OndexRDFUtils.iri(), bugfixing.

ondex-knet-builder/modules/neo4j-export/src/test/resources/text_mining_cytests/10_concept.cypher

@@ -1,13 +1,14 @@
 MATCH  
-  (toterm:TO { 
-  		iri: bkr + "to_0000233",
+  (toterm:TO {
   		prefName: "root volume",
   		altName: "RTVOL",
   		comment: "Is an indirect measure of root mass or density. Quantified in terms of cubic centimeters by water displacement method. ( Reference: GR:pj GR_REF:6917 )"
   }) - [ :is_a ] -> ( :TO { identifier: "TO:0000043" } ),
 
   (toterm) - [:identifier] -> (:Accession{ identifier: "TO:0000233" } ) 
            - [:dataSource] -> ({ iri: bk + "TO" })
+
+WHERE toterm.iri =~ bkr + "to_0000233.+"
 
 RETURN 
   COUNT ( toterm ) = 1

ondex-knet-builder/modules/rdf-common/src/main/java/net/sourceforge/ondex/rdf/OndexRDFUtils.java

@@ -66,12 +66,14 @@ public static String iri ( String ns, String classPart, String acc, int id, bool
 		.map ( StringUtils::trimToNull )
 		.map ( String::toLowerCase )
 		// To prevent cases like GO_GO:1234
-		.filter ( a -> !a.startsWith ( classPartNew ) )
 		.map ( OndexRDFUtils::idEncode )
 		.map ( a -> forceIdAddition ? a + "_" + id : a )
 		.orElse ( "" + id );
-
-		return ns + classPartNew + "_" + idPart;
+
+		return ns 
+			// To prevent cases like GO_GO:1234
+			+ (idPart.startsWith ( classPartNew ) ? "" : classPartNew + "_" )
+			+ idPart;
 	}
 
 	/**
@@ -84,6 +86,7 @@ public static String iri ( String ns, String classPart, String acc, int id )
 
 	/**
 	 * Don't use an ID, assuming the acc parameter is non empty.
+	 * @throws NullPointerException when acc is null
 	 * @throws IllegalArgumentException when acc is empty.
 	 * 
 	 * This is a wrapper of {@link #iri(String, String, String, int, boolean)}.

ondex-knet-builder/modules/rdf-common/src/test/java/net/sourceforge/ondex/rdf/OndexRDFUtilsTest.java

@@ -0,0 +1,78 @@
+package net.sourceforge.ondex.rdf;
+
+import static org.junit.Assert.assertEquals;
+
+import org.junit.Test;
+
+/**
+ * TODO: comment me!
+ *
+ * @author Marco Brandizi
+ * <dl><dt>Date:</dt><dd>11 Mar 2024</dd></dl>
+ *
+ */
+public class OndexRDFUtilsTest
+{
+	private static String NS = "http://foo.com/test/";
+
+	@Test
+	public void testIri ()
+	{
+		String cls = "TestConcept", acc = "A00";
+		int id = 1;
+
+		var iri = OndexRDFUtils.iri ( NS, cls, acc, id, false );
+		assertEquals ( "iri() failed!", (NS + cls + "_" + acc).toLowerCase (), iri );
+	}
+
+	@Test
+	public void testIriForceId ()
+	{
+		String cls = "TestConcept", acc = "A00";
+		int id = 1;
+
+		var iri = OndexRDFUtils.iri ( NS, cls, acc, id );
+		assertEquals ( "iri() failed!", (NS + cls + "_" + acc + "_" + id).toLowerCase (), iri );
+	}
+
+	@Test
+	public void testIriNoAcc ()
+	{
+		String cls = "TestConcept", acc = " ";
+		int id = 1;
+
+		var iri = OndexRDFUtils.iri ( NS, cls, acc, id );
+		assertEquals ( "iri() failed!", (NS + cls + "_" + id).toLowerCase (), iri );
+	}
+
+	@Test
+	public void testIriNoId ()
+	{
+		String cls = "TestConcept", acc = "A01";
+
+		var iri = OndexRDFUtils.iri ( NS, cls, acc );
+		assertEquals ( "iri() failed!", (NS + cls + "_" + acc).toLowerCase (), iri );
+	}
+
+	@Test ( expected = NullPointerException.class )
+	public void testIriNoAccNoId ()
+	{
+		String cls = "TestConcept";
+
+		OndexRDFUtils.iri ( NS, cls, null );
+	}
+
+	@Test
+	public void testIriRepeatedClass ()
+	{
+		String cls = "FOO", accCode = "001", acc = "FOO:" + accCode;
+		int id = 1;
+
+		var iri = OndexRDFUtils.iri ( NS, cls, acc, id );
+		assertEquals ( "iri() failed!", 
+			(NS + cls + "_" + accCode + "_" + id).toLowerCase (),
+			iri
+		);
+	}
+
+}