From 6bb2d3abcde920ef5ce2db425b2e95f678d29c63 Mon Sep 17 00:00:00 2001
From: ignazio <ignazio.palmisano@gmail.com>
Date: Sun, 14 Jan 2024 09:47:13 +0000
Subject: [PATCH] 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.
---
 .../obolibrary/oboformat/BasicsTestCase.java  | 10 ++---
 .../org/obolibrary/obo2owl/OWLAPIObo2Owl.java | 40 +++++++++----------
 2 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/contract/src/test/java/org/obolibrary/oboformat/BasicsTestCase.java b/contract/src/test/java/org/obolibrary/oboformat/BasicsTestCase.java
index 5b5dc15f4c..6fc050fff5 100644
--- a/contract/src/test/java/org/obolibrary/oboformat/BasicsTestCase.java
+++ b/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
diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java
index 3501203aed..0c6063f408 100644
--- a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java
+++ b/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");