Add support for converting MIRIAM URN to Xref

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/trunk@510 e3f1d335-44b1-4163-9530-9b341189ae98

org.bridgedb.bio/test/org/bridgedb/bio/Test.java

@@ -129,5 +129,23 @@ public void testAlias()
 		DataSource ds = DataSource.getByAlias("ensembl_gene_id");
 		assertSame(ds, BioDataSource.ENSEMBL);
 	}
+
+	@org.junit.Test
+	public void testFromUrn()
+	{
+		Xref ref = Xref.fromUrn("urn:miriam:entrez.gene:3643");
+		assertEquals (BioDataSource.ENTREZ_GENE, ref.getDataSource());
+		assertEquals ("3643", ref.getId());
+
+		ref = Xref.fromUrn("urn:miriam:blahblahblah:abc");
+		assertNull (ref);
+
+		ref = Xref.fromUrn("blahblahblha");
+		assertNull (ref);
+
+		ref = Xref.fromUrn("urn:miriam:obo.go:GO%3A00001234");
+		assertEquals (BioDataSource.GENE_ONTOLOGY, ref.getDataSource());
+		assertEquals ("GO:00001234", ref.getId());
+	}
 
 }

org.bridgedb/src/org/bridgedb/DataSource.java

@@ -59,6 +59,7 @@ public final class DataSource
 	private static Map<String, DataSource> byFullName = new HashMap<String, DataSource>();
 	private static Set<DataSource> registry = new HashSet<DataSource>();
 	private static Map<String, DataSource> byAlias = new HashMap<String, DataSource>();
+	private static Map<String, DataSource> byMiriamBase = new HashMap<String, DataSource>();
 
 	private String sysCode = null;
 	private String fullName = null;
@@ -310,6 +311,11 @@ else if (bySysCode.containsKey(sysCode))
 			registry.add (current);
 		}
 
+		if (current.urnBase != null)
+		{
+			byMiriamBase.put (current.urnBase, current);
+		}
+
 		current.sysCode = sysCode;
 		current.fullName = fullName;
 
@@ -465,4 +471,9 @@ public Object getOrganism()
 		return organism;
 	}
 
+	public static DataSource getByUrnBase(String base)
+	{
+		return byMiriamBase.get(base);
+	}
+
 }

org.bridgedb/src/org/bridgedb/Xref.java

@@ -16,6 +16,9 @@
 //
 package org.bridgedb;
 
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
+
 /**
  * Stores an id + {@link DataSource} combination, which represents
  * an unique gene product.
@@ -108,5 +111,27 @@ public String getURN()
 	{
 		return ds.getURN (id);
 	}
+
+	public static Xref fromUrn(String urn)
+	{
+		int pos = urn.lastIndexOf(":");
+		if (pos < 0) return null;
+
+		String base = urn.substring(0, pos);
+		String id;
+		try
+		{
+			id = URLDecoder.decode(urn.substring(pos + 1), "UTF-8");
+		}
+		catch (UnsupportedEncodingException e)
+		{
+			return null;
+		}
+
+		DataSource ds = DataSource.getByUrnBase(base);
+		if (ds == null) return null;
+
+		return new Xref (id, ds);
+	}
 
 }