/**
* Copyright (C) 2012-2013 Selventa, Inc.
*
* This file is part of the OpenBEL Framework.
*
* This program is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* The OpenBEL Framework is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
* License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.
*
* Additional Terms under LGPL v3:
*
* This license does not authorize you and you are prohibited from using the
* name, trademarks, service marks, logos or similar indicia of Selventa, Inc.,
* or, in the discretion of other licensors or authors of the program, the
* name, trademarks, service marks, logos or similar indicia of such authors or
* licensors, in any marketing or advertising materials relating to your
* distribution of the program or any covered product. This restriction does
* not waive or limit your obligation to keep intact all copyright notices set
* forth in the program as delivered to you.
*
* If you distribute the program in whole or in part, or any modified version
* of the program, and you assume contractual liability to the recipient with
* respect to the program or modified version, then you will indemnify the
* authors and licensors of the program for any liabilities that these
* contractual assumptions directly impose on those licensors and authors.
*/
package org.openbel.framework.api;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
import static org.openbel.framework.common.enums.FunctionEnum.BIOLOGICAL_PROCESS;
import static org.openbel.framework.common.enums.FunctionEnum.COMPLEX_ABUNDANCE;
import static org.openbel.framework.common.enums.FunctionEnum.KINASE_ACTIVITY;
import static org.openbel.framework.common.enums.FunctionEnum.PROTEIN_ABUNDANCE;
import static org.openbel.framework.common.enums.RelationshipType.ACTS_IN;
import static org.openbel.framework.common.enums.RelationshipType.DECREASES;
import static org.openbel.framework.common.enums.RelationshipType.HAS_COMPONENT;
import static org.openbel.framework.common.enums.RelationshipType.INCREASES;
import java.util.Collection;
import java.util.Iterator;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openbel.framework.api.Kam.KamEdge;
import org.openbel.framework.api.KamTestUtil.TestKamEdge;
import org.openbel.framework.api.KamTestUtil.TestKamNode;
import org.openbel.framework.api.internal.KamInfoUtil;
import org.openbel.framework.api.internal.KAMCatalogDao.KamInfo;
public class EdgeFilterTest {
private static Kam testKAM;
@Test
public void testSingleIncludeCriteria() {
// Test include HAS_COMPONENT relationship type criteria yields 2 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria rtcriteria =
new RelationshipTypeFilterCriteria();
rtcriteria.setInclude(true);
rtcriteria.add(HAS_COMPONENT);
edgeFilter.add(rtcriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(2, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(HAS_COMPONENT, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(HAS_COMPONENT, e2.getRelationshipType());
}
@Test
public void testSingleExcludeCriteria() {
// Test exclude HAS_COMPONENT relationship type criteria yields 3 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria rtcriteria =
new RelationshipTypeFilterCriteria();
rtcriteria.setInclude(false);
rtcriteria.add(HAS_COMPONENT);
edgeFilter.add(rtcriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(3, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(INCREASES, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(ACTS_IN, e2.getRelationshipType());
KamEdge e3 = edgeIt.next();
assertEquals(DECREASES, e3.getRelationshipType());
}
@Test
public void testMultipleIncludeCriteria() {
// Test include INCREASES AND DECREASES relationship type criteria yields 2 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria rtcriteria =
new RelationshipTypeFilterCriteria();
rtcriteria.setInclude(true);
rtcriteria.add(INCREASES);
rtcriteria.add(DECREASES);
edgeFilter.add(rtcriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(2, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(INCREASES, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(DECREASES, e2.getRelationshipType());
}
@Test
public void testMultipleExcludeCriteria() {
// Test exclude INCREASES AND DECREASES relationship type criteria yields 3 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria rtcriteria =
new RelationshipTypeFilterCriteria();
rtcriteria.setInclude(false);
rtcriteria.add(INCREASES);
rtcriteria.add(DECREASES);
edgeFilter.add(rtcriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(3, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(HAS_COMPONENT, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(HAS_COMPONENT, e2.getRelationshipType());
KamEdge e3 = edgeIt.next();
assertEquals(ACTS_IN, e3.getRelationshipType());
}
@Test
public void testCollidingIncludeExcludeCriteria() {
// Test include
// HAS_COMPONENT
// and exclude
// HAS_COMPONENT
// relationship type criterion yields 2 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria incriteria =
new RelationshipTypeFilterCriteria();
incriteria.setInclude(true);
incriteria.add(HAS_COMPONENT);
RelationshipTypeFilterCriteria excriteria =
new RelationshipTypeFilterCriteria();
excriteria.setInclude(false);
excriteria.add(HAS_COMPONENT);
edgeFilter.add(incriteria);
edgeFilter.add(excriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(5, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(HAS_COMPONENT, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(HAS_COMPONENT, e2.getRelationshipType());
KamEdge e3 = edgeIt.next();
assertEquals(INCREASES, e3.getRelationshipType());
KamEdge e4 = edgeIt.next();
assertEquals(ACTS_IN, e4.getRelationshipType());
KamEdge e5 = edgeIt.next();
assertEquals(DECREASES, e5.getRelationshipType());
}
@Test
public void testCollidingExcludeIncludeCriteria() {
// Test exclude
// HAS_COMPONENT
// and include
// HAS_COMPONENT
// relationship type criterion yields 2 edges
EdgeFilter edgeFilter = testKAM.createEdgeFilter();
RelationshipTypeFilterCriteria excriteria =
new RelationshipTypeFilterCriteria();
excriteria.setInclude(false);
excriteria.add(HAS_COMPONENT);
RelationshipTypeFilterCriteria incriteria =
new RelationshipTypeFilterCriteria();
incriteria.setInclude(true);
incriteria.add(HAS_COMPONENT);
edgeFilter.add(excriteria);
edgeFilter.add(incriteria);
Collection<KamEdge> edges = testKAM.getEdges(edgeFilter);
assertNotNull(edges);
assertEquals(3, edges.size());
Iterator<KamEdge> edgeIt = edges.iterator();
KamEdge e1 = edgeIt.next();
assertEquals(INCREASES, e1.getRelationshipType());
KamEdge e2 = edgeIt.next();
assertEquals(ACTS_IN, e2.getRelationshipType());
KamEdge e3 = edgeIt.next();
assertEquals(DECREASES, e3.getRelationshipType());
}
@BeforeClass
public static void setup() {
testKAM = createTestKAM();
assertNotNull(testKAM);
}
private static Kam createTestKAM() {
KamInfo testKAMInfo = null;
try {
testKAMInfo = KamInfoUtil.createKamInfo();
} catch (Exception e) {
e.printStackTrace();
fail(e.getMessage());
}
final TestKamNode[] testKamNodes = new TestKamNode[] {
new TestKamNode(1, COMPLEX_ABUNDANCE, "complex(p(1), p(2))"),
new TestKamNode(2, PROTEIN_ABUNDANCE, "p(1)"),
new TestKamNode(3, PROTEIN_ABUNDANCE, "p(2)"),
new TestKamNode(4, KINASE_ACTIVITY, "kin(p(2))"),
new TestKamNode(5, BIOLOGICAL_PROCESS, "bp(3)")
};
final TestKamEdge[] testKamEdges =
new TestKamEdge[] {
new TestKamEdge(1, testKamNodes[0], HAS_COMPONENT,
testKamNodes[1]),
new TestKamEdge(2, testKamNodes[0], HAS_COMPONENT,
testKamNodes[2]),
new TestKamEdge(3, testKamNodes[1], INCREASES,
testKamNodes[2]),
new TestKamEdge(4, testKamNodes[2], ACTS_IN,
testKamNodes[3]),
new TestKamEdge(5, testKamNodes[3], DECREASES,
testKamNodes[4])
};
return KamTestUtil.createKam(testKAMInfo, testKamNodes, testKamEdges);
}
}