Author: mes
Date: 2010-10-01 18:26:10 -0700 (Fri, 01 Oct 2010)
New Revision: 22136
Modified:
core3/session-api/trunk/src/main/java/org/cytoscape/session/CySession.java
core3/session-api/trunk/src/test/java/org/cytoscape/session/CySessionTest.java
Log:
added javadoc and unit tests
Modified:
core3/session-api/trunk/src/main/java/org/cytoscape/session/CySession.java
===================================================================
--- core3/session-api/trunk/src/main/java/org/cytoscape/session/CySession.java
2010-10-02 00:14:08 UTC (rev 22135)
+++ core3/session-api/trunk/src/main/java/org/cytoscape/session/CySession.java
2010-10-02 01:26:10 UTC (rev 22136)
@@ -43,7 +43,25 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-
+/**
+ * A session is an immutable snapshot of the data contents of Cytoscape.
+ * Sessions are only meant for saving and restoring the state of Cytoscape
+ * and are not meant to be used interactively for anything besides
+ * writing, reading, and restoring from session files.
+ * <br/>
+ * Using the data returned from the various methods in a CySession object
+ * should be sufficient to recreate all aspects of Cytoscape at the time
+ * the session was created.
+ * <br/>
+ * Creating an instance of CySession is done following the builder pattern.
+ * For example, the following code creates a session that only includes
+ * a list of networkViews and cytoscape properties, but nothing else.
+ * <br/>
+ * <pre>
+ * CySession session = new
CySession.Builder().networkViews(viewList).cytoscapeProperties(cyProps).build();
+ * </pre>
+ * <br/>
+ */
public final class CySession {
private final Set<CyNetworkView> netViews;
@@ -105,56 +123,130 @@
private Properties dProps;
private Map<String, List<File>> pluginFiles;
+ /**
+ * Returns a complete instance of CySession based upon the
methods
+ * called on this instance of Builder.
+ * @return A fully configured instanced of CySession.
+ */
public CySession build() { return new CySession(this); }
+ /**
+ * @param views A Set of CyNetworkView objects, presumably all
networks
+ * that exist in this instance of Cytoscape.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified network views.
+ */
public Builder networkViews(final Set<CyNetworkView> views) {
netViews = views;
return this;
}
+ /**
+ * @param t A Set of CyTable objects, presumably all tables
+ * that exist in this instance of Cytoscape.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified tables.
+ */
public Builder tables(final Set<CyTable> t) {
tables = t;
return this;
}
+ /**
+ * @param vs A map of CyNetworkViews to the names of the
VisualStyle
+ * currently applied to that network view, for presumably all
network views
+ * that exist in this instance of Cytoscape.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified network view visual style name map.
+ */
public Builder viewVisualStyleMap(final Map<CyNetworkView,String> vs)
{
vsMap = vs;
return this;
}
+ /**
+ * @param p A Properties object that contains the current
Cytoscape
+ * properties.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified properties.
+ */
public Builder cytoscapeProperties(final Properties p) {
cyProps = p;
return this;
}
+ /**
+ * @param p A Properties object that contains the current
VizMap
+ * properties for all VisualStyles in this instance of
Cytoscape.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified properties.
+ */
public Builder vizmapProperties(final Properties p) {
vProps = p;
return this;
}
+ /**
+ * @param p A Properties object that contains properties
defining
+ * the current state of the Desktop in Cytoscape.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified properties.
+ */
public Builder desktopProperties(final Properties p) {
dProps = p;
return this;
}
+ /**
+ * @param p A map of plugin names to a list of File objects
that the
+ * given plugin wants stored in the session file.
+ * @return An instance of Builder that has at least been
configured
+ * with the specified plugin file list map.
+ */
public Builder pluginFileListMap(final Map<String, List<File>>
p) {
this.pluginFiles = p;
return this;
}
}
+ /**
+ * @return A set of all CyNetworkView objects contained in this
Session.
+ */
public Set<CyNetworkView> getNetworkViews() { return netViews; }
+ /**
+ * @return A set of all CyTable objects contained in this Session.
+ */
public Set<CyTable> getTables() { return tables; }
+ /**
+ * @return A map of CyNetworkViews to the names of the VisualStyle
+ * applied to that network view in this session.
+ */
public Map<CyNetworkView,String> getViewVisualStyleMap() { return vsMap; }
+ /**
+ * @return A Propeties object containing all Cytoscape properties
+ * defined for this session.
+ */
public Properties getCytoscapeProperties() { return cyProps; }
+ /**
+ * @return A Propeties object containing all VisualStyles defined
+ * for this session.
+ */
public Properties getVizmapProperties() { return vProps; }
+ /**
+ * @return A Propeties object containing all desktop configuration
properties
+ * for this session.
+ */
public Properties getDesktopProperties() { return dProps; }
+ /**
+ * @return A map of plugin names to lists of File objects that are
stored
+ * as part of the session for the specified plugin.
+ */
public Map<String, List<File>> getPluginFileListMap() { return
pluginFiles; }
}
Modified:
core3/session-api/trunk/src/test/java/org/cytoscape/session/CySessionTest.java
===================================================================
---
core3/session-api/trunk/src/test/java/org/cytoscape/session/CySessionTest.java
2010-10-02 00:14:08 UTC (rev 22135)
+++
core3/session-api/trunk/src/test/java/org/cytoscape/session/CySessionTest.java
2010-10-02 01:26:10 UTC (rev 22136)
@@ -2,59 +2,242 @@
import static org.junit.Assert.*;
+import java.util.*;
+import java.io.File;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.model.CyTable;
import org.cytoscape.session.CySession;
import org.junit.Before;
import org.junit.Test;
+import static org.mockito.Mockito.*;
public class CySessionTest {
protected CySession session;
- @Before
- public void setUp() {
+
+ @Test
+ public void testDefaultGetNetworkViews() {
session = new CySession.Builder().build();
+ assertNotNull(session);
+ assertNotNull(session.getNetworkViews());
}
@Test
- public void testGetNetworkViews() {
+ public void testSetNullNetworkViews() {
+ session = new CySession.Builder().networkViews( null ).build();
assertNotNull(session);
assertNotNull(session.getNetworkViews());
+ assertEquals(0,session.getNetworkViews().size());
}
@Test
- public void testGetTables() {
+ public void testSetNetworkViews() {
+ CyNetworkView nv1 = mock(CyNetworkView.class);
+ CyNetworkView nv2 = mock(CyNetworkView.class);
+
+ Set<CyNetworkView> vs = new HashSet<CyNetworkView>();
+ vs.add( nv1 );
+ vs.add( nv2 );
+
+ session = new CySession.Builder().networkViews( vs ).build();
+
assertNotNull(session);
+ assertNotNull(session.getNetworkViews());
+ assertEquals(2,session.getNetworkViews().size());
+ assertTrue(session.getNetworkViews().contains( nv1 ));
+ assertTrue(session.getNetworkViews().contains( nv2 ));
+ }
+
+ @Test
+ public void testDefaultGetTables() {
+ session = new CySession.Builder().build();
+ assertNotNull(session);
assertNotNull(session.getTables());
}
+
+ @Test
+ public void testSetNullTables() {
+ session = new CySession.Builder().tables( null ).build();
+ assertNotNull(session);
+ assertNotNull(session.getTables());
+ assertEquals(0,session.getTables().size());
+ }
+
+ @Test
+ public void testSetTables() {
+ CyTable t1 = mock(CyTable.class);
+ CyTable t2 = mock(CyTable.class);
+
+ Set<CyTable> ts = new HashSet<CyTable>();
+ ts.add( t1 );
+ ts.add( t2 );
+
+ session = new CySession.Builder().tables( ts ).build();
+
+ assertNotNull(session);
+ assertNotNull(session.getTables());
+ assertEquals(2,session.getTables().size());
+ assertTrue(session.getTables().contains( t1 ));
+ assertTrue(session.getTables().contains( t2 ));
+ }
@Test
- public void testGetViewVisualStyleMap() {
+ public void testDefaultGetViewVisualStyleMap() {
+ session = new CySession.Builder().build();
assertNotNull(session);
assertNotNull(session.getViewVisualStyleMap());
}
+
+ @Test
+ public void testSetNullViewVisualStyleMap() {
+ session = new
CySession.Builder().viewVisualStyleMap(null).build();
+ assertNotNull(session);
+ assertNotNull(session.getViewVisualStyleMap());
+ assertEquals(0,session.getViewVisualStyleMap().size());
+ }
+
+ @Test
+ public void testSetViewVisualStyleMap() {
+ CyNetworkView nv1 = mock(CyNetworkView.class);
+ CyNetworkView nv2 = mock(CyNetworkView.class);
+
+ Map<CyNetworkView,String> vsm = new
HashMap<CyNetworkView,String>();
+ vsm.put(nv1,"vs1");
+ vsm.put(nv2,"vs2");
+
+ session = new
CySession.Builder().viewVisualStyleMap(vsm).build();
+ assertNotNull(session);
+ assertNotNull(session.getViewVisualStyleMap());
+ assertEquals(2,session.getViewVisualStyleMap().size());
+ assertTrue(session.getViewVisualStyleMap().containsKey(nv1));
+ assertTrue(session.getViewVisualStyleMap().containsKey(nv2));
+ assertEquals("vs1",session.getViewVisualStyleMap().get(nv1));
+ assertEquals("vs2",session.getViewVisualStyleMap().get(nv2));
+ }
@Test
- public void testGetCytoscapeProperties() {
+ public void testDefaultGetCytoscapeProperties() {
+ session = new CySession.Builder().build();
assertNotNull(session);
assertNotNull(session.getCytoscapeProperties());
}
@Test
- public void testGetVizmapProperties() {
+ public void testSetNullCytoscapeProperties() {
+ session = new
CySession.Builder().cytoscapeProperties(null).build();
assertNotNull(session);
+ assertNotNull(session.getCytoscapeProperties());
+ assertEquals(0,session.getCytoscapeProperties().size());
+ }
+
+ @Test
+ public void testSetCytoscapeProperties() {
+ session = new
CySession.Builder().cytoscapeProperties(getFakeProps()).build();
+ assertNotNull(session);
+ checkProps(session.getCytoscapeProperties());
+ }
+
+ @Test
+ public void testDefaultGetVizmapProperties() {
+ session = new CySession.Builder().build();
+ assertNotNull(session);
assertNotNull(session.getVizmapProperties());
}
@Test
- public void testGetDesktopProperties() {
+ public void testSetNullVizmapProperties() {
+ session = new
CySession.Builder().vizmapProperties(null).build();
assertNotNull(session);
+ assertNotNull(session.getVizmapProperties());
+ assertEquals(0,session.getVizmapProperties().size());
+ }
+
+ @Test
+ public void testSetVizmapProperties() {
+ session = new
CySession.Builder().vizmapProperties(getFakeProps()).build();
+ assertNotNull(session);
+ checkProps(session.getVizmapProperties());
+ }
+
+ @Test
+ public void testDefaultGetDesktopProperties() {
+ session = new CySession.Builder().build();
+ assertNotNull(session);
assertNotNull(session.getDesktopProperties());
}
@Test
- public void testGetPluginFileListMap() {
+ public void testSetNullDesktopProperties() {
+ session = new
CySession.Builder().desktopProperties(null).build();
assertNotNull(session);
+ assertNotNull(session.getDesktopProperties());
+ assertEquals(0,session.getDesktopProperties().size());
+ }
+
+ @Test
+ public void testSetDesktopProperties() {
+ session = new
CySession.Builder().desktopProperties(getFakeProps()).build();
+ assertNotNull(session);
+ checkProps(session.getDesktopProperties());
+ }
+
+ @Test
+ public void testDefaultGetPluginFileListMap() {
+ session = new CySession.Builder().build();
+ assertNotNull(session);
assertNotNull(session.getPluginFileListMap());
}
+
+ @Test
+ public void testSetNullPluginFileListMap() {
+ session = new
CySession.Builder().pluginFileListMap(null).build();
+ assertNotNull(session);
+ assertNotNull(session.getPluginFileListMap());
+ assertEquals(0,session.getPluginFileListMap().size());
+ }
+
+ @Test
+ public void testSetPluginFileListMap() {
+ File f1 = new File("f1");
+ File f2 = new File("f2");
+
+ List<File> l1 = new ArrayList<File>();
+ l1.add(f1);
+ l1.add(f2);
+
+ File f3 = new File("f3");
+ File f4 = new File("f4");
+
+ List<File> l2 = new ArrayList<File>();
+ l1.add(f3);
+ l1.add(f4);
+
+ Map<String,List<File>> pflm = new HashMap<String,List<File>>();
+ pflm.put("plugin1",l1);
+ pflm.put("plugin2",l2);
+
+ session = new
CySession.Builder().pluginFileListMap(pflm).build();
+ assertNotNull(session);
+ assertNotNull(session.getPluginFileListMap());
+ assertEquals(2,session.getPluginFileListMap().size());
+ assertEquals(l1,session.getPluginFileListMap().get("plugin1"));
+ assertEquals(l2,session.getPluginFileListMap().get("plugin2"));
+ }
+
+
+ private void checkProps(Properties p) {
+ assertNotNull(p);
+ assertEquals(2,p.size());
+ assertEquals("value1",p.getProperty("key1"));
+ assertEquals("value2",p.getProperty("key2"));
+ }
+
+ private Properties getFakeProps() {
+ Properties p = new Properties();
+ p.setProperty("key1","value1");
+ p.setProperty("key2","value2");
+ return p;
+ }
}
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