untranslatable axioms should not be logged
*/
public boolean isMuteUntranslatableAxioms() {
return muteUntranslatableAxioms;
}
/**
* @param muteUntranslatableAxioms true disables logging
*/
public void setMuteUntranslatableAxioms(boolean muteUntranslatableAxioms) {
this.muteUntranslatableAxioms = muteUntranslatableAxioms;
}
/**
* The Class UntranslatableAxiomException.
*/
public static class UntranslatableAxiomException extends Exception {
// generated
private static final long serialVersionUID = 40000L;
/**
* Instantiates a new untranslatable axiom exception.
*
* @param message the message
* @param cause the cause
*/
public UntranslatableAxiomException(String message, Throwable cause) {
super(message, cause);
}
/**
* Instantiates a new untranslatable axiom exception.
*
* @param message the message
*/
public UntranslatableAxiomException(String message) {
super(message);
}
}
/**
* Retrieve the identifier for a given {@link OWLObject}. This methods uses also shorthand hints
* to resolve the identifier. Should the translation process encounter a problem or not find an
* identifier the defaultValue is returned.
*
* @param obj the {@link OWLObject} to resolve
* @param ont the target ontology
* @param defaultValue the value to return in case of an error or no id
* @return identifier or the default value
*/
@Nonnull
public static String getIdentifierFromObject(@Nonnull OWLObject obj, @Nonnull OWLOntology ont,
@Nonnull String defaultValue) {
String id = defaultValue;
try {
id = getIdentifierFromObject(obj, ont);
if (id == null) {
id = defaultValue;
}
} catch (UntranslatableAxiomException e) {
LOG.error(e.getMessage(), e);
}
return id;
}
/**
* Retrieve the identifier for a given {@link OWLObject}. This methods uses also shorthand hints
* to resolve the identifier. Should the translation process encounter an unexpected axiom an
*
* @param obj the {@link OWLObject} to resolve
* @param ont the target ontology
* @return identifier or null
* @throws UntranslatableAxiomException the untranslatable axiom exception
* {@link UntranslatableAxiomException} is thrown.
*/
@SuppressWarnings("null")
@Nullable
public static String getIdentifierFromObject(OWLObject obj, @Nonnull OWLOntology ont)
throws UntranslatableAxiomException {
if (obj instanceof OWLObjectProperty || obj instanceof OWLAnnotationProperty) {
OWLEntity entity = (OWLEntity) obj;
Set axioms =
ont.getAnnotationAssertionAxioms(entity.getIRI());
for (OWLAnnotationAssertionAxiom ax : axioms) {
String propId = getIdentifierFromObject(ax.getProperty().getIRI(), ont);
// see BFOROXrefTest
// 5.9.3. Special Rules for Relations
if (propId.equals("shorthand")) {
OWLAnnotationValue value = ax.getValue();
if (value instanceof OWLLiteral) {
return ((OWLLiteral) value).getLiteral();
}
throw new UntranslatableAxiomException(
"Untranslatable axiom, expected literal value, but was: " + value
+ " in axiom: " + ax);
}
}
}
if (obj instanceof OWLEntity) {
return getIdentifier(((OWLEntity) obj).getIRI());
}
if (obj instanceof IRI) {
return getIdentifier((IRI) obj);
}
return null;
}
/**
* See table 5.9.2. Translation of identifiers
*
* @param iriId the iri id
* @return obo identifier or null
*/
@Nullable
public static String getIdentifier(@Nullable IRI iriId) {
if (iriId == null) {
return null;
}
String iri = iriId.toString();
// canonical IRIs
// if (iri.startsWith("http://purl.obolibrary.org/obo/")) {
// String canonicalId = iri.replace("http://purl.obolibrary.org/obo/",
// "");
// }
int indexSlash = iri.lastIndexOf('/');
String id = null;
if (indexSlash > -1) {
id = iri.substring(indexSlash + 1);
} else {
id = iri;
}
String[] s = id.split("#_");
// table 5.9.2 row 2 - NonCanonical-Prefixed-ID
if (s.length > 1) {
return s[0] + ':' + s[1];
}
// row 3 - Unprefixed-ID
s = id.split("#");
if (s.length > 1) {
// prefixURI = prefixURI + s[0] + "#";
// if(!(s[1].contains("#") || s[1].contains("_"))){
String prefix = "";
if ("owl".equals(s[0]) || "rdf".equals(s[0]) || "rdfs".equals(s[0])) {
prefix = s[0] + ':';
}
// TODO: the following implements behavior in current spec, but this
// leads to undesirable results
// else if (baseOntology != null) {
// String oid = getOntologyId(baseOntology); // OBO-style ID
// if (oid.equals(s[0]))
// prefix = "";
// else {
// return iri;
// }
// //prefix = s[0];
// }
return prefix + s[1];
}
// row 1 - Canonical-Prefixed-ID
s = id.split("_");
if (s.length == 2 && !id.contains("#") && !s[1].contains("_")) {
String localId;
try {
localId = java.net.URLDecoder.decode(s[1], "UTF-8");
return s[0] + ':' + localId;
} catch (UnsupportedEncodingException e) {
throw new OWLRuntimeException("UTF-8 not supported, JRE corrupted?", e);
}
}
if (s.length > 2 && !id.contains("#")
&& s[s.length - 1].replaceAll("[0-9]", "").isEmpty()) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < s.length; i++) {
if (i > 0) {
if (i == s.length - 1) {
sb.append(':');
} else {
sb.append('_');
}
}
sb.append(s[i]);
}
return sb.toString();
}
return iri;
}
/**
* Owl object to tag.
*
* @param obj the obj
* @return the string
*/
@Nullable
public static String owlObjectToTag(OWLObject obj) {
IRI iriObj = null;
if (obj instanceof OWLNamedObject) {
iriObj = ((OWLNamedObject) obj).getIRI();
} else if (obj instanceof IRI) {
iriObj = (IRI) obj;
}
if (iriObj == null) {
return null;
}
String iri = iriObj.toString();
String tag = ANNOTATIONPROPERTYMAP.get(iri);
if (tag == null) {
// hardcoded values for legacy annotation properties: (TEMPORARY)
if (iri.startsWith(Obo2OWLConstants.DEFAULT_IRI_PREFIX + "IAO_")) {
String legacyId = iri.replace(Obo2OWLConstants.DEFAULT_IRI_PREFIX, "");
if (legacyId.equals("IAO_xref")) {
return OboFormatTag.TAG_XREF.getTag();
}
if (legacyId.equals("IAO_id")) {
return OboFormatTag.TAG_ID.getTag();
}
if (legacyId.equals("IAO_namespace")) {
return OboFormatTag.TAG_NAMESPACE.getTag();
}
}
String prefix = Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
if (iri.startsWith(prefix)) {
tag = iri.substring(prefix.length());
}
}
return tag;
}
/**
* Gets the term frame.
*
* @param entity the entity
* @return the term frame
*/
protected Frame getTermFrame(@Nonnull OWLClass entity) {
String id = getIdentifier(entity.getIRI());
return getTermFrame(id);
}
private Frame getTermFrame(@Nonnull String id) {
Frame f = getObodoc().getTermFrame(id);
if (f == null) {
f = new Frame(FrameType.TERM);
f.setId(id);
f.addClause(new Clause(OboFormatTag.TAG_ID, id));
add(f);
}
return f;
}
/**
* Gets the typedef frame.
*
* @param entity the entity
* @return the typedef frame
*/
protected Frame getTypedefFrame(@Nonnull OWLEntity entity) {
String id = getIdentifier(entity);
return getTypedefFrame(id);
}
private Frame getTypedefFrame(@Nonnull String id) {
Frame f = getObodoc().getTypedefFrame(id);
if (f == null) {
f = new Frame(FrameType.TYPEDEF);
f.setId(id);
f.addClause(new Clause(OboFormatTag.TAG_ID, id));
add(f);
}
return f;
}
/**
* Tr.
*
* @param ax the ax
*/
@SuppressWarnings("null")
protected void tr(@Nonnull OWLClassAssertionAxiom ax) {
OWLObject cls = ax.getClassExpression();
if (!(cls instanceof OWLClass)) {
return;
}
String clsIRI = ((OWLClass) cls).getIRI().toString();
IRI labelPropertyIRI = OWLRDFVocabulary.RDFS_LABEL.getIRI();
if (IRI_CLASS_SYNONYMTYPEDEF.equals(clsIRI)) {
Frame f = getObodoc().getHeaderFrame();
Clause c = new Clause(OboFormatTag.TAG_SYNONYMTYPEDEF.getTag());
OWLNamedIndividual indv = (OWLNamedIndividual) ax.getIndividual();
String indvId = getIdentifier(indv);
// TODO: full specify this in the spec document.
// we may want to allow full IDs for subsets in future.
// here we would have a convention that an unprefixed
// subsetdef/synonymtypedef
// gets placed in a temp ID space, and only this id space is
// stripped
indvId = indvId.replaceFirst(".*:", "");
c.addValue(indvId);
c.addValue(indvId);
String nameValue = "";
String scopeValue = null;
for (OWLAnnotation ann : getAnnotationObjects(indv, getOWLOntology(), null)) {
String value = ((OWLLiteral) ann.getValue()).getLiteral();
if (ann.getProperty().getIRI().equals(labelPropertyIRI)) {
nameValue = '"' + value + '"';
} else {
scopeValue = value;
}
}
c.addValue(nameValue);
if (scopeValue != null) {
c.addValue(scopeValue);
}
f.addClause(c);
} else if (IRI_CLASS_SUBSETDEF.equals(clsIRI)) {
Frame f = getObodoc().getHeaderFrame();
Clause c = new Clause(OboFormatTag.TAG_SUBSETDEF.getTag());
OWLNamedIndividual indv = (OWLNamedIndividual) ax.getIndividual();
String indvId = getIdentifier(indv);
// TODO: full specify this in the spec document.
// we may want to allow full IDs for subsets in future.
// here we would have a convention that an unprefixed
// subsetdef/synonymtypedef
// gets placed in a temp ID space, and only this id space is
// stripped
indvId = indvId.replaceFirst(".*:", "");
c.addValue(indvId);
String nameValue = "";
for (OWLAnnotation ann : getAnnotationObjects(indv, getOWLOntology(), null)) {
String value = ((OWLLiteral) ann.getValue()).getLiteral();
if (ann.getProperty().getIRI().equals(labelPropertyIRI)) {
nameValue = '"' + value + '"';
}
}
c.addValue(nameValue);
f.addClause(c);
} else {
// TODO: individual
}
}
/**
* Tr.
*
* @param ax the ax
*/
@SuppressWarnings("null")
protected void tr(@Nonnull OWLSubClassOfAxiom ax) {
OWLClassExpression sub = ax.getSubClass();
OWLClassExpression sup = ax.getSuperClass();
if (sub.isOWLNothing() || sub.isTopEntity() || sup.isTopEntity() || sup.isOWLNothing()) {
error(TOP_BOTTOM_NONTRANSLATEABLE, ax, false);
return;
}
Set qvs = new HashSet<>();
// 5.2.2
if (sub instanceof OWLObjectIntersectionOf) {
Set xs = ((OWLObjectIntersectionOf) sub).getOperands();
// obo-format is limited to very restricted GCIs - the LHS of the
// axiom
// must correspond to ObjectIntersectionOf(cls
// ObjectSomeValuesFrom(p filler))
if (xs.size() == 2) {
OWLClass c = null;
OWLObjectSomeValuesFrom r = null;
OWLObjectProperty p = null;
OWLClass filler = null;
for (OWLClassExpression x : xs) {
if (x instanceof OWLClass) {
c = (OWLClass) x;
}
if (x instanceof OWLObjectSomeValuesFrom) {
r = (OWLObjectSomeValuesFrom) x;
if (r.getProperty() instanceof OWLObjectProperty
&& r.getFiller() instanceof OWLClass) {
p = (OWLObjectProperty) r.getProperty();
filler = (OWLClass) r.getFiller();
}
}
}
if (c != null && p != null && filler != null) {
sub = c;
qvs.add(new QualifierValue("gci_relation", getIdentifier(p)));
qvs.add(new QualifierValue("gci_filler", getIdentifier(filler)));
}
}
}
if (sub instanceof OWLClass) {
Frame f = getTermFrame((OWLClass) sub);
if (sup instanceof OWLClass) {
Clause c = new Clause(OboFormatTag.TAG_IS_A.getTag());
c.setValue(getIdentifier(sup));
c.setQualifierValues(qvs);
f.addClause(c);
addQualifiers(c, ax.getAnnotations());
} else if (sup instanceof OWLObjectCardinalityRestriction) {
// OWLObjectExactCardinality
// OWLObjectMinCardinality
// OWLObjectMaxCardinality
OWLObjectCardinalityRestriction cardinality = (OWLObjectCardinalityRestriction) sup;
OWLClassExpression filler = cardinality.getFiller();
if (filler.isBottomEntity() || filler.isTopEntity()) {
error(TOP_BOTTOM_NONTRANSLATEABLE, ax, false);
return;
}
String fillerId = getIdentifier(filler);
if (fillerId == null) {
error(ax, true);
return;
}
f.addClause(
createRelationshipClauseWithCardinality(cardinality, fillerId, qvs, ax));
} else if (sup instanceof OWLQuantifiedObjectRestriction) {
// OWLObjectSomeValuesFrom
// OWLObjectAllValuesFrom
OWLQuantifiedObjectRestriction r = (OWLQuantifiedObjectRestriction) sup;
OWLClassExpression filler = r.getFiller();
if (filler.isBottomEntity() || filler.isTopEntity()) {
error(TOP_BOTTOM_NONTRANSLATEABLE, ax, false);
return;
}
String fillerId = getIdentifier(filler);
if (fillerId == null) {
error(ax, true);
return;
}
if (r instanceof OWLObjectAllValuesFrom) {
qvs.add(new QualifierValue("all_only", "true"));
}
f.addClause(createRelationshipClauseWithRestrictions(r, fillerId, qvs, ax));
} else if (sup instanceof OWLObjectIntersectionOf) {
OWLObjectIntersectionOf i = (OWLObjectIntersectionOf) sup;
List clauses = new ArrayList<>();
for (OWLClassExpression operand : i.getOperands()) {
if (operand instanceof OWLObjectCardinalityRestriction) {
OWLObjectCardinalityRestriction restriction =
(OWLObjectCardinalityRestriction) operand;
OWLClassExpression filler = restriction.getFiller();
if (filler.isBottomEntity() || filler.isTopEntity()) {
error(TOP_BOTTOM_NONTRANSLATEABLE, ax, false);
return;
}
String fillerId = getIdentifier(filler);
if (fillerId == null) {
error(ax, true);
return;
}
clauses.add(createRelationshipClauseWithCardinality(restriction, fillerId,
new HashSet<>(qvs), ax));
} else if (operand instanceof OWLQuantifiedObjectRestriction) {
OWLQuantifiedObjectRestriction restriction =
(OWLQuantifiedObjectRestriction) operand;
OWLClassExpression filler = restriction.getFiller();
if (filler.isBottomEntity() || filler.isTopEntity()) {
error(TOP_BOTTOM_NONTRANSLATEABLE, ax, false);
return;
}
String fillerId = getIdentifier(filler);
if (fillerId == null) {
error(ax, true);
return;
}
clauses.add(createRelationshipClauseWithRestrictions(restriction, fillerId,
new HashSet<>(qvs), ax));
} else {
error(ax, true);
return;
}
}
if (clauses.isEmpty()) {
error(ax, true);
return;
}
clauses = normalizeRelationshipClauses(clauses);
for (Clause clause : clauses) {
f.addClause(clause);
}
} else {
error(ax, true);
return;
}
} else {
error(ax, true);
return;
}
}
/**
* Creates the relationship clause with restrictions.
*
* @param r the r
* @param fillerId the filler id
* @param qvs the qvs
* @param ax the ax
* @return the clause
*/
@Nonnull
protected Clause createRelationshipClauseWithRestrictions(
@Nonnull OWLQuantifiedObjectRestriction r, String fillerId,
@Nonnull Set qvs, @Nonnull OWLSubClassOfAxiom ax) {
Clause c = new Clause(OboFormatTag.TAG_RELATIONSHIP.getTag());
c.addValue(getIdentifier(r.getProperty()));
c.addValue(fillerId);
c.setQualifierValues(qvs);
addQualifiers(c, ax.getAnnotations());
return c;
}
/**
* Creates the relationship clause with cardinality.
*
* @param restriction the restriction
* @param fillerId the filler id
* @param qvs the qvs
* @param ax the ax
* @return the clause
*/
@Nonnull
protected Clause createRelationshipClauseWithCardinality(
@Nonnull OWLObjectCardinalityRestriction restriction, String fillerId,
@Nonnull Set qvs, @Nonnull OWLSubClassOfAxiom ax) {
Clause c = new Clause(OboFormatTag.TAG_RELATIONSHIP.getTag());
c.addValue(getIdentifier(restriction.getProperty()));
c.addValue(fillerId);
c.setQualifierValues(qvs);
String q = "cardinality";
if (restriction instanceof OWLObjectMinCardinality) {
q = MIN_CARDINALITY;
} else if (restriction instanceof OWLObjectMaxCardinality) {
q = MAX_CARDINALITY;
}
c.addQualifierValue(new QualifierValue(q, Integer.toString(restriction.getCardinality())));
addQualifiers(c, ax.getAnnotations());
return c;
}
/**
* Join clauses and its {@link QualifierValue} which have the same relationship type and target.
* Try to resolve conflicts for multiple statements. E.g., min=2 and min=3 is resolved to min=2,
* or max=2 and max=4 is resolved to max=4. It will not merge conflicting exact cardinality
* statements. TODO How to merge "all_some", and "all_only"?
*
* @param clauses the clauses
* @return normalized list of {@link Clause}
*/
@Nonnull
public static List normalizeRelationshipClauses(@Nonnull List clauses) {
List normalized = new ArrayList<>();
while (!clauses.isEmpty()) {
Clause target = clauses.remove(0);
assert target != null;
List similar = findSimilarClauses(clauses, target);
normalized.add(target);
mergeSimilarIntoTarget(target, similar);
}
return normalized;
}
/**
* Find similar clauses.
*
* @param clauses the clauses
* @param target the target
* @return the list
*/
@SuppressWarnings("null")
@Nonnull
static List findSimilarClauses(@Nonnull List clauses, @Nonnull Clause target) {
String targetTag = target.getTag();
Object targetValue = target.getValue();
Object targetValue2 = target.getValue2();
List similar = new ArrayList<>();
Iterator iterator = clauses.iterator();
while (iterator.hasNext()) {
Clause current = iterator.next();
Object currentValue = current.getValue();
Object currentValue2 = current.getValue2();
if (targetTag.equals(current.getTag()) && targetValue.equals(currentValue)
&& Objects.equals(targetValue2, currentValue2)) {
similar.add(current);
iterator.remove();
}
}
return similar;
}
/**
* Merge similar into target.
*
* @param target the target
* @param similar the similar
*/
static void mergeSimilarIntoTarget(@Nonnull Clause target, @Nonnull List similar) {
if (similar.isEmpty()) {
return;
}
Collection targetQVs = target.getQualifierValues();
for (Clause current : similar) {
Collection newQVs = current.getQualifierValues();
for (QualifierValue newQV : newQVs) {
String newQualifier = newQV.getQualifier();
// if min or max cardinality check for possible merges
if (MIN_CARDINALITY.equals(newQualifier) || MAX_CARDINALITY.equals(newQualifier)) {
QualifierValue match = findMatchingQualifierValue(newQV, targetQVs);
if (match != null) {
mergeQualifierValues(match, newQV);
} else {
target.addQualifierValue(newQV);
}
} else {
target.addQualifierValue(newQV);
}
}
}
}
/**
* Find matching qualifier value.
*
* @param query the query
* @param list the list
* @return the qualifier value
*/
@Nullable
static QualifierValue findMatchingQualifierValue(@Nonnull QualifierValue query,
@Nonnull Collection list) {
String queryQualifier = query.getQualifier();
for (QualifierValue qv : list) {
if (queryQualifier.equals(qv.getQualifier())) {
return qv;
}
}
return null;
}
/**
* Merge qualifier values.
*
* @param target the target
* @param newQV the new qv
*/
static void mergeQualifierValues(@Nonnull QualifierValue target,
@Nonnull QualifierValue newQV) {
// do nothing, if they are equal
if (!target.getValue().equals(newQV.getValue())) {
if (MIN_CARDINALITY.equals(target.getQualifier())) {
// try to merge, parse as integers
int currentValue = Integer.parseInt(target.getValue().toString());
int newValue = Integer.parseInt(newQV.getValue().toString());
int mergedValue = Math.min(currentValue, newValue);
target.setValue(Integer.toString(mergedValue));
} else if (MAX_CARDINALITY.equals(target.getQualifier())) {
// try to merge, parse as integers
int currentValue = Integer.parseInt(target.getValue().toString());
int newValue = Integer.parseInt(newQV.getValue().toString());
int mergedValue = Math.max(currentValue, newValue);
target.setValue(Integer.toString(mergedValue));
}
}
}
protected void error(String message, OWLAxiom ax, boolean shouldLogComplaint) {
untranslatableAxioms.add(ax);
error(message + ax, shouldLogComplaint);
}
protected void error(OWLAxiom ax, boolean shouldLogComplaint) {
untranslatableAxioms.add(ax);
error("the axiom is not translated : " + ax, shouldLogComplaint);
}
protected void error(String message, boolean shouldLogComplaint) {
if (strictConversion) {
throw new OWLRuntimeException("The conversion is halted: " + message);
} else {
if (!muteUntranslatableAxioms && shouldLogComplaint) {
LOG.error("MASKING ERROR «{}»", message, new Exception());
}
}
}
protected void warn(String message) {
if (strictConversion) {
throw new OWLRuntimeException("The conversion is halted: " + message);
} else {
LOG.warn("MASKING ERROR «{}»", message);
}
}
}