add test for multiple altids

otter606 · otter606 · commit a32f209ee975 · 2021-08-28T12:12:40.000+01:00
diff --git a/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java b/biojava-ontology/src/test/java/org/biojava/nbio/ontology/TestParseOBO.java
@@ -24,6 +24,7 @@
 
 import org.biojava.nbio.ontology.io.OboParser;
 import org.biojava.nbio.ontology.utils.Annotation;
+import org.junit.Before;
 import org.junit.Test;
 
 import java.io.*;
@@ -39,37 +40,50 @@
 
 public class TestParseOBO {
 
-	@Test
-	public void testNamespace() throws IOException, ParseException {
-
-		String testTermEntry = "\n[Term]\n" + "id: SO:0000691\n" 
-				+ "name: cleaved_initiator_methionine \n"
-				+ "namespace: sequence\n" 
-				+ "alt_id: BS:00067\n"
-				+ "def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n"
-				+ "subset: biosapiens\n" + "synonym: \"cleaved initiator methionine\" EXACT []\n"
-				+ "synonym: \"init_met\" RELATED [uniprot:feature_type]\n"
-				+ "synonym: \"initiator methionine\" RELATED []\n" + "is_a: SO:0100011 ! cleaved_peptide_region\n\n";
+	private OboParser parser;
 
-		OboParser parser = new OboParser();
-		InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());
+	final String testTermEntry = "\n[Term]\n" + "id: SO:0000691\n" + "name: cleaved_initiator_methionine \n"
+			+ "namespace: sequence\n" + "alt_id: BS:00067\n"
+			+ "def: \"The initiator methionine that has been cleaved from a mature polypeptide sequence.\" [EBIBS:GAR]\n"
+			+ "subset: biosapiens\n" + "synonym: \"cleaved initiator methionine\" EXACT []\n"
+			+ "synonym: \"init_met\" RELATED [uniprot:feature_type]\n"
+			+ "synonym: \"initiator methionine\" RELATED []\n" + "is_a: SO:0100011 ! cleaved_peptide_region\n\n";
+	private String replace;
 
+	public Ontology readObo(String input) throws ParseException, IOException {
+		parser = new OboParser();
+		InputStream inStream = new ByteArrayInputStream(input.getBytes());
 		assertNotNull(inStream);
-
-		BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream));
-		Ontology ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
+		BufferedReader oboFile = new  BufferedReader(new InputStreamReader(inStream));
+		return parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
 				"snippet from biosapiens protein feature ontology");
+	}
+
+	@Test
+	public void testNamespace() throws IOException, ParseException {
+		Ontology ontology = readObo(testTermEntry);
 
 		Set<Term> keys = ontology.getTerms();
 
 		assertTrue(keys.size() > 1);
 		assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE));
 		assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE));
-		assertTrue( getAnnotationForTerm(ontology).getProperty(ALT_ID) instanceof List);
+		assertTrue(getAnnotationForTerm(ontology).getProperty(ALT_ID) instanceof List);
+	}
 
+	@Test
+	public void testMultipleAltIds() throws IOException, ParseException {
+		
+		String replace = testTermEntry.replace("BS:00067", "BS:00067\nalt_id: BS:00068");
+		Ontology ontology = readObo(replace);
+		List<String> altIds = (List<String>) getAnnotationForTerm(ontology).getProperty(ALT_ID);
+		assertEquals(2, altIds.size());
+		assertEquals("BS:00067", altIds.get(0));
+		assertEquals("BS:00068", altIds.get(1));
 	}
 
 	private Annotation getAnnotationForTerm(Ontology ontology) {
 		return ontology.getTerm("SO:0000691").getAnnotation();
+
 	}
 }
