Biojava biojava#695: Stores namespace as annotation

tulay · tulay · commit a83dbc92543b · 2017-08-08T12:49:15.000-07:00
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
@@ -65,6 +65,7 @@ public class OboFileHandler implements OboFileEventListener {
 	public static final String DISJOINT_FROM = "disjoint_from";
 	public static final String SUBSET       = "subset";
 	public static final String INTERSECTION_OF = "intersection_of";
+	public static final String NAMESPACE = "namespace";
 
 
 	public static final String ALT_ID      = "alt_id";
@@ -171,6 +172,10 @@ else if (key.equals(NAME)){
 				Annotation anno = currentTerm.getAnnotation();
 				anno.setProperty(ALT_ID, value);
 			}
+            else if (key.equals(NAMESPACE)){
+                Annotation anno = currentTerm.getAnnotation();
+                anno.setProperty(NAMESPACE, value);
+            }
 
 			else {
 				//logger.info("unknown key {}", key);
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
@@ -0,0 +1,83 @@
+/*
+ *                    BioJava development code
+ *
+ * This code may be freely distributed and modified under the
+ * terms of the GNU Lesser General Public Licence.  This should
+ * be distributed with the code.  If you do not have a copy,
+ * see:
+ *
+ *      http://www.gnu.org/copyleft/lesser.html
+ *
+ * Copyright for this code is held jointly by the individual
+ * authors.  These should be listed in @author doc comments.
+ *
+ * For more information on the BioJava project and its aims,
+ * or to join the biojava-l mailing list, visit the home page
+ * at:
+ *
+ *      http://www.biojava.org/
+ *
+ * Created at 08 Aug 2017
+ */
+
+package org.biojava.nbio.ontology;
+
+import junit.framework.TestCase;
+import org.biojava.nbio.ontology.io.OboParser;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Set;
+
+import static org.biojava.nbio.ontology.obo.OboFileHandler.NAMESPACE;
+
+public class TestParseOBO extends TestCase {
+
+	private static final Logger logger = LoggerFactory.getLogger(TestParseOBO.class);
+
+	public void testNamespace(){
+
+		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();
+
+		try {
+
+
+            InputStream inStream = new ByteArrayInputStream(testTermEntry.getBytes());
+
+			assertNotNull(inStream);
+
+			BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
+
+			Ontology ontology;
+
+			ontology = parser.parseOBO(oboFile, "so-xp/subsets/biosapiens",
+                    "snippet from biosapiens protein feature ontology");
+			Set<Term> keys = ontology.getTerms();
+
+			assertTrue(keys.size() > 1);
+			assertTrue(ontology.getTerm("SO:0000691").getAnnotation().containsProperty(NAMESPACE));
+            assertEquals("sequence",ontology.getTerm("SO:0000691").getAnnotation().getProperty(NAMESPACE));
+
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			logger.error("Exception: ", e);
+			fail(e.getMessage());
+		}
+	}
+}
