OBO serialisation illegal axiom annotation (#1093)

fix for ontodev/robot#1089
owlcs · Feb 19, 2023 · 0176cf8 · 0176cf8
1 parent 97cca47
commit 0176cf8
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Showing 3 changed files with 68 additions and 3 deletions.
diff --git a/contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/Owl2OboTestCase.java b/contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/Owl2OboTestCase.java
@@ -1,8 +1,13 @@
 package org.semanticweb.owlapi.obolibrarytest.oboformat;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.IOException;
+import java.io.StringWriter;
 import java.util.Collection;
 import java.util.Optional;
 
@@ -20,6 +25,7 @@
 import org.semanticweb.owlapi.obolibrary.oboformat.model.Clause;
 import org.semanticweb.owlapi.obolibrary.oboformat.model.Frame;
 import org.semanticweb.owlapi.obolibrary.oboformat.model.OBODoc;
+import org.semanticweb.owlapi.obolibrary.oboformat.writer.OBOFormatWriter;
 import org.semanticweb.owlapi.vocab.OBOFormatConstants.OboFormatTag;
 import org.semanticweb.owlapi.vocab.Obo2OWLConstants;
 import org.semanticweb.owlapi.vocab.Obo2OWLConstants.Obo2OWLVocabulary;
@@ -170,4 +176,21 @@ void testOwl2OboProperty() {
         assertTrue(comment.isPresent());
         assertEquals(COMMENT, comment.get().getLiteral());
     }
+
+    @Test
+    void testIllegalOWLAxiomConversion() throws IOException {
+        File illegalOWLFile = getFile("illegal_property.owl");
+
+        OWLOntology illegalOntology = loadFrom(illegalOWLFile);
+        OBODoc oboDoc = convert(illegalOntology);
+
+        OBOFormatWriter writer = new OBOFormatWriter();
+        StringWriter stringWriter = new StringWriter();
+        BufferedWriter bw = new BufferedWriter(stringWriter);
+        writer.write(oboDoc, bw);
+
+        String illegalOutput = "{http://www.w3.org/1999/02/22-rdf-syntax-ns#type=\"owl:Axiom\"}";
+        assertFalse(stringWriter.toString().contains(illegalOutput),
+            String.format("Ilegal output '%s' exists in the output", illegalOutput));
+    }
 }
diff --git a/contract/src/test/resources/obo/illegal_property.owl b/contract/src/test/resources/obo/illegal_property.owl
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl#"
+     xml:base="http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl"
+     xmlns:obo="http://purl.obolibrary.org/obo/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+     xmlns:xml="http://www.w3.org/XML/1998/namespace"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/fbbt/fbbt-simple.owl">
+    </owl:Ontology>
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+        <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+        <rdfs:label>definition</rdfs:label>
+    </owl:AnnotationProperty>
+
+    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref">
+        <rdfs:label>database_cross_reference</rdfs:label>
+    </owl:AnnotationProperty>
+
+    <!-- THIS AXIOM IS ILLEGAL --> 
+    <owl:AnnotationProperty rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"/>
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/FBbt_00000006">
+        <obo:IAO_0000115>Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).</obo:IAO_0000115>
+        <oboInOwl:hasDbXref>UBERON:6000006</oboInOwl:hasDbXref>
+    </owl:Class>
+    <owl:Axiom>
+        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/FBbt_00000006"/>
+        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+        <owl:annotatedTarget>Any segment (FBbt:00000003) that is part of some head (FBbt:00000004).</owl:annotatedTarget>
+        <oboInOwl:hasDbXref>FlyBase:FBrf0075072</oboInOwl:hasDbXref>
+    </owl:Axiom>
+
+</rdf:RDF>
+
+<!-- See: https://github.com/ontodev/robot/issues/1089 -->
diff --git a/oboformat/src/main/java/org/semanticweb/owlapi/obolibrary/obo2owl/OWLAPIOwl2Obo.java b/oboformat/src/main/java/org/semanticweb/owlapi/obolibrary/obo2owl/OWLAPIOwl2Obo.java
@@ -122,9 +122,12 @@ public static Map<String, String> annotationPropertyMap() {
         Obo2OWLConstants.DEFAULT_IRI_PREFIX + "IAO_synonymtypedef";
     private static final String IRI_CLASS_SUBSETDEF =
         Obo2OWLConstants.DEFAULT_IRI_PREFIX + "IAO_subsetdef";
-    private static final Set<String> SKIPPED_QUALIFIERS =
-        new HashSet<>(Arrays.asList("gci_relation", "gci_filler", CARDINALITY, MIN_CARDINALITY,
-            MAX_CARDINALITY, "all_some", ALL_ONLY));
+    // RDF_TYPE added to guard against scenario when a syntactic triple is
+    // accidentally interpreted as an annotation.
+    // See https://github.com/ontodev/robot/issues/1089 for context
+    private static final Set<String> SKIPPED_QUALIFIERS = new HashSet<>(
+        Arrays.asList("gci_relation", "gci_filler", CARDINALITY, MIN_CARDINALITY, MAX_CARDINALITY,
+            "all_some", ALL_ONLY, "http://www.w3.org/1999/02/22-rdf-syntax-ns#type"));
     protected final Pattern absoluteURLPattern = Pattern.compile("<\\s*http.*?>");
     protected final Set<OWLAxiom> untranslatableAxioms = new HashSet<>();
     protected final Map<String, String> idSpaceMap = new HashMap<>();