Support old match_term_type metadata slot.

Initial versions of SSSOM used a single slot called 'match_term_type' to
indicate what was being mapped. This slot has been replaced in SSSOM
0.9.1 by two slots called 'subject_type' and 'object_type'. If a
'match_term_type' slot is found in a mapping set (and that set does not
contain 'subject_type' and 'object_type' slots), we convert it to its
modern equivalents.

cli/src/test/resources/updated-fields.sssom.tsv

@@ -1,6 +1,6 @@
 #curie_map:
 #  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
 #  UBERON: "http://purl.obolibrary.org/obo/UBERON_"
-subject_id	subject_label	predicate_id	object_id	mapping_justification
-FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	semapv:LexicalMatching
-FBbt:00000002	tagma	semapv:crossSpeciesExactMatch	UBERON:6000002	
+subject_id	subject_label	predicate_id	object_id	mapping_justification	subject_type	object_type
+FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	semapv:LexicalMatching		
+FBbt:00000002	tagma	semapv:crossSpeciesExactMatch	UBERON:6000002		owl class	owl class

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

@@ -0,0 +1,78 @@
+/*
+ * SSSOM-Java - SSSOM library for Java
+ * Copyright © 2023 Damien Goutte-Gattat
+ * 
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the Gnu General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package org.incenp.obofoundry.sssom;
+
+import java.util.Map;
+
+/**
+ * A YAML preprocessor to convert a dictionary containing a
+ * {@code match_term_type} metadata slot into its standardised equivalents.
+ * <p>
+ * Initial versions of the SSSOM specification described a
+ * {@code match_term_type} metadata slot which accepted values from a specific
+ * enumeration and was intended to describe what was being matched (e.g., it
+ * indicated that a given mapping was between two OWL classes, or between two
+ * SKOS concepts, etc.). In SSSOM 0.9.1, this slot was replaced by two distinct
+ * slots called {@code subject_type} and {@code object_type}.
+ */
+public class MatchTermTypeConverter implements IYAMLPreprocessor {
+
+    @Override
+    public void process(Map<String, Object> rawMap) throws SSSOMFormatException {
+        if ( rawMap.containsKey("match_term_type") && !rawMap.containsKey("subject_type")
+                && !rawMap.containsKey("object_type") ) {
+            Object rawValue = rawMap.get("match_term_type");
+            String value = null;
+            if ( rawValue != null ) {
+                if ( String.class.isInstance(rawValue) ) {
+                    switch ( String.class.cast(rawValue) ) {
+                    case "ConceptMatch":
+                        value = "skos concept";
+                        break;
+                    case "ClassMatch":
+                        value = "owl class";
+                        break;
+                    case "ObjectPropertyMatch":
+                        value = "owl object property";
+                        break;
+                    case "IndividualMatch":
+                        value = "owl named indivdual";
+                        break;
+                    case "DataPropertyMatch":
+                        value = "owl data property";
+                        break;
+                    case "TermMatch":
+                        // FIXME: It's unclear what is the equivalent of TermMatch in the new enum.
+                        value = "rdf literal";
+                        break;
+                    }
+                }
+
+                if ( value == null ) {
+                    throw new SSSOMFormatException("Typing error when parsing 'match_term_type'");
+                }
+            }
+
+            rawMap.remove("match_term_type");
+            rawMap.put("subject_type", value);
+            rawMap.put("object_type", value);
+        }
+    }
+
+}

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

@@ -49,6 +49,7 @@ public YAMLConverter() {
 
         preprocessors = new ArrayList<IYAMLPreprocessor>();
         preprocessors.add(new MatchTypeConverter());
+        preprocessors.add(new MatchTermTypeConverter());
 
         setSlotMaps = new HashMap<String, Slot<MappingSet>>();
         for ( Slot<MappingSet> slot : SlotHelper.getMappingSetHelper().getSlots() ) {

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

@@ -25,6 +25,7 @@
 import java.util.List;
 
 import org.apache.commons.io.FileUtils;
+import org.incenp.obofoundry.sssom.model.EntityType;
 import org.incenp.obofoundry.sssom.model.Mapping;
 import org.incenp.obofoundry.sssom.model.MappingSet;
 import org.junit.jupiter.api.Assertions;
@@ -273,9 +274,15 @@ void testSlotPropagation() throws IOException, SSSOMFormatException {
     void testObsoleteFields() throws IOException, SSSOMFormatException {
         TSVReader reader = new TSVReader("src/test/resources/obsolete-fields.sssom.tsv");
         MappingSet ms = reader.read();
-
-        Assertions.assertEquals("https://w3id.org/semapv/vocab/LexicalMatching",
-                ms.getMappings().get(0).getMappingJustification());
-        Assertions.assertNull(ms.getMappings().get(1).getMappingJustification());
+        Mapping m1 = ms.getMappings().get(0);
+        Mapping m2 = ms.getMappings().get(1);
+
+        Assertions.assertEquals("https://w3id.org/semapv/vocab/LexicalMatching", m1.getMappingJustification());
+        Assertions.assertNull(m2.getMappingJustification());
+
+        Assertions.assertNull(m1.getSubjectType());
+        Assertions.assertNull(m1.getObjectType());
+        Assertions.assertEquals(EntityType.OWL_CLASS, m2.getSubjectType());
+        Assertions.assertEquals(EntityType.OWL_CLASS, m2.getObjectType());
     }
 }

core/src/test/resources/obsolete-fields.sssom.tsv

@@ -1,6 +1,6 @@
 #curie_map:
 #  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
 #  UBERON: "http://purl.obolibrary.org/obo/UBERON_"
-subject_id	subject_label	predicate_id	object_id	match_type
-FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	Lexical
-FBbt:00000002	tagma	semapv:crossSpeciesExactMatch	UBERON:6000002	
+subject_id	subject_label	predicate_id	object_id	match_type	match_term_type
+FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	Lexical	
+FBbt:00000002	tagma	semapv:crossSpeciesExactMatch	UBERON:6000002		ClassMatch