Fix incorrect IRI for linkml:Uriorcurie.

The IRI of the LinkML type "uriorcurie" is not https://w3id.org/linkml/uriOrCurie but https://w3id.org/linkml/Uriorcurie We fix the code that deals with extension definitions to expect the correct IRI, while still accepting the incorrect one for backwards compatibility.
gouttegd · Jul 23, 2024 · 2bedd9f · 2bedd9f
1 parent 65f9f15
commit 2bedd9f
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Showing 4 changed files with 15 additions and 5 deletions.
diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/model/ValueType.java b/core/src/main/java/org/incenp/obofoundry/sssom/model/ValueType.java
@@ -32,7 +32,7 @@ public enum ValueType {
     BOOLEAN("http://www.w3.org/2001/XMLSchema#boolean"),
     DATE("http://www.w3.org/2001/XMLSchema#date"),
     DATETIME("http://www.w3.org/2001/XMLSchema#datetime"),
-    IDENTIFIER("https://w3id.org/linkml/uriOrCurie"),
+    IDENTIFIER("https://w3id.org/linkml/Uriorcurie", "https://w3id.org/linkml/uriOrCurie"),
     OTHER(null);
 
     private final static Map<String, ValueType> MAP;
@@ -42,16 +42,26 @@ public enum ValueType {
         for ( ValueType vt : ValueType.values() ) {
             if ( vt != ValueType.OTHER ) {
                 map.put(vt.iri, vt);
+                if ( vt.alias != null ) {
+                    map.put(vt.alias, vt);
+                }
             }
         }
 
         MAP = Collections.unmodifiableMap(map);
     }
 
     private final String iri;
+    private final String alias;
 
     ValueType(String iri) {
         this.iri = iri;
+        this.alias = null;
+    }
+
+    ValueType(String iri, String alias) {
+        this.iri = iri;
+        this.alias = alias;
     }
 
     @Override

diff --git a/core/src/test/java/org/incenp/obofoundry/sssom/TSVReaderTest.java b/core/src/test/java/org/incenp/obofoundry/sssom/TSVReaderTest.java
@@ -350,7 +350,7 @@ void testAcceptDefinedExtensions() throws IOException, SSSOMFormatException {
         compare(new ExtensionDefinition("ext_bar", "https://example.org/properties/barProperty",
                 "http://www.w3.org/2001/XMLSchema#integer"), definitions.get("ext_bar"));
         compare(new ExtensionDefinition("ext_baz", "https://example.org/properties/bazProperty",
-                "https://w3id.org/linkml/uriOrCurie"), definitions.get("ext_baz"));
+                "https://w3id.org/linkml/Uriorcurie"), definitions.get("ext_baz"));
         compare(new ExtensionDefinition("ext_foo", "https://example.org/properties/fooProperty"),
                 definitions.get("ext_foo"));
 
@@ -389,7 +389,7 @@ void testAcceptAllExtensions() throws IOException, SSSOMFormatException {
         compare(new ExtensionDefinition("ext_bar", "https://example.org/properties/barProperty",
                 "http://www.w3.org/2001/XMLSchema#integer"), definitions.get("ext_bar"));
         compare(new ExtensionDefinition("ext_baz", "https://example.org/properties/bazProperty",
-                "https://w3id.org/linkml/uriOrCurie"), definitions.get("ext_baz"));
+                "https://w3id.org/linkml/Uriorcurie"), definitions.get("ext_baz"));
         compare(new ExtensionDefinition("ext_foo", "https://example.org/properties/fooProperty"),
                 definitions.get("ext_foo"));
         compare(new ExtensionDefinition("ext_undeclared_baz", "http://sssom.invalid/ext_undeclared_baz"),

diff --git a/core/src/test/resources/output/test-extensions-defined.sssom.tsv b/core/src/test/resources/output/test-extensions-defined.sssom.tsv
@@ -21,7 +21,7 @@
 #    type_hint: xsd:integer
 #  - slot_name: ext_baz
 #    property: EXPROP:bazProperty
-#    type_hint: linkml:uriOrCurie
+#    type_hint: linkml:Uriorcurie
 #  - slot_name: ext_foo
 #    property: EXPROP:fooProperty
 #ext_undeclared_foo: Foo B

diff --git a/core/src/test/resources/sets/exo2c-with-extensions.sssom.tsv b/core/src/test/resources/sets/exo2c-with-extensions.sssom.tsv
@@ -17,7 +17,7 @@
 #    type_hint: xsd:integer
 #  - slot_name: ext_baz
 #    property: EXPROP:bazProperty
-#    type_hint: linkml:uriOrCurie
+#    type_hint: linkml:Uriorcurie
 #  - slot_name: ext_foo
 #    property: EXPROP:fooProperty
 #ext_foo: Foo A