Followed #54 - polished tests and added more comments.

json-converter/src/test/java/org/biopax/paxtools/io/jsonld/JsonldBiopaxConverterTest.java

@@ -10,7 +10,7 @@
 public class JsonldBiopaxConverterTest {
 
 	@Test
-	final void test() throws IOException {
+	final void testPc5BmpSignalingPathway() throws IOException {
 		File jsonldTestFileName = File.createTempFile("test", ".jsonld");
 		File rdfTestFileName = File.createTempFile("test", ".rdf");
 
@@ -26,10 +26,16 @@ final void test() throws IOException {
 	}
 
 	@Test
-	final void test2() throws IOException {
+	final void testSomePc14DemoPathway() throws IOException {
 		JsonldConverter converter = new JsonldBiopaxConverter();
+
 		// convert owl test file in resource directory to jsonld format
-		InputStream in = getClass().getResourceAsStream("/demo-pathway-xsd.owl");
+		InputStream in = getClass().getResourceAsStream("/demo-pathway.owl");
+		//- there is no rdf:datatype=... anymore; should be fine as the datatypes are defined in the biopax-level3.owl spec!
+		//todo: for some reason, Jena libs v4 or v5 fail at e.g. rdf:about="TEST_CHEBI:cs_26d67131a0608673ae6a683d1dad18f7",
+		//but jena v3 just prints warnings, e.g.: org.apache.jena.riot - [line: 155, col: 82] {W107} Bad URI: <TEST_CHEBI:cs_26d67131a0608673ae6a683d1dad18f7> Code: 0/ILLEGAL_CHARACTER in SCHEME: The character violates the grammar rules for URIs/IRIs.
+		//howver, removing the underscore from TEST_CHEBI - makes those warning/errors go away...
+
 		ByteArrayOutputStream baos = new ByteArrayOutputStream();
 		converter.convertToJsonld(in, baos);
 		String res = baos.toString("UTF-8");
@@ -40,27 +46,10 @@ final void test2() throws IOException {
 				() -> Assertions.assertDoesNotThrow(() -> URI.create("http://bioregistry.io/chebi:20")), //good valid absolute URI
 				() -> Assertions.assertTrue(res.contains("@id\" : \"http://bioregistry.io/chebi:20")),
 				() -> Assertions.assertTrue(res.contains("@id\" : \"http://bioregistry.io/mi:0361")),//as long as it has 'http://' (valid abs. uri w/o schema would fail here due Jena bug)
-				() -> Assertions.assertTrue(res.contains("@id\" : \"chebi:20")), //unchanged
-				() -> Assertions.assertTrue(res.contains("\"@id\" : \"http://www.biopax.org/release/biopax-level3.owl#displayName\""))
-		);
-	}
-
-	@Test
-	final void test3() throws IOException {
-		JsonldConverter converter = new JsonldBiopaxConverter();
-		// convert owl test file in resource directory to jsonld format
-		InputStream in = getClass().getResourceAsStream("/demo-pathway-noxsd.owl");
-		ByteArrayOutputStream baos = new ByteArrayOutputStream();
-		converter.convertToJsonld(in, baos);
-		String res = baos.toString("UTF-8");
-		Assertions.assertAll(
-				() -> Assertions.assertThrows(IllegalArgumentException.class, () -> URI.create("http://")),
-				() -> Assertions.assertDoesNotThrow(() -> URI.create("bioregistry.io/chebi:20")),
-				() -> Assertions.assertDoesNotThrow(() -> URI.create("chebi:20")),
-				() -> Assertions.assertDoesNotThrow(() -> URI.create("http://bioregistry.io/chebi:28")),
-				() -> Assertions.assertTrue(res.contains("@id\" : \"http://bioregistry.io/chebi:28")),
+				() -> Assertions.assertTrue(res.contains("@id\" : \"chebi:20")), //CURIE of a standard/normalized SMR's UnificationXref
 				() -> Assertions.assertTrue(res.contains("\"@id\" : \"http://www.biopax.org/release/biopax-level3.owl#displayName\"")),
-				() -> Assertions.assertTrue(res.contains("@id\" : \"chebi:28"))
+				() -> Assertions.assertTrue(res.contains("\"displayName\" : \"(+)-camphene\"")), //chebi:20
+				() -> Assertions.assertTrue(res.contains("\"id\" : \"CHEBI:20\"")) //with jena v3 (e.g. 3.2.0 or 3.17.0)
 		);
 	}