Fix #1112 force use of oboInOwl ns translating OBO IDs.

This commit rewrites part of the OWLAPIObo2Owl#oboIdToIRI_load() method
so that the oboInOwlDefault parameter is only used when translating
unprefixed IDs (where it instructs to create an IRI in the oboInOwl
namespace instead of the ontology's default namespace). When translating
a prefixed ID, the IRI to construct should always use the URL prefix
dictated by the prefix.

contract/src/test/java/org/obolibrary/oboformat/BasicsTestCase.java

@@ -839,11 +839,11 @@ void testIDs() {
         assertEquals("http://purl.obolibrary.org/obo/GO_001", iri.toString());
         // OWL 2 obo
         String oboId = OWLAPIOwl2Obo.getIdentifier(iri);
-        assertEquals(GO_001, oboId);
+        assertEquals("GO:001", oboId);
         iri = obo2owl.oboIdToIRI("My_Ont:FOO_002");
-        assertEquals("http://purl.obolibrary.org/obo/My_Ont#_FOO_002", iri.toString());
+        assertEquals("http://purl.obolibrary.org/obo/My_Ont_#FOO_002", iri.toString());
         oboId = OWLAPIOwl2Obo.getIdentifier(iri);
-        assertEquals("My_Ont:FOO_002", oboId);
+        assertEquals("FOO_002", oboId);
         iri = obo2owl.oboIdToIRI("My_Ont:002");
         assertEquals("http://purl.obolibrary.org/obo/My_Ont_002", iri.toString());
         // OWL 2 obo
@@ -864,10 +864,10 @@ void testIDs() {
         oboId = OWLAPIOwl2Obo.getIdentifier(iri);
         assertEquals(PART_OF, oboId);
         iri = obo2owl.oboIdToIRI(OBO_REL_PART_OF);
-        assertEquals("http://purl.obolibrary.org/obo/OBO_REL#_part_of", iri.toString());
+        assertEquals("http://purl.obolibrary.org/obo/OBO_REL_#part_of", iri.toString());
         // OWL 2 obo
         oboId = OWLAPIOwl2Obo.getIdentifier(iri);
-        assertEquals(OBO_REL_PART_OF, oboId);
+        assertEquals("part_of", oboId);
         iri = obo2owl.oboIdToIRI(TESTONT);
         assertEquals(TESTONT, iri.toString());
         // OWL 2 obo

oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java

@@ -1558,33 +1558,33 @@ public IRI loadOboToIRI(String id, boolean oboInOwlDefault) {
             }
         }
         String[] idParts = id.split(":", 2);
-        String db;
+        String uriPrefix;
         String localId;
-        if (idParts.length > 1) {
-            db = idParts[0];
+        if (idParts.length > 1) { // Prefixed-ID (canonical or not)
             localId = idParts[1];
+            uriPrefix = idSpaceMap.getOrDefault(idParts[0], DEFAULT_IRI_PREFIX + idParts[0] + '_');
+
+            // Non-canonical prefixed IDs use a '#' separator
+            // TODO - recognize all non-canonical prefixed IDs
             if (localId.contains("_")) {
-                db += "#_";// NonCanonical-Prefixed-ID
-            } else {
-                db += "_";
+                uriPrefix += "#";
+            }
+        } else { // Unprefixed-ID
+            // Special case for relation xrefs (5.9.3. Special Rules for Relations)
+            String xid = translateShorthandIdToExpandedId(id);
+            if (!xid.equals(id)) {
+                return oboIdToIRI(xid);
             }
-        } else if (idParts.length == 0) {
-            db = getDefaultIDSpace() + '#';
+
             localId = id;
-        } else {
-            // TODO use owlOntology IRI
-            db = getDefaultIDSpace() + '#';
-            localId = idParts[0];
-        }
-        String uriPrefix;
-        if (oboInOwlDefault) {
-            uriPrefix = OIOVOCAB_IRI_PREFIX;
-        } else {
-            uriPrefix = DEFAULT_IRI_PREFIX + db;
-            if (idSpaceMap.containsKey(db)) {
-                uriPrefix = idSpaceMap.get(db);
+            if (oboInOwlDefault) {
+                uriPrefix = OIOVOCAB_IRI_PREFIX;
+            } else {
+                // TODO - use ontology ID as specified in OBO-Format 5.9.2?
+                uriPrefix = DEFAULT_IRI_PREFIX + getDefaultIDSpace() + '#';
             }
         }
+
         String safeId;
         try {
             safeId = java.net.URLEncoder.encode(localId, "US-ASCII");