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additional cmd --obsolete-replace
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@cmungall
cmungall committed Oct 6, 2017
1 parent 4879157 commit 67c2aa1
Showing 1 changed file with 78 additions and 12 deletions.
90 changes: 78 additions & 12 deletions OWLTools-Runner/src/main/java/owltools/cli/CommandRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1463,6 +1463,11 @@ else if (opts.nextEq("-x")) {
}
esmu.merge();
}
else if (opts.nextEq("--replace-annotations")) {
opts.info("[-p PROP]", "Replace annotation assertions of type PROP for equivalent classes");
// TODO

}
else if (opts.nextEq("--merge-equivalent-classes")) {
opts.info("[-f FROM-URI-PREFIX]* [-t TO-URI-PREFIX] [-a] [-sa]", "merges equivalent classes, from source(s) to target ontology");
List<String> prefixFroms = new Vector<String>();
Expand Down Expand Up @@ -1504,7 +1509,9 @@ else if (opts.nextEq("-sa|--prioritize-annotations-from-source")) {
// we use equivalence axioms from the full complement of ontologies
// TODO - allow arbitrary entities
Map<Integer,Integer> binSizeMap = new HashMap<Integer,Integer>();
for (OWLClass e : g.getSourceOntology().getClassesInSignature()) {
int nMatches = 0;

for (OWLClass e : g.getAllOWLClasses()) {
//LOG.info(" testing "+c+" ECAs: "+g.getSourceOntology().getEquivalentClassesAxioms(c));
// TODO - may be more efficient to invert order of testing
String iriStr = e.getIRI().toString();
Expand All @@ -1518,6 +1525,7 @@ else if (opts.nextEq("-sa|--prioritize-annotations-from-source")) {
if (prefixFroms.size()==0)
isMatch = true;
if (isMatch) {
nMatches ++;
Set<OWLClass> ecs = new HashSet<OWLClass>();
if (reasoner != null) {
ecs = reasoner.getEquivalentClasses(e).getEntities();
Expand All @@ -1534,6 +1542,7 @@ else if (opts.nextEq("-sa|--prioritize-annotations-from-source")) {
}
}
int size = ecs.size();
LOG.debug("Equiv mappings for : "+e+" = "+ecs);
if (binSizeMap.containsKey(size)) {
binSizeMap.put(size, binSizeMap.get(size) +1);
}
Expand All @@ -1547,6 +1556,7 @@ else if (opts.nextEq("-sa|--prioritize-annotations-from-source")) {

// add to mapping. Renaming will happen later
e2iri.put(e, d.getIRI()); // TODO one-to-many
LOG.debug("mapping "+e+" -> "+d);

// annotation collapsing. In OBO, max cardinality of label, comment and definition is 1
// note that this not guaranteed to work if multiple terms are being merged in
Expand Down Expand Up @@ -1581,12 +1591,12 @@ else if (opts.nextEq("-sa|--prioritize-annotations-from-source")) {
}
}
}
LOG.info("Num matches = "+nMatches);
for (Integer k : binSizeMap.keySet()) {
LOG.info(" | Bin( "+k+" classes ) | = "+binSizeMap.get(k));
}
g.getManager().removeAxioms(g.getSourceOntology(), rmAxioms);
LOG.info("Mapping "+e2iri.size()+" entities");
// TODO - this is slow
List<OWLOntologyChange> changes = oer.changeIRI(e2iri);
g.getManager().applyChanges(changes);
LOG.info("Mapped "+e2iri.size()+" entities!");
Expand Down Expand Up @@ -3268,14 +3278,65 @@ else if (opts.nextEq("--obsolete-class")) {
}
else if (opts.nextEq("--obsolete-replace")) {
opts.info("ID REPLACEMENT-ID", "Add a deprecation axiom");
OWLObject obj = resolveEntity( opts);
OWLObject obsObj = resolveEntity( opts);
OWLObject repl = resolveEntity( opts);
OWLEntityRenamer oer = new OWLEntityRenamer(g.getManager(), g.getAllOntologies());
Set<OWLAxiom> rmAxioms = new HashSet<>();
OWLOntology ont = g.getSourceOntology();
IRI obsObjIRI = ((HasIRI) obsObj).getIRI();
IRI replIRI = ((HasIRI) repl).getIRI();
String origLabel = g.getLabel(obsObj);
String label = "obsolete "+origLabel;
for (OWLAnnotationAssertionAxiom a : ont.getAnnotationAssertionAxioms(obsObjIRI)) {
if (a.getProperty().isLabel()) {
rmAxioms.add(a);
}
if (a.getProperty().isComment()) {
rmAxioms.add(a);
}
if (a.getProperty().getIRI().equals(Obo2OWLVocabulary.IRI_IAO_0000115.getIRI())) {
//if (g.getDef(((HasIRI) repl).getIRI()) != null) {
rmAxioms.add(a);
//}
}
}
LOG.info("REMOVING: "+rmAxioms);
g.getManager().removeAxioms(ont, rmAxioms);

Map<OWLEntity,IRI> e2iri = new HashMap<OWLEntity,IRI>();
e2iri.put((OWLEntity) obsObj, replIRI);
List<OWLOntologyChange> changes = oer.changeIRI(e2iri);
g.getManager().applyChanges(changes);
OWLDataFactory df = g.getDataFactory();
Set<OWLAxiom> newAxioms = new HashSet<>();
OWLAnnotationProperty synp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_hasExactSynonym.getIRI());
OWLAnnotationProperty xp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_hasDbXref.getIRI());
OWLAnnotation synAnn = df.getOWLAnnotation(xp, df.getOWLLiteral(g.getIdentifier(obsObjIRI)));
Set<OWLAnnotation> synAnns = Collections.singleton(synAnn);
newAxioms.add(df.getOWLDeclarationAxiom((OWLClass)obsObj));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLDeprecated(), obsObjIRI, df.getOWLLiteral(true)));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getRDFSLabel(), obsObjIRI, df.getOWLLiteral(label)));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(synp, replIRI, df.getOWLLiteral(origLabel), synAnns));

OWLAnnotationProperty rp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0100001.getIRI());
newAxioms.add(df.getOWLAnnotationAssertionAxiom(rp, obsObjIRI,
df.getOWLLiteral(g.getIdentifier(repl))));

g.getManager().addAxioms(ont, newAxioms);

}
else if (opts.nextEq("--replace-annotations")) {
opts.info("[-p PROP]", "Replace annotation assertions of type PROP for equivalent classes");
OWLObject obsObj = resolveEntity( opts);
OWLObject repl = resolveEntity( opts);
OWLEntityRenamer oer = new OWLEntityRenamer(g.getManager(), g.getAllOntologies());
Set<OWLAxiom> rmAxioms = new HashSet<>();
OWLOntology ont = g.getSourceOntology();
IRI objIRI = ((HasIRI) obj).getIRI();
String label = "obsolete "+g.getLabel(obj);
for (OWLAnnotationAssertionAxiom a : ont.getAnnotationAssertionAxioms(objIRI)) {
IRI obsObjIRI = ((HasIRI) obsObj).getIRI();
IRI replIRI = ((HasIRI) repl).getIRI();
String origLabel = g.getLabel(obsObj);
String label = "obsolete "+origLabel;
for (OWLAnnotationAssertionAxiom a : ont.getAnnotationAssertionAxioms(obsObjIRI)) {
if (a.getProperty().isLabel()) {
rmAxioms.add(a);
}
Expand All @@ -3292,23 +3353,28 @@ else if (opts.nextEq("--obsolete-replace")) {
g.getManager().removeAxioms(ont, rmAxioms);

Map<OWLEntity,IRI> e2iri = new HashMap<OWLEntity,IRI>();
e2iri.put((OWLEntity) obj, ((HasIRI) repl).getIRI());
e2iri.put((OWLEntity) obsObj, replIRI);
List<OWLOntologyChange> changes = oer.changeIRI(e2iri);
g.getManager().applyChanges(changes);
OWLDataFactory df = g.getDataFactory();
Set<OWLAxiom> newAxioms = new HashSet<>();
newAxioms.add(df.getOWLDeclarationAxiom((OWLClass)obj));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLDeprecated(), objIRI, df.getOWLLiteral(true)));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getRDFSLabel(), objIRI, df.getOWLLiteral(label)));
OWLAnnotationProperty synp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_hasExactSynonym.getIRI());
OWLAnnotationProperty xp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_hasDbXref.getIRI());
OWLAnnotation synAnn = df.getOWLAnnotation(xp, df.getOWLLiteral(g.getIdentifier(obsObjIRI)));
Set<OWLAnnotation> synAnns = Collections.singleton(synAnn);
newAxioms.add(df.getOWLDeclarationAxiom((OWLClass)obsObj));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getOWLDeprecated(), obsObjIRI, df.getOWLLiteral(true)));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(df.getRDFSLabel(), obsObjIRI, df.getOWLLiteral(label)));
newAxioms.add(df.getOWLAnnotationAssertionAxiom(synp, replIRI, df.getOWLLiteral(origLabel), synAnns));

OWLAnnotationProperty rp = df.getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0100001.getIRI());
newAxioms.add(df.getOWLAnnotationAssertionAxiom(rp, objIRI,
newAxioms.add(df.getOWLAnnotationAssertionAxiom(rp, obsObjIRI,
df.getOWLLiteral(g.getIdentifier(repl))));

g.getManager().addAxioms(ont, newAxioms);

}
else if (opts.nextEq("-d") || opts.nextEq("--draw")) {
else if (opts.nextEq("-d") || opts.nextEq("--draw")) {
opts.info("[-o FILENAME] [-f FMT] LABEL/ID", "generates a file tmp.png made using QuickGO code");
String imgf = "tmp.png";
String fmt = "png";
Expand Down

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