use list as an annotation value for Alt_id

otter606 · otter606 · commit c44cdc5e821c · 2021-08-28T11:56:00.000+01:00
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileEventListener.java
@@ -33,40 +33,37 @@
  */
 public interface OboFileEventListener {
 
-	/** starting to parse a new OBO file
-	 *
-	 *
+	/** 
+	 * starting to parse a new OBO file
 	 */
-	public void documentStart();
+	 void documentStart();
 
-	/** end of parsing a new OBO file
-	 *
-	 *
+	/** 
+	 * end of parsing a new OBO file
 	 */
-	public void documentEnd();
+	 void documentEnd();
 
-	/** parsed a new OBO file header
-	 *
-	 *
+	/**
+	 *  parsed a new OBO file header
 	 */
-	public void newOboFileHeader();
+	 void newOboFileHeader();
 
-	/** parsed a new stanza in the file
-	 *
+	/**
+	 *  parsed a new stanza in the file
 	 * @param stanza
 	 */
-	public void newStanza(String stanza);
+	 void newStanza(String stanza);
 
-	/**found a new key in the file
-	 *
+	/**
+	 * found a new key in the file
 	 * @param key
 	 * @param value
 	 */
-	public void newKey(String key, String value );
+	 void newKey(String key, String value );
 
 	/** a new synonym has been found
 	 *
 	 * @param synonym
 	 */
-	public void newSynonym(Synonym synonym);
+	 void newSynonym(Synonym synonym);
 }
diff --git a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/obo/OboFileHandler.java
@@ -80,7 +80,6 @@ public OboFileHandler(Ontology ontology){
 
 		//Term isa = onto.importTerm(OntoTools.IS_A, null);
 		//Term partof = onto.importTerm(OntoTools.PART_OF, null);;
-
 	}
 
 	@Override
@@ -108,7 +107,6 @@ public void newStanza(String stanza) {
 		} else {
 			isTerm = false;
 		}
-
 	}
 
 	@Override
@@ -174,8 +172,16 @@ else if (key.equals(NAME)){
 				Annotation anno = currentTerm.getAnnotation();
 				anno.setProperty(COMMENT, value);
 			} else if (key.equals(ALT_ID)){
+				// #964
 				Annotation anno = currentTerm.getAnnotation();
-				anno.setProperty(ALT_ID, value);
+				if (anno.containsProperty(ALT_ID)) {
+					List<String> alts = (List<String>) anno.getProperty(ALT_ID);
+					alts.add(value);
+				} else {
+					List<String> alts = new ArrayList<>();
+					alts.add(value);
+					anno.setProperty(ALT_ID, alts);
+				}
 			}
 			else if (key.equals(REPLACED_BY)) {
 				Annotation anno = currentTerm.getAnnotation();
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
@@ -23,44 +23,53 @@
 package org.biojava.nbio.ontology;
 
 import org.biojava.nbio.ontology.io.OboParser;
-import org.junit.Assert;
+import org.biojava.nbio.ontology.utils.Annotation;
 import org.junit.Test;
 
 import java.io.*;
 import java.text.ParseException;
+import java.util.List;
 import java.util.Set;
 
 import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;
+import static org.biojava.nbio.ontology.obo.OboFileHandler.ALT_ID;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
 
 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";
+		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";
 
-	OboParser parser = new OboParser();
-	InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());
+		OboParser parser = new OboParser();
+		InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());
 
-		Assert.assertNotNull(inStream);
+		assertNotNull(inStream);
 
-		BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
+		BufferedReader oboFile = new BufferedReader(new InputStreamReader(inStream));
 		Ontology ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
-		    "snippet from biosapiens protein feature ontology");
+				"snippet from biosapiens protein feature ontology");
+
 		Set<Term> keys = ontology.getTerms();
 
-		Assert.assertTrue(keys.size() > 1);
-		Assert.assertTrue(ontology.getTerm("SO:0000691").getAnnotation().containsProperty(NAMESPACE));
-	Assert.assertEquals("sequence", ontology.getTerm("SO:0000691").getAnnotation().getProperty(NAMESPACE));
+		assertTrue(keys.size() > 1);
+		assertTrue(getAnnotationForTerm(ontology).containsProperty(NAMESPACE));
+		assertEquals("sequence", getAnnotationForTerm(ontology).getProperty(NAMESPACE));
+		assertTrue( getAnnotationForTerm(ontology).getProperty(ALT_ID) instanceof List);
+
+	}
+
+	private Annotation getAnnotationForTerm(Ontology ontology) {
+		return ontology.getTerm("SO:0000691").getAnnotation();
 	}
 }
