Test.java

// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
// Copyright 2006-2009 BridgeDb developers
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
package org.bridgedb.webservice.picr;

import java.util.HashSet;
import java.util.Map;
import java.util.Set;

import org.bridgedb.AttributeMapper;
import org.bridgedb.BridgeDb;
import org.bridgedb.DataSource;
import org.bridgedb.IDMapper;
import org.bridgedb.IDMapperException;
import org.bridgedb.Xref;
import org.junit.Assert;
import org.junit.Before;


public class Test {
	
	@Before
	public void setUp() throws ClassNotFoundException
	{
		Class.forName ("org.bridgedb.webservice.picr.IDMapperPicr");
	}
	
	@org.junit.Test
	public void test() throws IDMapperException
	{
		IDMapper idmap = BridgeDb.connect ("idmapper-picr:");
		AttributeMapper amap = (AttributeMapper)idmap;
		
		Set<DataSource> dslist = idmap.getCapabilities().getSupportedTgtDataSources();
		
		final DataSource SGD = DataSource.getByFullName("SGD");
		final DataSource PDB  = DataSource.getByFullName("PDB");
		final DataSource ENSEMBL_YEAST = DataSource.getByFullName("ENSEMBL_S_CEREVISIAE");
		Assert.assertTrue (dslist.contains(SGD));
		Assert.assertTrue (dslist.contains(PDB));
		Assert.assertTrue (dslist.contains(ENSEMBL_YEAST));
		
		Xref src1 = new Xref ("YER095W", ENSEMBL_YEAST);
		for (DataSource ds : dslist) System.out.println (ds.getFullName());
		
		Set<Xref> srcRefs = new HashSet<Xref>();
		srcRefs.add (src1);
		DataSource[] targets = new DataSource[] { SGD, PDB, ENSEMBL_YEAST }; 
		Map<Xref, Set<Xref>> result = idmap.mapID(srcRefs, targets);
		
		/*
		This list is expected:
		RAD51 SGD
		YER095W SGD
		YER095W ENSEMBL_S_CEREVISIAE
		1SZP PDB
		S000000897 SGD
		*/
		for (Xref ref : result.get(src1)) System.out.println (ref.getId() + " "  + ref.getDataSource().getFullName());

		System.out.println (amap.getAttributes(src1, "Sequence").iterator().next());
	}
		
}