Author: pwang
Date: 2012-08-03 15:05:58 -0700 (Fri, 03 Aug 2012)
New Revision: 30086
Added:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/nnf/
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/nnf/NNFReaderTest.java
Log:
Port from 2.8
Added:
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/nnf/NNFReaderTest.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/nnf/NNFReaderTest.java
(rev 0)
+++
core3/impl/trunk/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/nnf/NNFReaderTest.java
2012-08-03 22:05:58 UTC (rev 30086)
@@ -0,0 +1,192 @@
+package org.cytoscape.io.internal.read.nnf;
+
+import static org.junit.Assert.*;
+import static org.mockito.Mockito.mock;
+import org.cytoscape.io.internal.read.AbstractNetworkReaderTest;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyNode;
+import java.io.IOException;
+import org.cytoscape.model.CyNetwork;
+import java.io.FileInputStream;
+import org.junit.Test;
+import java.util.Iterator;
+import org.cytoscape.model.CyRow;
+
+
+/**
+ * Test code for Nested Network Format file reader.
+ *
+ * @author kono, ruschein
+ * @since Cytoscape 2.7.0
+ */
+public class NNFReaderTest extends AbstractNetworkReaderTest {
+
+ // All test data files are in this directory.
+ private static final String FILE_LOCATION =
"src/test/resources/testData/NNFData/";
+
+
+ @Test
+ public void testGood1() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good1.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertEquals("root",
reader.getNetworks()[0].getRow(reader.getNetworks()[0]).get(CyNetwork.NAME,
String.class));
+ }
+
+ @Test
+ public void testGood2() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good2.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertEquals("root",
reader.getNetworks()[0].getRow(reader.getNetworks()[0]).get(CyNetwork.NAME,
String.class));
+ }
+
+
+ @Test
+ public void testGood3() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good3.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertEquals("Module_Overview",
reader.getNetworks()[0].getRow(reader.getNetworks()[0]).get(CyNetwork.NAME,
String.class));
+
+ CyNetwork targetNetwork = reader.getNetworks()[0];
+
+ assertEquals("Module_Overview",
targetNetwork.getRow(targetNetwork).get(CyNetwork.NAME, String.class));
+ assertEquals(4, targetNetwork.getNodeCount());
+ assertEquals(5, targetNetwork.getEdgeCount());
+ }
+
+
+ public void testGood4() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good4.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertEquals("Top_Level_Network",
reader.getNetworks()[0].getRow(reader.getNetworks()[0]).get(CyNetwork.NAME,
String.class));
+
+ final CyNetwork[] networks = reader.getNetworks()
;//this.networkManager.getNetworkSet();
+ CyNetwork targetNetwork = null;
+ for (CyNetwork net : networks) {
+ if (net.getRow(net).get(CyNetwork.NAME,
String.class).equals("M3")) {
+ targetNetwork = net;
+ }
+ }
+
+ assertNotNull(targetNetwork);
+ assertEquals("M3",
targetNetwork.getRow(targetNetwork).get(CyNetwork.NAME, String.class));
+ assertEquals(4, targetNetwork.getNodeCount());
+ assertEquals(3, targetNetwork.getEdgeCount());
+
+ // Find node M2
+ CyNode m2 = null; // = Cytoscape.getCyNode("M2");
+ for (CyNetwork net : networks) {
+ Iterator<CyRow> rowsIt =
net.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, "M2").iterator();
+ while(rowsIt.hasNext()){
+ CyRow row = rowsIt.next();
+ Long suid = row.get("suid", Long.class);
+ m2 = net.getNode(suid);
+ }
+ }
+
+ assertNotNull(m2);
+ CyNetwork nestedNetwork = m2.getNetworkPointer();
+ assertNotNull(nestedNetwork);
+
assertTrue(((CyNetwork)nestedNetwork).getRow(((CyNetwork)nestedNetwork)).get(CyNetwork.NAME,
String.class).equals("M2"));
+ assertEquals(1, nestedNetwork.getNodeCount());
+ assertEquals(0, nestedNetwork.getEdgeCount());
+ }
+
+
+ @Test
+ public void testGood5() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good5.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertEquals("TopLevelNetwork",
reader.getNetworks()[0].getRow(reader.getNetworks()[0]).get(CyNetwork.NAME,
String.class));
+ }
+
+ @Test
+ public void testGood6() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good6.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+ reader.run(taskMonitor);
+
+ assertNotNull(reader.getNetworks()[0]);
+ assertNotNull(reader.getNetworks()[1]);
+ }
+
+
+ public void testBad1() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "bad1.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+ try {
+ reader.run(taskMonitor);
+ } catch (IOException e) {
+ e.printStackTrace();
+ assertNotNull(reader.getNetworks()[0]);
+ return;
+ }
+
+ //If not caught by the above, something is wrong!
+ fail();
+ }
+
+ @Test
+ public void testBad2() throws Exception {
+ final NNFNetworkReader reader = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "bad2.nnf"), layouts,
+ viewFactory, netFactory,
mock(CyNetworkManager.class));
+
+ try {
+ reader.run(taskMonitor);
+ } catch (IOException e) {
+ e.printStackTrace();
+ assertNull(reader.getNetworks());
+ return;
+ }
+
+ //If not caught by the above, something is wrong!
+ fail();
+ }
+
+// @Test
+// public void testMultipleFiles() throws Exception {
+//
+// final NNFNetworkReader reader1 = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good3.nnf"), layouts,
+// viewFactory, netFactory,
mock(CyNetworkManager.class));
+//
+// reader1.run(taskMonitor);
+//
+// final NNFNetworkReader reader2 = new NNFNetworkReader(new
FileInputStream(FILE_LOCATION + "good4.nnf"), layouts,
+// viewFactory, netFactory, networkManager);
+//
+// reader2.run(taskMonitor);
+//
+// // Find node m3 and the network M3 belongs to
+// final Set<CyNetwork> networks =
this.networkManager.getNetworkSet();
+// CyNetwork targetNetwork = null;
+// for (CyNetwork net : networks) {
+// if (net.getRow(net).get(CyNetwork.NAME,
String.class).equals("M3")) {
+// targetNetwork = net;
+// }
+// }
+//
+// assertNotNull(targetNetwork);
+// assertEquals("M3",
targetNetwork.getRow(targetNetwork).get(CyNetwork.NAME, String.class));
+// assertEquals(6, targetNetwork.getNodeCount());
+// assertEquals(4, targetNetwork.getEdgeCount());
+// }
+}
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