Allow arbitrary annotation properties as qualifier tags in OBO #1099

Allowing arbitrary defined annotation properties as qualifier tags. Use oboInOWL as the default namespace when looking up tag IRIs. This helps with backwards compatibility for undeclared annotation properties. Enforce oio namespace for created_by and creation_date.
owlcs · Jan 13, 2024 · 8dda5c8 · 8dda5c8
1 parent b683b03
commit 8dda5c8
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Showing 10 changed files with 203 additions and 29 deletions.
diff --git a/contract/src/test/java/org/obolibrary/oboformat/LoadAnonymousTestCase.java b/contract/src/test/java/org/obolibrary/oboformat/LoadAnonymousTestCase.java
@@ -5,6 +5,7 @@
 import static org.semanticweb.owlapi.vocab.OWL2Datatype.XSD_STRING;
 
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.junit.jupiter.api.Test;
 import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
@@ -94,7 +95,10 @@ void shouldLoad() {
             AnnotationAssertion(Annotation(hasDbXref, literal), iao0000115, uo0.getIRI(),
                 literal("A unit of measurement is a standardized quantity of a physical quality.")),
             AnnotationAssertion(Annotation(hasDbXref, literal), iao0000115, uo1.getIRI(),
-                literal("A unit which is a standard measure of the distance between two points.")));
-        assertEquals(expected, asUnorderedSet(ontology.axioms()));
+                literal("A unit which is a standard measure of the distance between two points.")),
+            AnnotationAssertion(RDFSLabel(), createdBy.getIRI(), literal("created by")),
+            AnnotationAssertion(RDFSLabel(), id.getIRI(), literal("id")));
+
+        assertEquals(expected.stream().map(Object::toString).sorted().collect(Collectors.joining("\n")), ontology.axioms().map(Object::toString).sorted().collect(Collectors.joining("\n")));
     }
 }
diff --git a/contract/src/test/java/org/obolibrary/oboformat/RoundTripTestBasics.java b/contract/src/test/java/org/obolibrary/oboformat/RoundTripTestBasics.java
@@ -12,6 +12,7 @@
 import org.obolibrary.oboformat.diff.OBODocDiffer;
 import org.obolibrary.oboformat.model.FrameStructureException;
 import org.obolibrary.oboformat.model.OBODoc;
+import org.semanticweb.owlapi.formats.OBODocumentFormat;
 import org.semanticweb.owlapi.io.StringDocumentTarget;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
@@ -43,14 +44,19 @@ public List<Diff> roundTripOBODoc(OBODoc obodoc, boolean isExpectRoundtrip)
         OWLOntology oo = convert(obodoc);
         StringDocumentTarget oo1 = saveOntology(oo);
         OBODoc obodoc2 = convert(oo);
-        StringDocumentTarget oo2 = saveOntology(convert(obodoc2));
+        OWLOntology o2 = convert(obodoc2);
+        StringDocumentTarget oo2 = saveOntology(o2);
         String s1 = oo1.toString();
         String s2 = oo2.toString();
         assertEquals(s1, s2);
         obodoc2.check();
         List<Diff> diffs = OBODocDiffer.getDiffs(obodoc, obodoc2);
         if (isExpectRoundtrip) {
-            assertEquals(0, diffs.size(), "Expected no diffs but " + diffs);
+            if (diffs.size() > 0) {
+                StringDocumentTarget out1 = saveOntology(oo, new OBODocumentFormat());
+                StringDocumentTarget out2 = saveOntology(o2, new OBODocumentFormat());
+                assertEquals(out1.toString(), out2.toString());
+            }
         }
         return diffs;
     }

diff --git a/contract/src/test/java/org/obolibrary/oboformat/RoundTripTestCase.java b/contract/src/test/java/org/obolibrary/oboformat/RoundTripTestCase.java
@@ -229,7 +229,7 @@ void testRoundTripOWLRO() {
                 Collection<QualifierValue> values = clause.getQualifierValues();
                 assertEquals(1, values.size());
                 QualifierValue value = values.iterator().next();
-                assertEquals("http://purl.obolibrary.org/obo/IAO_0000116", value.getQualifier());
+                assertEquals("IAO:0000116", value.getQualifier());
                 assertEquals("From Allen terminology", value.getValue());
                 found = true;
             }

diff --git a/contract/src/test/java/org/obolibrary/oboformat/TagIRIsTest.java b/contract/src/test/java/org/obolibrary/oboformat/TagIRIsTest.java
@@ -0,0 +1,69 @@
+package org.obolibrary.oboformat;
+
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.Collections;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.junit.jupiter.api.Test;
+import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+
+class TagIRIsTest extends TestBase {
+
+    @Test
+    void testTagIRIMapping() {
+        OWLAnnotationProperty definition =
+            df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/IAO_0000115"));
+        OWLAnnotationProperty oioCreatedBy = df.getOWLAnnotationProperty(
+            IRI.create("http://www.geneontology.org/formats/oboInOwl#created_by"));
+        OWLAnnotationProperty oioInventedBy = df.getOWLAnnotationProperty(
+            IRI.create("http://www.geneontology.org/formats/oboInOwl#invented_by"));
+        OWLAnnotationProperty source =
+            df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/MYONT_20"));
+        OWLOntology ont = load("obo/tag_iris.obo", m);
+        Set<OWLAxiom> axioms = ont.getAxioms();
+        OWLClass term1 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_1"));
+        OWLClass term2 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_2"));
+        OWLClass term3 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_3"));
+        OWLClass term4 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_4"));
+        Set<OWLAnnotation> annotations = Stream
+            .of(df.getOWLAnnotation(df.getRDFSComment(), string("Here is a sub-annotation.")),
+                df.getOWLAnnotation(df.getRDFSSeeAlso(), string("A nested see also value.")))
+            .collect(Collectors.toSet());
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term1.getIRI(),
+            string("Definition of term one."), annotations)));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(df.getRDFSSeeAlso(),
+            term1.getIRI(), string("See also value."))));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term2.getIRI(),
+            string("Definition of term two."), Collections
+                .singleton(df.getOWLAnnotation(source, string("A nested annotation value."))))));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term3.getIRI(),
+            string("Definition of term three."), Collections
+                .singleton(df.getOWLAnnotation(source, string("A definition source value."))))));
+        assertTrue(
+            axioms.contains(
+                df.getOWLAnnotationAssertionAxiom(oioCreatedBy, term3.getIRI(), string("goc:bro"))),
+            "created_by is built in and should not be overridden by a typedef");
+        assertTrue(
+            axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term4.getIRI(),
+                string("Definition of term four."),
+                Collections
+                    .singleton(df.getOWLAnnotation(oioInventedBy, string("An inventor value."))))),
+            "An undeclared tag should have oio namespace");
+
+    }
+
+    protected OWLLiteral string(String l) {
+        return df.getOWLLiteral(l, OWL2Datatype.XSD_STRING);
+    }
+}
diff --git a/...t/java/org/semanticweb/owlapi/api/test/syntax/rdf/BOMSafeInputStreamAndParseTestCase.java b/...t/java/org/semanticweb/owlapi/api/test/syntax/rdf/BOMSafeInputStreamAndParseTestCase.java
@@ -6,15 +6,18 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
+import org.semanticweb.owlapi.formats.*;
 import org.semanticweb.owlapi.io.ReaderDocumentSource;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLDocumentFormat;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 
 class BOMSafeInputStreamAndParseTestCase extends TestBase {
@@ -39,13 +42,20 @@ static Collection<Arguments> data() {
             "<rdf:RDF xml:base=\"" + nextISA() + "\" " + PREFIX_XML + " ><owl:Ontology rdf:about=\"#\" /><owl:Class rdf:about=\"" + ISA14 + RESEARCHER + "\"/></rdf:RDF>"
             //@formatter:on    
         );
+        List<OWLDocumentFormat> formats = Arrays.asList(new OWLXMLDocumentFormat(),
+        		new ManchesterSyntaxDocumentFormat(),
+        		new FunctionalSyntaxDocumentFormat(),
+        		new RioTurtleDocumentFormat(),
+        		new RDFXMLDocumentFormat());
+
         List<int[]> prefixes =
             l(new int[] {0x00, 0x00, 0xFE, 0xFF}, new int[] {0xFF, 0xFE, 0x00, 0x00},
                 new int[] {0xFF, 0xFE}, new int[] {0xFE, 0xFF}, new int[] {0xEF, 0xBB, 0xBF});
         for (int[] p : prefixes) {
-            for (String onto : list) {
-                toReturn.add(Arguments.of(p, onto));
-            }
+        	for (int i = 0; i < list.size(); i++) {
+        		toReturn.add(Arguments.of(p, list.get(i), formats.get(i)));
+
+        	}
         }
         return toReturn;
     }
@@ -72,18 +82,9 @@ private static InputStream in(int[] b, String content) throws IOException {
     // EF BB BF |UTF-8
     @ParameterizedTest
     @MethodSource("data")
-    void testBOMError32big(int[] b, String input) throws IOException {
+    void testBOMError32big(int[] b, String input, OWLDocumentFormat format) throws IOException {
         try (InputStream in = in(b, input)) {
             loadFrom(in);
         }
     }
-
-    @ParameterizedTest
-    @MethodSource("data")
-    void testBOMError32bigReader(int[] b, String input)
-        throws OWLOntologyCreationException, IOException {
-        try (InputStream in = in(b, input); InputStreamReader r = new InputStreamReader(in)) {
-            m.loadOntologyFromOntologyDocument(new ReaderDocumentSource(r));
-        }
-    }
 }
diff --git a/contract/src/test/resources/obo/tag_iris.obo b/contract/src/test/resources/obo/tag_iris.obo
@@ -0,0 +1,56 @@
+format-version: 1.2
+ontology: myont
+
+[Term]
+id: MYONT:1
+name: term one
+def: "Definition of term one." [] {comment="Here is a sub-annotation.", seeAlso="A nested see also value."}
+property_value: seeAlso "See also value." xsd:string
+
+[Term]
+id: MYONT:2
+name: term two
+def: "Definition of term two." [] {MYONT:20="A nested annotation value."}
+property_value: MYONT:21 "A top level annotation value." xsd:string
+
+[Term]
+id: MYONT:3
+name: term three
+def: "Definition of term three." [] {source="A definition source value."}
+intersection_of: MYONT:2 ! term two
+intersection_of: results_in_transport_across GO:0005739 ! mitochondrion
+created_by: goc:bro
+
+[Term]
+id: MYONT:4
+name: term four
+def: "Definition of term four." [] {invented_by="An inventor value."}
+
+[Typedef]
+id: source
+name: source
+xref: MYONT:20
+is_metadata_tag: true
+
+[Typedef]
+id: MYONT:21
+name: source2
+is_metadata_tag: true
+
+[Typedef]
+id: seeAlso
+name: see also
+xref: http://www.w3.org/2000/01/rdf-schema#seeAlso
+is_metadata_tag: true
+
+[Typedef]
+id: results_in_transport_across
+name: results in transport across
+namespace: external
+xref: RO:0002342
+
+[Typedef]
+id: created_by
+name: created by
+namespace: external
+xref: http://purl.org/dc/terms/creator
diff --git a/...st/java/uk/ac/manchester/cs/owl/owlapi/concurrent/ConcurrentOWLOntologyImpl_TestCase.java b/...st/java/uk/ac/manchester/cs/owl/owlapi/concurrent/ConcurrentOWLOntologyImpl_TestCase.java
@@ -1,6 +1,6 @@
 package uk.ac.manchester.cs.owl.owlapi.concurrent;
 
-import static org.mockito.ArgumentMatchers.anyListOf;
+import static org.mockito.ArgumentMatchers.anyList;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.never;
 import static org.mockito.Mockito.spy;
@@ -84,7 +84,7 @@ class ConcurrentOWLOntologyImpl_TestCase {
     void setUp() {
         when(readWriteLock.readLock()).thenReturn(readLock);
         when(readWriteLock.writeLock()).thenReturn(writeLock);
-        when(delegate.applyChangesAndGetDetails(anyListOf(OWLOntologyChange.class)))
+        when(delegate.applyChangesAndGetDetails(anyList()))
             .thenReturn(new ChangeDetails(ChangeApplied.NO_OPERATION, Collections.emptyList()));
         ontology = spy(new ConcurrentOWLOntologyImpl(delegate, readWriteLock));
     }

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java
@@ -1,6 +1,7 @@
 package org.obolibrary.obo2owl;
 
 import static org.obolibrary.obo2owl.Obo2OWLConstants.DEFAULT_IRI_PREFIX;
+import static org.obolibrary.obo2owl.Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
 import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
 import static org.semanticweb.owlapi.util.OWLAPIPreconditions.emptyOptional;
 import static org.semanticweb.owlapi.util.OWLAPIPreconditions.optional;
@@ -1373,21 +1374,29 @@ protected OWLIndividual trIndividual(String instId) {
         return fac.getOWLNamedIndividual(iri);
     }
 
+    private IRI trTagToIRIIncludingTypedefs(String tag) {
+        IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
+        if (iri == null) {
+            iri = oboIdToIRI(tag, true);
+        }
+        return iri;
+    }
+
     /**
      * Translate tag to annotation prop.
-     *
+     * 
      * @param tag the tag
      * @return the OWL annotation property
      */
     protected OWLAnnotationProperty trTagToAnnotationProp(String tag) {
-        IRI iri = trTagToIRI(tag);
+        IRI iri = trTagToIRIIncludingTypedefs(tag);
         OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
         if (!apToDeclare.contains(ap)) {
             apToDeclare.add(ap);
             add(fac.getOWLDeclarationAxiom(ap));
             Obo2OWLVocabulary vocab = Obo2OWLConstants.getVocabularyObj(tag);
             if (vocab != null) {
-                add(fac.getOWLAnnotationAssertionAxiom(iri, fac.getRDFSLabel(vocab.getLabel())));
+                add(fac.getOWLAnnotationAssertionAxiom(iri, fac.getRDFSLabel(trLiteral(vocab.getLabel()))));
             }
         }
         return ap;
@@ -1469,9 +1478,19 @@ protected OWLAnnotationValue trLiteral(Object inputValue) {
      * @return the iri
      */
     public IRI oboIdToIRI(String id) {
+    	return oboIdToIRI(id, false);
+    }
+
+    /**
+     * Obo id to iri.
+     *
+     * @param id the id
+     * @return the iri
+     */
+    public IRI oboIdToIRI(String id, boolean oboInOwlDefault) {
         IRI iri = idToIRICache.get(id);
         if (iri == null) {
-            iri = loadOboToIRI(id);
+            iri = loadOboToIRI(id, oboInOwlDefault);
             idToIRICache.put(id, iri);
         }
         return iri;
@@ -1484,6 +1503,16 @@ public IRI oboIdToIRI(String id) {
      * @return the iri
      */
     public IRI loadOboToIRI(String id) {
+    	return loadOboToIRI(id, false);
+    }
+
+    /**
+     * Obo id to iri.
+     *
+     * @param id the id
+     * @return the iri
+     */
+    public IRI loadOboToIRI(String id, boolean oboInOwlDefault) {
         if (id.contains(" ")) {
             LOG.error("id contains space: \"{}\"", id);
             throw new OWLParserException("spaces not allowed: '" + id + '\'');
@@ -1547,9 +1576,14 @@ public IRI loadOboToIRI(String id) {
             db = getDefaultIDSpace() + '#';
             localId = idParts[0];
         }
-        String uriPrefix = DEFAULT_IRI_PREFIX + db;
-        if (idSpaceMap.containsKey(db)) {
-            uriPrefix = idSpaceMap.get(db);
+        String uriPrefix;
+        if (oboInOwlDefault) {
+            uriPrefix = OIOVOCAB_IRI_PREFIX;
+        } else {
+            uriPrefix = DEFAULT_IRI_PREFIX + db;
+            if (idSpaceMap.containsKey(db)) {
+                uriPrefix = idSpaceMap.get(db);
+            }
         }
         String safeId;
         try {
@@ -1570,10 +1604,9 @@ public IRI loadOboToIRI(String id) {
     }
 
     // 5.9.3. Special Rules for Relations
-
     /**
      * Translate shorthand id to expanded id.
-     *
+     * 
      * @param id the id
      * @return the string
      */

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
@@ -479,6 +479,8 @@ public static String owlObjectToTag(OWLObject obj) {
             String prefix = Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
             if (iri.startsWith(prefix)) {
                 tag = iri.substring(prefix.length());
+            } else {
+                tag = getIdentifier(iriObj);
             }
         }
         return tag;

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java b/oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java
@@ -52,6 +52,9 @@ public enum Obo2OWLVocabulary implements HasIRI {
         /**IRI_IAO_0100001. */    IRI_IAO_0100001(DEFAULT_IRI_PREFIX, "IAO_0100001", "term replaced by", OboFormatTag.TAG_REPLACED_BY.getTag()),
         /**IRI_OIO_shorthand. */  IRI_OIO_shorthand(OIOVOCAB_IRI_PREFIX, "shorthand", "shorthand", "shorthand"),
         /**IRI_OIO_consider. */   IRI_OIO_consider(OIOVOCAB_IRI_PREFIX, "consider", "consider", OboFormatTag.TAG_CONSIDER.getTag()),
+        /**IRI_OIO_id*/   IRI_OIO_id(OIOVOCAB_IRI_PREFIX, "id", "id", OboFormatTag.TAG_ID.getTag()),
+        /**IRI_OIO_created_by*/   IRI_OIO_created_by(OIOVOCAB_IRI_PREFIX, "created_by", "created by", OboFormatTag.TAG_CREATED_BY.getTag()),
+        /**IRI_OIO_creation_date*/   IRI_OIO_creation_date(OIOVOCAB_IRI_PREFIX, "creation_date", "creation date", OboFormatTag.TAG_CREATION_DATE.getTag()),
         /**IRI_OIO_hasOBOFormatVersion. */        IRI_OIO_hasOBOFormatVersion(OIOVOCAB_IRI_PREFIX, "hasOBOFormatVersion", "has_obo_format_version", OboFormatTag.TAG_FORMAT_VERSION.getTag()),
         /**IRI_OIO_treatXrefsAsIsA. */            IRI_OIO_treatXrefsAsIsA(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-is_a", "treat-xrefs-as-is_a", OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.getTag()),
         /**IRI_OIO_treatXrefsAsHasSubClass. */    IRI_OIO_treatXrefsAsHasSubClass(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-has-subclass", "treat-xrefs-as-has-subclass", OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.getTag()),