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org.obolibrary.oboformat.parser.XrefExpander Maven / Gradle / Ivy
package org.obolibrary.oboformat.parser;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import javax.annotation.Nonnull;
import org.obolibrary.oboformat.model.Clause;
import org.obolibrary.oboformat.model.Frame;
import org.obolibrary.oboformat.model.Frame.FrameType;
import org.obolibrary.oboformat.model.FrameMergeException;
import org.obolibrary.oboformat.model.OBODoc;
import org.obolibrary.oboformat.model.Xref;
import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/** xref expander */
public class XrefExpander {
protected static final Logger LOG = LoggerFactory.getLogger(XrefExpander.class);
OBODoc sourceOBODoc;
OBODoc targetOBODoc;
String targetBase;
@Nonnull
Map treatMap = new HashMap<>();
@Nonnull
Map targetDocMap = new HashMap<>();
/**
* @param src
* src
* @throws InvalidXrefMapException
* InvalidXrefMapException
*/
public XrefExpander(@Nonnull OBODoc src) {
sourceOBODoc = src;
Frame shf = src.getHeaderFrame();
String ontId = shf.getTagValue(OboFormatTag.TAG_ONTOLOGY, String.class);
String tgtOntId = ontId + "/xref_expansions";
targetOBODoc = new OBODoc();
Frame thf = new Frame(FrameType.HEADER);
thf.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, tgtOntId));
targetOBODoc.setHeaderFrame(thf);
sourceOBODoc.addImportedOBODoc(targetOBODoc);
setUp();
}
/**
* @param src
* src
* @param targetBase
* targetBase
* @throws InvalidXrefMapException
* InvalidXrefMapException
*/
public XrefExpander(OBODoc src, String targetBase) {
sourceOBODoc = src;
this.targetBase = targetBase;
setUp();
}
/**
* @param src
* src
* @param tgt
* tgt
* @throws InvalidXrefMapException
* InvalidXrefMapException
*/
public XrefExpander(OBODoc src, OBODoc tgt) {
sourceOBODoc = src;
targetOBODoc = tgt;
setUp();
}
/**
* @throws InvalidXrefMapException
* InvalidXrefMapException
*/
public final void setUp() {
// required for translation of IDs
// obo2owl = new Obo2Owl();
// obo2owl.setObodoc(sourceOBODoc);
Map relationsUseByIdSpace = new HashMap<>();
for (Clause c : sourceOBODoc.getHeaderFrame().getClauses()) {
String[] parts;
String v = c.getValue(String.class);
if (v == null) {
LOG.error("problem with header clause in xref expansion: {}", c);
continue;
}
parts = v.split("\\s");
String relation = null;
String idSpace = parts[0];
if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_EQUIVALENT.getTag())) {
addRule(parts[0], new EquivalenceExpansion());
// addMacro(idSpace,"is_specific_equivalent_of","Class: ?X
// EquivalentTo: ?Y and "+oboIdToIRI(parts[1])+" some
// "+oboIdToIRI(parts[2]));
} else if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_GENUS_DIFFERENTIA.getTag())) {
addRule(idSpace, new GenusDifferentiaExpansion(parts[1], parts[2]));
// addMacro(idSpace,"is_generic_equivalent_of","Class: ?Y
// EquivalentTo: ?X and "+oboIdToIRI(parts[1])+" some
// "+oboIdToIRI(parts[2]));
relationsUseByIdSpace.put(idSpace, parts[1]);
relation = parts[1];
} else if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_REVERSE_GENUS_DIFFERENTIA.getTag())) {
addRule(idSpace, new ReverseGenusDifferentiaExpansion(parts[1], parts[2]));
// addMacro(idSpace,"is_generic_equivalent_of","Class: ?Y
// EquivalentTo: ?X and "+oboIdToIRI(parts[1])+" some
// "+oboIdToIRI(parts[2]));
relationsUseByIdSpace.put(idSpace, parts[1]);
relation = parts[1];
} else if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.getTag())) {
addRule(idSpace, new HasSubClassExpansion());
} else if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.getTag())) {
addRule(idSpace, new IsaExpansion());
} else if (c.getTag().equals(OboFormatTag.TAG_TREAT_XREFS_AS_RELATIONSHIP.getTag())) {
addRule(idSpace, new RelationshipExpansion(parts[1]));
relationsUseByIdSpace.put(idSpace, parts[1]);
relation = parts[1];
} else {
continue;
}
if (targetBase != null) {
// create a new bridge ontology for every expansion macro
OBODoc tgt = new OBODoc();
Frame thf = new Frame(FrameType.HEADER);
thf.addClause(new Clause(OboFormatTag.TAG_ONTOLOGY, targetBase + "-" + idSpace.toLowerCase()));
tgt.setHeaderFrame(thf);
targetDocMap.put(idSpace, tgt);
sourceOBODoc.addImportedOBODoc(tgt);
if (relation != null) {
// See 4.4.2
// "In addition, any Typedef frames for relations used in a
// header macro
// are also copied into the corresponding bridge ontology
Frame tdf = sourceOBODoc.getTypedefFrame(relation);
if (tdf != null) {
try {
tgt.addTypedefFrame(tdf);
} catch (FrameMergeException e) {
LOG.debug("frame merge failed", e);
}
}
}
}
}
}
/**
* @param idSpace
* idSpace
* @return target doc
*/
public OBODoc getTargetDoc(String idSpace) {
if (targetOBODoc != null) {
return targetOBODoc;
}
return targetDocMap.get(idSpace);
}
private void addRule(String db, @Nonnull Rule rule) {
if (treatMap.containsKey(db)) {
throw new InvalidXrefMapException(db);
}
rule.idSpace = db;
treatMap.put(db, rule);
}
/** expand xrefs */
public void expandXrefs() {
for (Frame f : sourceOBODoc.getTermFrames()) {
String id = f.getTagValue(OboFormatTag.TAG_ID, String.class);
Collection clauses = f.getClauses(OboFormatTag.TAG_XREF);
for (Clause c : clauses) {
Xref x = c.getValue(Xref.class);
if (x != null) {
String xid = x.getIdref();
String s = getIDSpace(xid);
if (treatMap.containsKey(s)) {
treatMap.get(s).expand(f, id, xid);
}
}
}
}
}
private static String getIDSpace(@Nonnull String x) {
String[] parts = x.split(":", 2);
return parts[0];
}
/** rule */
public abstract class Rule {
protected String xref;
/** id space */
public String idSpace;
/**
* @param sf
* sf
* @param id
* id
* @param xRef
* xref
*/
public abstract void expand(@Nonnull Frame sf, String id, String xRef);
@Nonnull
protected Frame getTargetFrame(String id) {
Frame f = getTargetDoc(idSpace).getTermFrame(id);
if (f == null) {
f = new Frame();
f.setId(id);
try {
getTargetDoc(idSpace).addTermFrame(f);
} catch (FrameMergeException e) {
// this should be impossible
LOG.error("Frame merge exceptions should not be possible", e);
}
}
return f;
}
}
/** equivalence expansion */
public class EquivalenceExpansion extends Rule {
@Override
public void expand(@Nonnull Frame sf, String id, String xRef) {
Clause c = new Clause(OboFormatTag.TAG_EQUIVALENT_TO, xRef);
sf.addClause(c);
}
}
/** subclass expansion */
public class HasSubClassExpansion extends Rule {
@Override
public void expand(Frame sf, String id, String xRef) {
Clause c = new Clause(OboFormatTag.TAG_IS_A, id);
getTargetFrame(xRef).addClause(c);
}
}
/** genus diff expansion */
public class GenusDifferentiaExpansion extends Rule {
protected final String rel;
protected final String tgt;
/**
* @param rel
* rel
* @param tgt
* tgt
*/
public GenusDifferentiaExpansion(String rel, String tgt) {
this.rel = rel;
this.tgt = tgt;
}
@Override
public void expand(Frame sf, String id, String xRef) {
Clause gc = new Clause(OboFormatTag.TAG_INTERSECTION_OF, xRef);
Clause dc = new Clause(OboFormatTag.TAG_INTERSECTION_OF);
dc.setValue(rel);
dc.addValue(tgt);
getTargetFrame(id).addClause(gc);
getTargetFrame(id).addClause(dc);
}
}
/** reverse genus differentia expansion */
public class ReverseGenusDifferentiaExpansion extends Rule {
protected final String rel;
protected final String tgt;
/**
* @param rel
* rel
* @param tgt
* tgt
*/
public ReverseGenusDifferentiaExpansion(String rel, String tgt) {
this.rel = rel;
this.tgt = tgt;
}
@Override
public void expand(Frame sf, String id, String xRef) {
Clause gc = new Clause(OboFormatTag.TAG_INTERSECTION_OF, id);
Clause dc = new Clause(OboFormatTag.TAG_INTERSECTION_OF);
dc.setValue(rel);
dc.addValue(tgt);
getTargetFrame(xRef).addClause(gc);
getTargetFrame(xRef).addClause(dc);
}
}
/** is a expansion */
public class IsaExpansion extends Rule {
@Override
public void expand(Frame sf, String id, String xRef) {
Clause c = new Clause(OboFormatTag.TAG_IS_A, xRef);
getTargetFrame(id).addClause(c);
}
}
/** relationship expansion */
public class RelationshipExpansion extends Rule {
protected final String rel;
/**
* @param rel
* rel
*/
public RelationshipExpansion(String rel) {
this.rel = rel;
}
@Override
public void expand(Frame sf, String id, String xRef) {
Clause c = new Clause(OboFormatTag.TAG_RELATIONSHIP, rel);
c.addValue(xRef);
getTargetFrame(id).addClause(c);
}
}
}
