Accept non-ambiguous invalid enum values.

When reading from SSSOM/TSV or SSSOM/JSON, accept a `sssom_version`
value provided as a floating point value, even though strictly speaking
it should be a string. That is, accept `sssom_version: 1.1` as
equivalent to `sssom_version: "1.1"`.

Likewise, accept `entity_type_enum` values provided as CURIEs. For
example, accept `owl:Class` as equivalent to `owl class`.

In both cases, this is when parsing only. When writing, the version
number is always written as a string and entity type values are alwayrs
written using their canonical string form.

Author: gouttegd

core/src/main/java/org/incenp/obofoundry/sssom/YAMLConverter.java

@@ -173,6 +173,9 @@ public MappingSet convertMappingSet(Map<String, Object> rawMap) throws SSSOMForm
             if ( String.class.isInstance(rawVersion) ) {
                 version = Version.fromString(String.class.cast(rawVersion));
                 rawMap.remove("sssom_version");
+            } else if ( Double.class.isInstance(rawVersion) ) {
+                version = Version.fromString(Double.class.cast(rawVersion).toString());
+                rawMap.remove("sssom_version");
             } else {
                 throw getTypingError("sssom_version");
             }

core/src/main/java/org/incenp/obofoundry/sssom/model/EntityType.java

@@ -28,42 +28,54 @@
  * Represents the type of an entity that is being mapped.
  */
 public enum EntityType {
-    OWL_CLASS("http://www.w3.org/2002/07/owl#Class"),
-    OWL_OBJECT_PROPERTY("http://www.w3.org/2002/07/owl#ObjectProperty"),
-    OWL_DATA_PROPERTY("http://www.w3.org/2002/07/owl#DataProperty"),
-    OWL_ANNOTATION_PROPERTY("http://www.w3.org/2002/07/owl#AnnotationProperty"),
-    OWL_NAMED_INDIVIDUAL("http://www.w3.org/2002/07/owl#NamedIndividual"),
-    SKOS_CONCEPT("http://www.w3.org/2004/02/skos/core#Concept"),
-    RDFS_RESOURCE("http://www.w3.org/2000/01/rdf-schema#Resource"),
-    RDFS_CLASS("http://www.w3.org/2000/01/rdf-schema#Class"),
-    RDFS_LITERAL("http://www.w3.org/2000/01/rdf-schema#Literal"),
-    RDFS_DATATYPE("http://www.w3.org/2000/01/rdf-schema#Datatype"),
-    RDF_PROPERTY("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"),
+    OWL_CLASS("http://www.w3.org/2002/07/owl#Class", "owl:Class"),
+    OWL_OBJECT_PROPERTY("http://www.w3.org/2002/07/owl#ObjectProperty", "owl:ObjectProperty"),
+    OWL_DATA_PROPERTY("http://www.w3.org/2002/07/owl#DataProperty", "owl:DataProperty"),
+    OWL_ANNOTATION_PROPERTY("http://www.w3.org/2002/07/owl#AnnotationProperty", "owl:AnnotationProperty"),
+    OWL_NAMED_INDIVIDUAL("http://www.w3.org/2002/07/owl#NamedIndividual", "owl:NamedIndividual"),
+    SKOS_CONCEPT("http://www.w3.org/2004/02/skos/core#Concept", "skos:Concept"),
+    RDFS_RESOURCE("http://www.w3.org/2000/01/rdf-schema#Resource", "rdfs:Resource"),
+    RDFS_CLASS("http://www.w3.org/2000/01/rdf-schema#Class", "rdfs:Class"),
+    RDFS_LITERAL("http://www.w3.org/2000/01/rdf-schema#Literal", "rdfs:Literal"),
+    RDFS_DATATYPE("http://www.w3.org/2000/01/rdf-schema#Datatype", "rdfs:Datatype"),
+    RDF_PROPERTY("http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "rdf:Property"),
     COMPOSED_ENTITY_EXPRESSION("https://w3id.org/sssom/ComposedEntityExpression");
 
     private final static Map<String, EntityType> MAP;
     private final static Map<String, EntityType> URI_MAP;
+    private final static Map<String, EntityType> SYN_MAP;
 
     static {
         Map<String, EntityType> map = new HashMap<String, EntityType>();
         Map<String, EntityType> uri_map = new HashMap<String, EntityType>();
+        Map<String, EntityType> syn_map = new HashMap<String, EntityType>();
         for ( EntityType value : EntityType.values() ) {
             map.put(value.toString(), value);
             if ( value.iri != null ) {
                 uri_map.put(value.iri, value);
             }
+            if ( value.synonym != null ) {
+                syn_map.put(value.synonym, value);
+            }
         }
 
         MAP = Collections.unmodifiableMap(map);
         URI_MAP = Collections.unmodifiableMap(uri_map);
+        SYN_MAP = Collections.unmodifiableMap(syn_map);
     }
 
     private String iri;
+    private String synonym;
 
     EntityType(String iri) {
         this.iri = iri;
     }
 
+    EntityType(String iri, String synonym) {
+        this.iri = iri;
+        this.synonym = synonym;
+    }
+
     @Override
     public String toString() {
         return name().toLowerCase().replace('_', ' ');
@@ -91,6 +103,26 @@ public static EntityType fromString(String v) {
         return MAP.get(v);
     }
 
+    /**
+     * Parses a string into a entity type enum value.
+     * <p>
+     * This is similar to {@link #fromString(String)}, but optionally allows to
+     * recognise “synonyms”.
+     * 
+     * @param v   The string to parse.
+     * @param lax If {@code true}, will attempt to match the provided value against
+     *            known synonyms of the expected values.
+     * @return The corresponding enumeration value, or {@code null} if the provided
+     *         value does not match any entity type.
+     */
+    public static EntityType fromString(String v, boolean lax) {
+        EntityType et = MAP.get(v);
+        if ( et == null && lax ) {
+            et = SYN_MAP.get(v);
+        }
+        return et;
+    }
+
     /**
      * Parses an IRI into the corresponding entity type enum value.
      * <p>

core/src/main/java/org/incenp/obofoundry/sssom/slots/EntityTypeSlot.java

@@ -59,7 +59,7 @@ public void setValue(T object, String value) {
         if ( value != null ) {
             et = EntityType.fromIRI(value);
             if ( et == null ) {
-                et = EntityType.fromString(value);
+                et = EntityType.fromString(value, true);
             }
             if ( et == null ) {
                 throw new IllegalArgumentException();

core/src/test/java/org/incenp/obofoundry/sssom/TSVReaderTest.java

@@ -787,6 +787,27 @@ void testRelativeURIs() throws IOException {
         }
     }
 
+    @Test
+    void testAcceptingLaxEnumValues() throws IOException {
+        TSVReader reader = new TSVReader("src/test/resources/sets/test-lax-enum-values.sssom.tsv");
+        MappingSet ms;
+
+        try {
+            ms = reader.read();
+            Assertions.assertEquals(Version.SSSOM_1_1, ms.getSssomVersion());
+            Assertions.assertEquals(EntityType.OWL_CLASS, ms.getMappings().get(0).getSubjectType());
+            Assertions.assertEquals(EntityType.OWL_ANNOTATION_PROPERTY, ms.getMappings().get(1).getSubjectType());
+            Assertions.assertEquals(EntityType.OWL_OBJECT_PROPERTY, ms.getMappings().get(2).getSubjectType());
+            Assertions.assertEquals(EntityType.OWL_DATA_PROPERTY, ms.getMappings().get(3).getSubjectType());
+            Assertions.assertEquals(EntityType.RDFS_RESOURCE, ms.getMappings().get(4).getSubjectType());
+            Assertions.assertEquals(EntityType.RDFS_CLASS, ms.getMappings().get(5).getSubjectType());
+            Assertions.assertEquals(EntityType.RDF_PROPERTY, ms.getMappings().get(6).getSubjectType());
+            Assertions.assertEquals(EntityType.SKOS_CONCEPT, ms.getMappings().get(7).getSubjectType());
+        } catch ( SSSOMFormatException e ) {
+            Assertions.fail(e);
+        }
+    }
+
     private void compare(ExtensionDefinition expected, ExtensionDefinition actual) {
         Assertions.assertEquals(expected.getSlotName(), actual.getSlotName());
         Assertions.assertEquals(expected.getProperty(), actual.getProperty());

core/src/test/resources/sets/test-lax-enum-values.sssom.tsv

@@ -0,0 +1,22 @@
+#sssom_version: 1.1
+#curie_map:
+#  COMENT: https://example.com/entities/
+#  COMPID: https://example.com/people/
+#  ORGENT: https://example.org/entities/
+#  ORGPID: https://example.org/people/
+#mapping_set_id: https://example.org/sets/exo2c
+#mapping_set_title: O2C set
+#creator_id:
+#  - ORGPID:0000-0000-0001-1234
+#  - COMPID:0000-0000-0002-5678
+#license: https://creativecommons.org/licenses/by/4.0/
+#publication_date: 2023-09-13
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	subject_type
+ORGENT:0001	alice	skos:closeMatch	COMENT:0011	alpha	semapv:ManualMappingCuration	owl:Class
+ORGENT:0002	bob	skos:closeMatch	COMENT:0012	beta	semapv:ManualMappingCuration	owl:AnnotationProperty
+ORGENT:0004	daphne	skos:closeMatch	COMENT:0014	delta	semapv:ManualMappingCuration	owl:ObjectProperty
+ORGENT:0005	eve	skos:closeMatch	COMENT:0015	epsilon	semapv:ManualMappingCuration	owl:DataProperty
+ORGENT:0006	fanny	skos:closeMatch	COMENT:0016	zeta	semapv:ManualMappingCuration	rdfs:Resource
+ORGENT:0007	gavin	skos:exactMatch	COMENT:0013	gamma	semapv:ManualMappingCuration	rdfs:Class
+ORGENT:0008	hector	skos:closeMatch	COMENT:0017	eta	semapv:ManualMappingCuration	rdf:Property
+ORGENT:0009	ivan	skos:exactMatch	COMENT:0019	iota	semapv:ManualMappingCuration	skos:Concept