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Remint #236

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07eeeef
remint
cmungall Jan 20, 2018
34ac462
added remint command
cmungall Jan 27, 2018
b4cc2e8
logging
cmungall Feb 15, 2018
1bb770a
added option --exclude-seen-literals for copy-axioms
cmungall Feb 19, 2018
3bfe279
minting
cmungall Apr 19, 2018
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1 change: 1 addition & 0 deletions OWLTools-Annotation/src/main/java/owltools/gaf/inference/FoldBasedPredictor.java
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Expand Up @@ -171,6 +171,7 @@ public List<Prediction> predictForBioEntities(Map<Bioentity, ? extends Collectio
// step 2: reasoner
reasoner = new ExpressionMaterializingReasonerFactory(new ElkReasonerFactory()).createReasoner(generatedContainer);
reasoner.setIncludeImports(true);
LOG.info("Materializing expressions for props: "+defaultProperties);
reasoner.materializeExpressions(defaultProperties);


Expand Down
221 changes: 208 additions & 13 deletions OWLTools-Core/src/main/java/owltools/mooncat/AxiomCopier.java
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@@ -1,11 +1,14 @@
package owltools.mooncat;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.log4j.Logger;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
Expand All @@ -22,12 +25,14 @@
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.semanticweb.owlapi.util.OWLEntityRenamer;

import uk.ac.manchester.cs.owlapi.modularity.ModuleType;
import uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor;
Expand All @@ -47,12 +52,22 @@
*/
public class AxiomCopier {

private static Logger LOG = Logger.getLogger(AxiomCopier.class);

/**
* If true, copy axiom over even if it exists in target.
* We may want to do this if we want to annotate an axiom with all sources
*/
public boolean isCopyDuplicates = false;


public boolean isCopyDuplicatesOnly = false;

/**
* If true, exclude annotation axiom if we already have seen the literal
* (regardless of axiom)
*/
public boolean isFreshLiteralsOnly = false;

/**
* If true, check all incoming axioms to ensure they do not cause
* incoherency
Expand All @@ -63,9 +78,15 @@ public class AxiomCopier {
* We have 2 strategies; see below
*/
public boolean isUseConservative = true;
public OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

public boolean isIncludeUnmapped = false;

public OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();

public boolean isCopyLabelToExactSynonym = false;

public boolean isIncludeInferred = false;


/**
* Simple IRI-value pairs representing an Annotation minus property
Expand Down Expand Up @@ -157,6 +178,7 @@ public String toString() {
* @throws OWLOntologyCreationException
*/
public Set<OWLAxiom> copyAxioms(OWLOntology sourceOnt, OWLOntology targetOnt, OWLOntology mapOnt) throws OWLOntologyCreationException {
LOG.info("Copying axioms...");

// axioms in targetOnt (minus annotations)
Set<OWLAxiom> axiomsExisting = new HashSet<>();
Expand All @@ -170,6 +192,11 @@ public Set<OWLAxiom> copyAxioms(OWLOntology sourceOnt, OWLOntology targetOnt, OW
// reflexive mappings of classes S->T
Map<OWLClass, OWLClass> eqMap = new HashMap<>();

// all literals encountered
Set<String> literals = new HashSet<String>();



OWLDataFactory df = targetOnt.getOWLOntologyManager().getOWLDataFactory();

Set<OWLAxiom> targetAxioms = targetOnt.getAxioms(Imports.EXCLUDED);
Expand All @@ -195,6 +222,15 @@ else if (ax instanceof OWLAnnotationAssertionAxiom) {
OWLAnnotationAssertionAxiom aax = (OWLAnnotationAssertionAxiom)ax;
AnnTuple tup = getAnnTuple(aax);
annTuples.add(tup);
literals.add(tup.val);
}
}
LOG.info("AnnTuples = "+annTuples.size());

if (isIncludeUnmapped) {
// seed with reflexive mappings
for (OWLClass c : sourceOnt.getClassesInSignature(Imports.EXCLUDED)) {
eqMap.put(c, c);
}
}

Expand All @@ -213,12 +249,42 @@ else if (ax instanceof OWLAnnotationAssertionAxiom) {
}
}
}
LOG.info("eqMap = "+eqMap.size());

Set<OWLAxiom> axiomsToAdd = new HashSet<>();

Set<OWLAxiom> srcAxioms = sourceOnt.getAxioms(Imports.EXCLUDED);

Set<OWLAxiom> inferredSrcAxioms = new HashSet<>();
if (isIncludeInferred) {

LOG.info("computing inferred source axioms; orig = "+srcAxioms.size());
OWLReasoner reasoner = reasonerFactory.createReasoner(sourceOnt);
for (OWLClass c : sourceOnt.getClassesInSignature()) {

Set<OWLClass> ancs = new HashSet<>(reasoner.getSuperClasses(c, false).getFlattened());
ancs.removeAll(reasoner.getSuperClasses(c, true).getFlattened());
LOG.info("C= "+c +" ancs = "+ancs.size());
for (OWLClass a : ancs) {
String id = c.getIRI().toString();
id = id.replaceAll(".*/", "");
id = id.replaceAll("_", ":");

OWLAnnotationProperty p =
df.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#source"));
OWLAnnotation ann = df.getOWLAnnotation(p, df.getOWLLiteral(id+"/inferred"));
OWLSubClassOfAxiom ax = df.getOWLSubClassOfAxiom(c, a, Collections.singleton(ann));
srcAxioms.add(ax);
inferredSrcAxioms.add(ax);
}

}
LOG.info("computed inferred source axioms; total = "+srcAxioms.size());
}

if (isTestForCoherency) {
LOG.info("testing for coherency");

Set<OWLAxiom> badAxioms = findIncoherentAxioms(reasonerFactory, sourceOnt, targetOnt, mapOnt);
System.out.println("ORIG:"+srcAxioms.size());
System.out.println("INCOHERENCY-CAUSING AXIOMS:"+badAxioms.size());
Expand Down Expand Up @@ -253,9 +319,24 @@ else if (ax instanceof OWLAnnotationAssertionAxiom) {
eqMap.get(supc),
anns(df, srcClass, false));

// preserve original annotations for inferred
// (we previously stamp these)
if (inferredSrcAxioms.contains(ax)) {
newAxiom = df.getOWLSubClassOfAxiom(eqMap.get(srcClass),
eqMap.get(supc),
ax.getAnnotations());
}

boolean isAdd = false;
// add copy to list
if (isCopyDuplicates ||
!axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations())) {
isAdd = true;
}
if (isCopyDuplicatesOnly) {
isAdd = axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations());
}
if (isAdd) {
axiomsToAdd.add(newAxiom);
}
}
Expand All @@ -276,11 +357,19 @@ else if (!sca.getSubClass().isAnonymous() && sca.getSuperClass().isAnonymous())
df.getOWLObjectSomeValuesFrom(x.getProperty(), eqMap.get(supc)),
anns(df, srcClass, false));

boolean isAdd = false;
// add copy to list
if (isCopyDuplicates ||
!axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations())) {
isAdd = true;
}
if (isCopyDuplicatesOnly) {
isAdd = axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations());
}
if (isAdd) {
axiomsToAdd.add(newAxiom);
}

}
}
}
Expand All @@ -305,26 +394,44 @@ else if (ax instanceof OWLAnnotationAssertionAxiom){

// OBO convention: xref annotations are treated differently for
// axiom annotations (as are defs)
boolean isXrefAnn = aax.getProperty().getIRI().toString().contains("Synonym");

OWLAnnotationAssertionAxiom newAxiom = df.getOWLAnnotationAssertionAxiom(aax.getProperty(),
eqMap.get(srcClass).getIRI(),
aax.getValue(),
anns(df, srcClass, isXrefAnn));
AnnTuple tup = getAnnTuple(newAxiom);
boolean isXrefAnn =
aax.getProperty().getIRI().toString().contains("Synonym") ||
aax.getProperty().getIRI().toString().equals("http://purl.obolibrary.org/obo/IAO_0000115");
OWLAnnotationProperty ap1 = aax.getProperty();
Set<OWLAnnotationProperty> aps = new HashSet<>();
aps.add(ap1);
if (ap1.isLabel()) {
if (isCopyLabelToExactSynonym) {
OWLAnnotationProperty sp =
df.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"));

aps.add(sp);
}
}
for (OWLAnnotationProperty ap: aps) {
OWLAnnotationAssertionAxiom newAxiom = df.getOWLAnnotationAssertionAxiom(ap,
eqMap.get(srcClass).getIRI(),
aax.getValue(),
anns(df, srcClass, isXrefAnn));
AnnTuple tup = getAnnTuple(newAxiom);

boolean isDupe = annTuples.contains(tup) ||
axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations());
if (isCopyDuplicates || !isDupe) {
boolean isDupe = annTuples.contains(tup) ||
axiomsExisting.contains(newAxiom.getAxiomWithoutAnnotations());
if (isFreshLiteralsOnly && literals.contains(tup.val))
isDupe = true;
if (isCopyDuplicates || !isDupe) {
axiomsToAdd.add(newAxiom);
}
}
axiomsToAdd.add(df.getOWLDeclarationAxiom(eqMap.get(srcClass)));
}
}
else {
//System.out.println("SKIP:"+ax);

}
}
LOG.info("Axioms to add = "+axiomsToAdd.size());
return axiomsToAdd;
}

Expand Down Expand Up @@ -359,6 +466,7 @@ private AnnTuple getAnnTuple(OWLAnnotationAssertionAxiom aax) {
v = av.toString();
}
v = v.toLowerCase();
v = v.replaceAll("^ +", "").replaceAll(" +$", "");
return new AnnTuple((IRI)aax.getSubject(), v);
}

Expand Down Expand Up @@ -440,6 +548,93 @@ public Set<OWLAxiom> findIncoherentAxioms(OWLReasonerFactory rf,
return badAxioms;

}


public class IdAssigner {
public OWLOntology ontology;
public String prefix;
Integer lastId = 0;
Set<String> taken = null;
}

public IRI getNextId(IdAssigner ida) {
//int id = ida.lastId;
Set<String> taken = ida.taken;

if (taken == null) {
taken = new HashSet<>();
for (OWLClass cls : ida.ontology.getClassesInSignature()) {
String frag = cls.getIRI().getFragment();
String[] parts = frag.split("_");
if (parts.length == 2) {
String id = parts[0] + ":" + parts[1];
taken.add(id);
String prefix = parts[0];
if (ida.prefix == null)
ida.prefix = prefix;
if (ida.prefix.equals(prefix)) {

}
else {
//
}
}
else {
// warn
}
}
}
String id = null;
while (id == null) {
ida.lastId ++;
String nextid = ida.prefix + String.format(":%07d", ida.lastId);
if (!taken.contains(nextid)) {
id = nextid;
}
}

return IRI.create(id);

}

public void remintOntologyIds(OWLOntology ontology, String prefix, boolean isCreateLabels) {
IdAssigner ida = new IdAssigner();
ida.ontology = ontology;
ida.prefix = prefix;
remintOntologyIds(ontology, ida, isCreateLabels);
}

/**
* Mint new IDs for all classes in an ontology
*
* @param ontology
* @param ida
*/
public void remintOntologyIds(OWLOntology ontology, IdAssigner ida, boolean isCreateLabels) {
if (ida == null) {
ida = new IdAssigner();
ida.ontology = ontology;
}
OWLOntologyManager m = ontology.getOWLOntologyManager();
OWLDataFactory df = m.getOWLDataFactory();
Map<IRI, IRI> iriMap = new HashMap<>();
OWLEntityRenamer renamer = new OWLEntityRenamer(m,
ontology.getImportsClosure());
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange> ();
for (OWLClass c : ontology.getClassesInSignature()) {
IRI id = getNextId(ida);
iriMap.put(c.getIRI(), id);
List<OWLOntologyChange> ch =
renamer.changeIRI(c.getIRI(), id);
changes.addAll(ch);
if (isCreateLabels) {
String label = c.getIRI().getFragment();
label = label.replaceAll("_", " ");
OWLAnnotationValue value = df.getOWLLiteral(label);
OWLAnnotationAssertionAxiom ax =
df.getOWLAnnotationAssertionAxiom(df.getRDFSLabel(), id, value);
m.addAxiom(ontology, ax);
}
}
m.applyChanges(changes);
}
}
6 changes: 5 additions & 1 deletion OWLTools-Core/src/test/java/owltools/mooncat/ProvenanceReasonerWrapperTest.java
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Expand Up @@ -7,6 +7,8 @@
import org.junit.Test;
import org.semanticweb.elk.owlapi.ElkReasonerFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
import org.semanticweb.owlapi.util.PriorityCollection;

import owltools.OWLToolsTestBasics;
import owltools.io.CatalogXmlIRIMapper;
Expand All @@ -23,7 +25,9 @@ public class ProvenanceReasonerWrapperTest extends OWLToolsTestBasics {
@Test
public void testReason() throws Exception {
ParserWrapper pw = new ParserWrapper();
pw.getManager().getIRIMappers().add(new CatalogXmlIRIMapper(getResource("mooncat/eq-lattice/catalog-v001.xml")));
CatalogXmlIRIMapper cm = new CatalogXmlIRIMapper(getResource("mooncat/eq-lattice/catalog-v001.xml"));
PriorityCollection<OWLOntologyIRIMapper> im = pw.getManager().getIRIMappers();
im.add(cm);

OWLOntology o = pw.parseOWL(getResourceIRIString("mooncat/eq-lattice/eq-with-imports.owl"));

Expand Down
2 changes: 1 addition & 1 deletion OWLTools-Parent/pom.xml
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Expand Up @@ -18,7 +18,7 @@
</issueManagement>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<owlapi.version>4.5.0</owlapi.version>
<owlapi.version>4.2.8</owlapi.version>
<slf4j.version>1.7.10</slf4j.version>
</properties>

Expand Down
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