Add more tests for the JSON format.

Add a new test for the JSONReader, to check that non-string-typed slots
(e.g. double-typed and enum-typed slots) are parsed correctly.

Also add some roundtrip tests for both the JSONReader and the
JSONWriter, including some TSV-to-JSON-to-TSV roundtripping tests.

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

@@ -175,6 +175,9 @@ public MappingSet convertMappingSet(Map<String, Object> rawMap) throws SSSOMForm
         // Process the bulk of the metadata slots
         Map<String, ExtensionValue> extensionSlots = new HashMap<String, ExtensionValue>();
         for ( String key : rawMap.keySet() ) {
+            if ( key.equals("mappings") ) { // To be processed separately
+                continue;
+            }
             if ( setSlotMaps.containsKey(key) ) {
                 setSlotValue(setSlotMaps.get(key), ms, rawMap.get(key));
             } else {

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

@@ -21,6 +21,7 @@
 import java.io.IOException;
 import java.time.LocalDate;
 
+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;
@@ -160,4 +161,13 @@ void testSlotPropagation() throws IOException, SSSOMFormatException {
         // Second mapping has its own mapping tool value
         Assertions.assertEquals("bar mapper", ms.getMappings().get(1).getMappingTool());
     }
+
+    @Test
+    void testParsingNonStringValues() throws IOException, SSSOMFormatException {
+        JSONReader reader = new JSONReader("src/test/resources/sets/test-non-string-values.sssom.json");
+        MappingSet ms = reader.read();
+
+        Assertions.assertEquals(EntityType.OWL_CLASS, ms.getMappings().get(0).getSubjectType());
+        Assertions.assertEquals(0.7, ms.getMappings().get(0).getConfidence());
+    }
 }

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

@@ -92,6 +92,54 @@ void testEscapingJSON() throws IOException, SSSOMFormatException {
         assertWrittenAsExpected(ms, "test-escaping-json", null, null);
     }
 
+    @Test
+    void testBasicRoundtrip() throws IOException, SSSOMFormatException {
+        JSONReader reader = new JSONReader("src/test/resources/sets/exo2c.sssom.json");
+        MappingSet ms = reader.read();
+
+        assertWrittenAsExpected(ms, "exo2c", "test-basic-roundtrip", null);
+    }
+
+    @Test
+    void testTSVAndJSONRoundtrips() throws IOException, SSSOMFormatException {
+        TSVtoJSONtoTSVRoundtrip("exo2c", ExtraMetadataPolicy.NONE);
+        TSVtoJSONtoTSVRoundtrip("test-extensions-defined", ExtraMetadataPolicy.DEFINED);
+    }
+
+    private void TSVtoJSONtoTSVRoundtrip(String tsvFilename, ExtraMetadataPolicy policy)
+            throws IOException, SSSOMFormatException {
+        File origTSV = new File("src/test/resources/sets/" + tsvFilename + ".sssom.tsv");
+        if ( !origTSV.exists() ) {
+            origTSV = new File("src/test/resources/output/" + tsvFilename + ".sssom.tsv");
+        }
+
+        TSVReader tsvReader = new TSVReader(origTSV);
+        tsvReader.setExtraMetadataPolicy(policy);
+        MappingSet ms = tsvReader.read();
+
+        File json = new File("src/test/resources/output/" + tsvFilename + ".sssom.json.out");
+        JSONWriter jsonWriter = new JSONWriter(json);
+        jsonWriter.setShortenIRIs(true);
+        jsonWriter.setExtraMetadataPolicy(policy);
+        jsonWriter.write(ms);
+
+        JSONReader jsonReader = new JSONReader(json);
+        jsonReader.setExtraMetadataPolicy(policy);
+        ms = jsonReader.read();
+
+        File newTSV = new File("src/test/resources/output/" + tsvFilename + ".sssom.tsv.out");
+        TSVWriter tsvWriter = new TSVWriter(newTSV);
+        tsvWriter.setExtraMetadataPolicy(policy);
+        tsvWriter.write(ms);
+
+        boolean same = FileUtils.contentEquals(origTSV, newTSV);
+        Assertions.assertTrue(same);
+        if ( same ) {
+            json.delete();
+            newTSV.delete();
+        }
+    }
+
     /*
      * Checks that a mapping set is written exactly as we expect. This method will
      * write the provided set to a temporary file and compares the written file with

core/src/test/resources/sets/test-non-string-values.sssom.json

@@ -0,0 +1,20 @@
+{
+  "curie_map": {
+    "COMENT": "https://example.com/entities/",
+    "ORGENT": "https://example.org/entities/"
+  },
+  "mapping_set_id": "https://example.org/sets/exo2c",
+  "mapping_set_title": "O2C set",
+  "mappings": [
+    {
+      "subject_id": "ORGENT:0001",
+      "subject_label": "alice",
+      "predicate_id": "skos:closeMatch",
+      "object_id": "COMENT:0011",
+      "object_label": "alpha",
+      "mapping_justification": "semapv:ManualMappingCuration",
+      "subject_type": "owl class",
+      "confidence": 0.7
+    }
+  ]
+}