Author: pwang
Date: 2012-05-30 17:49:00 -0700 (Wed, 30 May 2012)
New Revision: 29404
Added:
core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/Cy263SimpleSessionLodingTest.java
core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/session2x/v263SessionLarge.cys
Log:
Original creation
Added:
core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/Cy263SimpleSessionLodingTest.java
===================================================================
---
core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/Cy263SimpleSessionLodingTest.java
(rev 0)
+++
core3/impl/trunk/session-impl/integration-test/src/test/java/org/cytoscape/session/Cy263SimpleSessionLodingTest.java
2012-05-31 00:49:00 UTC (rev 29404)
@@ -0,0 +1,202 @@
+package org.cytoscape.session;
+
+import static org.junit.Assert.*;
+import java.awt.Color;
+import java.awt.Paint;
+import java.io.File;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.Set;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
+import org.cytoscape.view.presentation.property.LineTypeVisualProperty;
+import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
+import org.cytoscape.view.presentation.property.values.LineType;
+import org.cytoscape.view.presentation.property.values.NodeShape;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
+import org.cytoscape.work.TaskIterator;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.ops4j.pax.exam.junit.ExamReactorStrategy;
+import org.ops4j.pax.exam.junit.JUnit4TestRunner;
+import org.ops4j.pax.exam.spi.reactors.AllConfinedStagedReactorFactory;
+import org.cytoscape.model.CyTableUtil;
+import org.cytoscape.model.CyTable;
+
+/**
+ * Test for sample file in Cytoscape 2.6.3 distribution
+ *
+ */
+@RunWith(JUnit4TestRunner.class)
+@ExamReactorStrategy(AllConfinedStagedReactorFactory.class)
+public class Cy263SimpleSessionLodingTest extends BasicIntegrationTest {
+
+ @Before
+ public void setup() throws Exception {
+ sessionFile = new
File("./src/test/resources/testData/session2x/", "v263SessionLarge.cys");
+ checkBasicConfiguration();
+ }
+
+ @Test
+ public void testLoadSession() throws Exception {
+ final TaskIterator ti =
openSessionTF.createTaskIterator(sessionFile);
+ tm.execute(ti);
+ }
+
+ @After
+ public void confirm() {
+ // test overall status of current session.
+ checkGlobalStatus();
+
+ checkVisualStyles();
+
+ final Set<CyNetwork> networks = networkManager.getNetworkSet();
+ final Iterator<CyNetwork> itr = networks.iterator();
+
+ // get the parent network in the session
+ CyNetwork gdNetwork = null;
+ while (itr.hasNext()){
+ CyNetwork network = itr.next();
+
+ // Check title
+ String title = network.getRow(network).get("name",
String.class);
+ if
(title.equalsIgnoreCase("gene_disease_network4.txt")){
+ gdNetwork = network;
+ break;
+ }
+ }
+
+ checkAttributes(gdNetwork);
+ checkNetwork(gdNetwork);
+ }
+
+ private void checkGlobalStatus() {
+ assertEquals(7, networkManager.getNetworkSet().size());
+ assertEquals(7, viewManager.getNetworkViewSet().size());
+
+ // Since this test runs in headless mode, this should be zero.
+ assertEquals(0,
renderingEngineManager.getAllRenderingEngines().size());
+
+ assertEquals(42, tableManager.getAllTables(true).size());
+ assertEquals(21, tableManager.getAllTables(false).size());
+
+ }
+
+ private void checkVisualStyles() {
+
+ Set<VisualStyle> vsSet = vmm.getAllVisualStyles();
+
+ VisualStyle gda_geneCentric = null;
+ VisualStyle gda_diseaseCentric = null;
+ VisualStyle gda_wholeNetwork = null;
+
+ Iterator<VisualStyle> it = vsSet.iterator();
+
+ while (it.hasNext()){
+ VisualStyle vs = it.next();
+ if (vs.getTitle().equalsIgnoreCase("gda_geneCentric")){
+ gda_geneCentric = vs;
+ }
+ if
(vs.getTitle().equalsIgnoreCase("gda_diseaseCentric")){
+ gda_diseaseCentric = vs;
+ }
+ if (vs.getTitle().equalsIgnoreCase("gda_wholeNetwork")){
+ gda_wholeNetwork = vs;
+ }
+ }
+
+ assertNotNull(gda_geneCentric);
+ assertNotNull(gda_diseaseCentric);
+ assertNotNull(gda_wholeNetwork);
+
+ checkVisualStyle(gda_wholeNetwork);
+ }
+
+
+ private void checkVisualStyle(final VisualStyle style) {
+
+ // Collection<VisualMappingFunction<?, ?>>
mappings = style.getAllVisualMappingFunctions();
+ // assertEquals(4, mappings.size());
+
+ // Test defaults
+ NodeShape defaultShape =
style.getDefaultValue(BasicVisualLexicon.NODE_SHAPE);
+ Paint nodeColor =
style.getDefaultValue(BasicVisualLexicon.NODE_FILL_COLOR);
+ Integer fontSize =
style.getDefaultValue(BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
+ Integer transparency =
style.getDefaultValue(BasicVisualLexicon.NODE_TRANSPARENCY);
+ Double w = style.getDefaultValue(BasicVisualLexicon.NODE_WIDTH);
+ Double h =
style.getDefaultValue(BasicVisualLexicon.NODE_HEIGHT);
+
+ Paint edgeLabelColor =
style.getDefaultValue(BasicVisualLexicon.EDGE_LABEL_COLOR);
+
+ assertEquals(NodeShapeVisualProperty.RECTANGLE, defaultShape);
+ assertEquals(Color.WHITE, nodeColor);
+ assertEquals(Integer.valueOf(12), fontSize);
+ assertEquals(Integer.valueOf(255), transparency);
+ assertEquals(Double.valueOf(70), w);
+ assertEquals(Double.valueOf(30), h);
+
+ // Check each mapping
+ VisualMappingFunction<?, String> nodeLabelMapping = style
+
.getVisualMappingFunction(BasicVisualLexicon.NODE_LABEL);
+ VisualMappingFunction<?, String> edgeLabelMapping = style
+
.getVisualMappingFunction(BasicVisualLexicon.EDGE_LABEL);
+
+ assertTrue(nodeLabelMapping instanceof PassthroughMapping);
+
+ assertEquals("Name", nodeLabelMapping.getMappingColumnName());
+ assertEquals(String.class,
nodeLabelMapping.getMappingColumnType());
+
+ // Node Color mapping
+ VisualMappingFunction<?, Paint> nodeColorMapping = style
+
.getVisualMappingFunction(BasicVisualLexicon.NODE_FILL_COLOR);
+ assertTrue(nodeColorMapping instanceof DiscreteMapping);
+ assertEquals("NodeType",
nodeColorMapping.getMappingColumnName());
+ assertEquals(String.class,
nodeColorMapping.getMappingColumnType());
+
+ VisualMappingFunction<?, ?> edgeWidthMapping = style
+
.getVisualMappingFunction(BasicVisualLexicon.EDGE_WIDTH);
+ assertTrue(edgeWidthMapping instanceof ContinuousMapping);
+ assertEquals("AsssociationCount",
edgeWidthMapping.getMappingColumnName());
+ }
+
+ private void checkAttributes(final CyNetwork network){
+
+ CyTable nodeTable = network.getDefaultNodeTable();
+
+ // check attribute name
+
assertTrue(CyTableUtil.getColumnNames(nodeTable).contains("NodeType"));
+
assertTrue(CyTableUtil.getColumnNames(nodeTable).contains("OMIM_ID"));
+
+ // check attribute values
+ Object[] rows1 = nodeTable.getMatchingRows("Name",
"Obesity").toArray();
+ CyRow row1 = (CyRow)rows1[0];
+ assertEquals("Disease",row1.get("NodeType", String.class));
+ assertEquals(null,row1.get("OMIM_ID", String.class));
+
+ Object[] rows2 = nodeTable.getMatchingRows("Name",
"ACE").toArray();
+ CyRow row2 = (CyRow)rows2[0];
+ assertEquals("Gene",row2.get("NodeType", String.class));
+ assertEquals(106180,row2.get("OMIM_ID",
Integer.class).intValue());
+ }
+
+
+ private void checkNetwork(final CyNetwork network) {
+ assertEquals(4133, network.getNodeCount());
+ assertEquals(14558, network.getEdgeCount());
+
+ // Selection state
+ Collection<CyRow> selectedNodes =
network.getDefaultNodeTable().getMatchingRows(CyNetwork.SELECTED, true);
+ Collection<CyRow> selectedEdges =
network.getDefaultEdgeTable().getMatchingRows(CyNetwork.SELECTED, true);
+ assertEquals(0, selectedNodes.size());
+ assertEquals(0, selectedEdges.size());
+ }
+}
Added:
core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/session2x/v263SessionLarge.cys
===================================================================
(Binary files differ)
Property changes on:
core3/impl/trunk/session-impl/integration-test/src/test/resources/testData/session2x/v263SessionLarge.cys
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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