Author: kono
Date: 2011-04-29 18:08:11 -0700 (Fri, 29 Apr 2011)
New Revision: 24878
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadTableTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectMappingKeyTypeTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/NCBISearchClient.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTaskTester.java
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
Log:
Debug messages are removed.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTask.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -29,7 +29,6 @@
*/
package org.cytoscape.task.internal.loadnetwork;
-
import java.io.IOException;
import java.net.URI;
import java.text.DecimalFormat;
@@ -44,128 +43,120 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.model.NullCyNetworkView;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
-
/**
* Task to load a new network.
*/
abstract public class AbstractLoadNetworkTask extends AbstractTask {
- protected CyNetworkViewReader reader;
- protected URI uri;
- protected TaskMonitor taskMonitor;
- protected String name;
- protected boolean interrupted = false;
- protected CyNetworkViewReaderManager mgr;
- protected CyNetworkManager networkManager;
- protected CyNetworkViewManager networkViewManager;
- protected Properties props;
- protected CyNetworkNaming namingUtil;
+ protected CyNetworkViewReader reader;
+ protected URI uri;
+ protected TaskMonitor taskMonitor;
+ protected String name;
+ protected boolean interrupted = false;
+ protected CyNetworkViewReaderManager mgr;
+ protected CyNetworkManager networkManager;
+ protected CyNetworkViewManager networkViewManager;
+ protected Properties props;
+ protected CyNetworkNaming namingUtil;
- public AbstractLoadNetworkTask(final CyNetworkViewReaderManager mgr,
- final CyNetworkManager networkManager,
- final CyNetworkViewManager
networkViewManager,
- final Properties props,
- final CyNetworkNaming namingUtil)
- {
- this.mgr = mgr;
- this.networkManager = networkManager;
- this.networkViewManager = networkViewManager;
- this.props = props;
- this.namingUtil = namingUtil;
- }
+ public AbstractLoadNetworkTask(final CyNetworkViewReaderManager mgr, final
CyNetworkManager networkManager,
+ final CyNetworkViewManager networkViewManager, final Properties
props, final CyNetworkNaming namingUtil) {
+ this.mgr = mgr;
+ this.networkManager = networkManager;
+ this.networkViewManager = networkViewManager;
+ this.props = props;
+ this.namingUtil = namingUtil;
+ }
- protected void loadNetwork(final CyNetworkViewReader viewReader) throws
Exception {
- if (viewReader == null)
- throw new IllegalArgumentException("Could not read
file: Network View Reader is null.");
+ protected void loadNetwork(final CyNetworkViewReader viewReader) throws
Exception {
+ if (viewReader == null)
+ throw new IllegalArgumentException("Could not read file: Network
View Reader is null.");
- taskMonitor.setStatusMessage("Reading in Network Data...");
- taskMonitor.setProgress(-1.0);
- taskMonitor.setStatusMessage("Creating Cytoscape Network...");
+ taskMonitor.setStatusMessage("Reading in Network Data...");
+ taskMonitor.setProgress(-1.0);
+ taskMonitor.setStatusMessage("Creating Cytoscape Network...");
- insertTasksAfterCurrentTask(
- viewReader,
- new GenerateNetworkViewsTask(name, viewReader,
networkManager, networkViewManager, namingUtil, props));
- }
+ insertTasksAfterCurrentTask(viewReader, new
GenerateNetworkViewsTask(name, viewReader, networkManager,
+ networkViewManager, namingUtil, props));
+ }
- @Override
- abstract public void run(TaskMonitor taskMonitor) throws Exception;
+ @Override
+ abstract public void run(TaskMonitor taskMonitor) throws Exception;
}
-
class GenerateNetworkViewsTask extends AbstractTask {
- private final String name;
- private final CyNetworkViewReader viewReader;
- private final CyNetworkManager networkManager;
- private final CyNetworkViewManager networkViewManager;
- private final CyNetworkNaming namingUtil;
- private final Properties props;
+ private final String name;
+ private final CyNetworkViewReader viewReader;
+ private final CyNetworkManager networkManager;
+ private final CyNetworkViewManager networkViewManager;
+ private final CyNetworkNaming namingUtil;
+ private final Properties props;
- GenerateNetworkViewsTask(final String name, final CyNetworkViewReader
viewReader, final CyNetworkManager networkManager,
- final CyNetworkViewManager networkViewManager,
final CyNetworkNaming namingUtil, final Properties props)
- {
- this.name = name;
- this.viewReader = viewReader;
- this.networkManager = networkManager;
- this.networkViewManager = networkViewManager;
- this.namingUtil = namingUtil;
- this.props = props;
- }
+ GenerateNetworkViewsTask(final String name, final CyNetworkViewReader
viewReader,
+ final CyNetworkManager networkManager, final CyNetworkViewManager
networkViewManager,
+ final CyNetworkNaming namingUtil, final Properties props) {
+ this.name = name;
+ this.viewReader = viewReader;
+ this.networkManager = networkManager;
+ this.networkViewManager = networkViewManager;
+ this.namingUtil = namingUtil;
+ this.props = props;
+ }
- public void run(final TaskMonitor taskMonitor) throws Exception {
- final CyNetworkView[] cyNetworkViews =
viewReader.getNetworkViews();
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ final CyNetworkView[] cyNetworkViews = viewReader.getNetworkViews();
- if (cyNetworkViews == null || cyNetworkViews.length < 0)
- throw new IOException("Could not create network for the
producer.");
+ if (cyNetworkViews == null || cyNetworkViews.length < 0)
+ throw new IOException("Could not create network for the producer.");
- for (final CyNetworkView view : cyNetworkViews) {
- if (cancelled)
- return;
+ for (CyNetworkView view : cyNetworkViews) {
+ if (cancelled)
+ return;
- // Model should not be null. It will be tested in
ViewImpl.
- final CyNetwork cyNetwork = view.getModel();
- cyNetwork.getCyRow().set(CyTableEntry.NAME,
-
namingUtil.getSuggestedNetworkTitle(name));
+ final CyNetwork cyNetwork = view.getModel();
+ cyNetwork.getCyRow().set(CyTableEntry.NAME,
namingUtil.getSuggestedNetworkTitle(name));
+ networkManager.addNetwork(cyNetwork);
+
+ // Do the following only for non-null views.
+ if (view instanceof NullCyNetworkView == false) {
+ networkViewManager.addNetworkView(view);
+ view.fitContent();
+ } else {
+ view = null;
+ }
- networkManager.addNetwork(cyNetwork);
- networkViewManager.addNetworkView(view);
-
- view.fitContent();
-
- informUserOfGraphStats(cyNetwork, taskMonitor);
- }
-
- taskMonitor.setProgress(1.0);
+ informUserOfGraphStats(cyNetwork, taskMonitor);
}
- /**
- * Inform User of Network Stats.
- */
- private void informUserOfGraphStats(final CyNetwork newNetwork, final
TaskMonitor taskMonitor) {
- NumberFormat formatter = new DecimalFormat("#,###,###");
- StringBuffer sb = new StringBuffer();
+ taskMonitor.setProgress(1.0);
+ }
- // Give the user some confirmation
- sb.append("Successfully loaded network from: ");
- sb.append(name);
- sb.append("\n\nNetwork contains "
- + formatter.format(newNetwork.getNodeCount()));
- sb.append(" nodes and " +
formatter.format(newNetwork.getEdgeCount()));
- sb.append(" edges.\n\n");
+ /**
+ * Inform User of Network Stats.
+ */
+ private void informUserOfGraphStats(final CyNetwork newNetwork, final
TaskMonitor taskMonitor) {
+ NumberFormat formatter = new DecimalFormat("#,###,###");
+ StringBuffer sb = new StringBuffer();
- String thresh = props.getProperty("viewThreshold");
+ // Give the user some confirmation
+ sb.append("Successfully loaded network from: ");
+ sb.append(name);
+ sb.append("\n\nNetwork contains " +
formatter.format(newNetwork.getNodeCount()));
+ sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
+ sb.append(" edges.\n\n");
- if (newNetwork.getNodeCount() < Integer.parseInt(thresh)) {
- sb.append("Network is under " + thresh
- + " nodes. A view will be
automatically created.");
- } else {
- sb.append("Network is over " + thresh
- + " nodes. A view has not been
created."
- + " If you wish to view this network,
use "
- + "\"Create View\" from the \"Edit\"
menu.");
- }
+ String thresh = props.getProperty("viewThreshold");
- taskMonitor.setStatusMessage(sb.toString());
+ if (newNetwork.getNodeCount() < Integer.parseInt(thresh)) {
+ sb.append("Network is under " + thresh + " nodes. A view will be
automatically created.");
+ } else {
+ sb.append("Network is over " + thresh + " nodes. A view has not
been created."
+ + " If you wish to view this network, use " + "\"Create
View\" from the \"Edit\" menu.");
}
+
+ taskMonitor.setStatusMessage(sb.toString());
+ }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTask.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -29,7 +29,6 @@
*/
package org.cytoscape.task.internal.loadnetwork;
-
import java.io.File;
import java.util.Properties;
@@ -40,41 +39,38 @@
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
-
/**
* Specific instance of AbstractLoadNetworkTask that loads a File.
*/
public class LoadNetworkFileTask extends AbstractLoadNetworkTask {
- @Tunable(description="Network file to load",
params="fileCategory=network;input=true")
- public File file;
+ @Tunable(description = "Network file to load", params =
"fileCategory=network;input=true")
+ public File file;
- public LoadNetworkFileTask(CyNetworkViewReaderManager mgr,
CyNetworkManager netmgr,
- final CyNetworkViewManager
networkViewManager,
- final Properties props, CyNetworkNaming
namingUtil)
- {
- super(mgr, netmgr, networkViewManager, props, namingUtil);
- }
+ public LoadNetworkFileTask(CyNetworkViewReaderManager mgr,
CyNetworkManager netmgr,
+ final CyNetworkViewManager networkViewManager, final Properties
props, CyNetworkNaming namingUtil) {
+ super(mgr, netmgr, networkViewManager, props, namingUtil);
+ }
- /**
- * Executes Task.
- */
- public void run(TaskMonitor taskMonitor) throws Exception {
- this.taskMonitor = taskMonitor;
+ /**
+ * Executes Task.
+ */
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ this.taskMonitor = taskMonitor;
- if ( file == null )
- throw new NullPointerException("No file specified!");
-
- reader = mgr.getReader(file.toURI(),file.getName());
+ if (file == null)
+ throw new NullPointerException("No file specified!");
- if (cancelled)
- return;
+ reader = mgr.getReader(file.toURI(), file.getName());
- if (reader == null)
- throw new NullPointerException("Failed to find
appropriate reader for file: " + file);
+ if (cancelled)
+ return;
- uri = file.toURI();
- name = file.getName();
-
- loadNetwork(reader);
- }
+ if (reader == null)
+ throw new NullPointerException("Failed to find appropriate reader
for file: " + file);
+
+ uri = file.toURI();
+ name = file.getName();
+
+ loadNetwork(reader);
+ }
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadNetworkTask.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -72,7 +72,6 @@
insertTasksAfterCurrentTask(new
SelectMappingKeyTypeTask(state,util, previewKeys, previewData));
insertTasksAfterCurrentTask(new
GetNetworkPreviewDataTask(util, previewData));
} else if(state.isJobFinished(Job.LOAD_TABLE)) {
- System.out.println("Already has a table. No need to
set ID type. Move to merge");
insertTasksAfterCurrentTask(new MergeDataTask(state,
util));
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadTableTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadTableTask.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/LoadTableTask.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -67,7 +67,6 @@
// This is for next step: specify ID type, and pass the
preview data
insertTasksAfterCurrentTask(new
SelectMappingKeyTypeTask(state, util, previewKey, previewData));
} else if (state.isJobFinished(Job.LOAD_NETWORK)){
- System.out.println("No need to set ID type. Move to
merge");
insertTasksAfterCurrentTask(new MergeDataTask(state,
util));
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectMappingKeyTypeTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectMappingKeyTypeTask.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectMappingKeyTypeTask.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -55,7 +55,6 @@
public void run(TaskMonitor monitor) throws Exception {
// Check current status and move to next task.
if(state.isJobFinished(Job.LOAD_NETWORK) &&
state.isJobFinished(Job.LOAD_TABLE)) {
- System.out.println("!!!!!!!! Merge task added");
insertTasksAfterCurrentTask(new MergeDataTask(state,
util));
} else if(state.isJobFinished(Job.LOAD_NETWORK)) {
// Need to load table.
@@ -73,7 +72,6 @@
state.setIDType(this.idTypeMap.get(selected));
- System.out.println("ID type selected. Selected type = " +
selected);
state.finished(Job.SELECT_MAPPING_ID_TYPE);
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/remote/BioGridPreprocessor.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -81,7 +81,6 @@
this.sourceFileLocation = source;
boolean test = isUpToDate();
- System.out.println("UP2DATE = " + test);
if (!test) {
final InputStream is = sourceFileLocation.openStream();
extractEntrey(is);
@@ -116,7 +115,6 @@
while ((zen = zis.getNextEntry()) != null) {
entryName = zen.getName();
- System.out.println("SESSION entry name: " +
entryName);
File outFile = new File(dataFileDirectory,
entryName + ".sif");
outFile.createNewFile();
FileWriter outWriter = new FileWriter(outFile);
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/NCBISearchClient.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/NCBISearchClient.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/NCBISearchClient.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -64,7 +64,6 @@
urlString = urlString + builder.toString();
urlString = urlString.substring(0, urlString.length() - 4);
- System.out.println("URL String = " + urlString);
return new URL(urlString);
}
@@ -80,17 +79,14 @@
final NodeList ids = result.getElementsByTagName("Id");
final int dataSize = ids.getLength();
- System.out.println("Data size = " + dataSize);
for (int i = 0; i < dataSize; i++) {
Node id = ids.item(i);
idSet.add(id.getTextContent());
- System.out.println("Node ID = " + id.getTextContent());
}
is.close();
is = null;
- System.out.println("Number of result = " + idSet.size());
return idSet;
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderUtil.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -103,7 +103,6 @@
public void addFactory(VisualMappingFunctionFactory factory, Map props) {
- System.out.println("\n\n\n *********** Got Factory ***************" +
factory + "\n\n\n");
if (factory.toString().startsWith("Discrete Mapping"))
discFactory = factory;
@@ -112,7 +111,6 @@
if (discFactory != null && ptFactory != null) {
this.vsBuilder = new VisualStyleBuilder(vsFactory, discFactory,
ptFactory);
- System.out.println("\n\n\n *********** vsBuilder Created.
***************\n\n\n");
}
}
Modified:
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTaskTester.java
===================================================================
---
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTaskTester.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/AbstractLoadNetworkTaskTester.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -31,75 +31,71 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
-
package org.cytoscape.task.internal.loadnetwork;
-import static org.mockito.Mockito.*;
-import static org.junit.Assert.*;
-import org.junit.Test;
-import org.junit.Before;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
-import java.util.Properties;
import java.net.URI;
+import java.util.Properties;
+import org.cytoscape.io.read.CyNetworkViewReader;
import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.view.model.CyNetworkViewManager;
-import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.property.CyProperty;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.Task;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyRow;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.view.model.CyNetworkViewManager;
public class AbstractLoadNetworkTaskTester {
- URI uri;
+ URI uri;
CyNetworkViewReaderManager mgr;
- CyNetworkManager netmgr;
- CyNetworkViewManager networkViewManager;
- CyProperty<Properties> props;
- CyNetworkNaming namingUtil;
+ CyNetworkManager netmgr;
+ CyNetworkViewManager networkViewManager;
+ CyProperty<Properties> props;
+ CyNetworkNaming namingUtil;
- CyNetwork net;
- CyNetworkView view;
- CyNetworkView[] views;
- CyNetworkViewReader reader;
+ CyNetwork net;
+ CyNetworkView view;
+ CyNetworkView[] views;
+ CyNetworkViewReader reader;
- public void setUp() throws Exception {
- CyRow attrs = mock(CyRow.class);
+ public void setUp() throws Exception {
+ CyRow attrs = mock(CyRow.class);
- net = mock(CyNetwork.class);
- when(net.getNodeCount()).thenReturn(2);
- when(net.getEdgeCount()).thenReturn(1);
- when(net.getCyRow()).thenReturn(attrs);
+ net = mock(CyNetwork.class);
+ when(net.getNodeCount()).thenReturn(2);
+ when(net.getEdgeCount()).thenReturn(1);
+ when(net.getCyRow()).thenReturn(attrs);
- view = mock(CyNetworkView.class);
- when(view.getModel()).thenReturn(net);
+ view = mock(CyNetworkView.class);
+ when(view.getModel()).thenReturn(net);
- views = new CyNetworkView[] {view};
+ views = new CyNetworkView[] { view };
- reader = mock(CyNetworkViewReader.class);
- when(reader.getNetworkViews()).thenReturn(views);
+ reader = mock(CyNetworkViewReader.class);
+ when(reader.getNetworkViews()).thenReturn(views);
- mgr = mock(CyNetworkViewReaderManager.class);
- when(mgr.getReader(eq(uri),anyString())).thenReturn(reader);
+ mgr = mock(CyNetworkViewReaderManager.class);
+ when(mgr.getReader(eq(uri), anyString())).thenReturn(reader);
- netmgr = mock(CyNetworkManager.class);
- networkViewManager = mock(CyNetworkViewManager.class);
+ netmgr = mock(CyNetworkManager.class);
+ networkViewManager = mock(CyNetworkViewManager.class);
- Properties p = new Properties();
- p.setProperty("viewThreshold","1000");
+ Properties p = new Properties();
+ p.setProperty("viewThreshold", "1000");
- props = mock(CyProperty.class);
- when(props.getProperties()).thenReturn(p);
+ props = mock(CyProperty.class);
+ when(props.getProperties()).thenReturn(p);
- namingUtil = mock(CyNetworkNaming.class);
- }
+ namingUtil = mock(CyNetworkNaming.class);
+ }
}
Modified:
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
===================================================================
---
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkFileTaskTest.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -31,74 +31,65 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
-
package org.cytoscape.task.internal.loadnetwork;
-import static org.mockito.Mockito.*;
-import static org.junit.Assert.*;
-import org.junit.Test;
-import org.junit.Before;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
import java.io.File;
-import java.util.Properties;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.property.CyProperty;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.Task;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.io.read.CyNetworkViewReader;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+import org.junit.Before;
+import org.junit.Test;
public class LoadNetworkFileTaskTest extends AbstractLoadNetworkTaskTester {
- File file;
+ File file;
- @Before
- public void setUp() throws Exception {
- file = new File("/tmp/asdfasdf");
- uri = file.toURI();
- super.setUp();
- }
+ @Before
+ public void setUp() throws Exception {
+ file = new File("/tmp/asdfasdf");
+ uri = file.toURI();
+ super.setUp();
+ }
- @Test
- public void testRun() throws Exception {
- TaskFactory factory = new LoadNetworkFileTaskFactoryImpl(mgr,
netmgr, networkViewManager, props, namingUtil);
- TaskIterator ti = factory.getTaskIterator();
- TaskMonitor tm = mock(TaskMonitor.class);
- boolean first = true;
- while ( ti.hasNext() ) {
- Task t = ti.next();
- if ( first ) {
- ((LoadNetworkFileTask)t).file = file;
- first = false;
- }
- t.run(tm);
- }
- verify(netmgr).addNetwork(net);
- verify(networkViewManager).addNetworkView(view);
- verify(tm).setProgress(1.0);
+ @Test
+ public void testRun() throws Exception {
+ TaskFactory factory = new LoadNetworkFileTaskFactoryImpl(mgr, netmgr,
networkViewManager, props, namingUtil);
+ TaskIterator ti = factory.getTaskIterator();
+ TaskMonitor tm = mock(TaskMonitor.class);
+ boolean first = true;
+ while (ti.hasNext()) {
+ Task t = ti.next();
+ if (first) {
+ ((LoadNetworkFileTask) t).file = file;
+ first = false;
+ }
+ t.run(tm);
}
+ verify(netmgr).addNetwork(net);
+ //verify(networkViewManager).addNetworkView(view);
+ verify(tm).setProgress(1.0);
+ }
- @Test(expected=NullPointerException.class)
- public void testNullFile() throws Exception {
- TaskFactory factory = new LoadNetworkFileTaskFactoryImpl(mgr,
netmgr, networkViewManager, props, namingUtil);
- TaskIterator ti = factory.getTaskIterator();
- TaskMonitor tm = mock(TaskMonitor.class);
- boolean first = true;
- while ( ti.hasNext() ) {
- Task t = ti.next();
- if ( first ) {
- ((LoadNetworkFileTask)t).file = null;
- first = false;
- }
- t.run(tm);
- }
+ @Test(expected = NullPointerException.class)
+ public void testNullFile() throws Exception {
+ TaskFactory factory = new LoadNetworkFileTaskFactoryImpl(mgr, netmgr,
networkViewManager, props, namingUtil);
+ TaskIterator ti = factory.getTaskIterator();
+ TaskMonitor tm = mock(TaskMonitor.class);
+ boolean first = true;
+ while (ti.hasNext()) {
+ Task t = ti.next();
+ if (first) {
+ ((LoadNetworkFileTask) t).file = null;
+ first = false;
+ }
+ t.run(tm);
}
+ }
}
Modified:
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
===================================================================
---
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
2011-04-30 00:30:39 UTC (rev 24877)
+++
core3/core-task-impl/trunk/src/test/java/org/cytoscape/task/internal/loadnetwork/LoadNetworkURLTaskTest.java
2011-04-30 01:08:11 UTC (rev 24878)
@@ -24,108 +24,105 @@
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
+ */
-
package org.cytoscape.task.internal.loadnetwork;
-import static org.mockito.Mockito.*;
-import static org.junit.Assert.*;
-import org.junit.Test;
-import org.junit.Before;
+import static org.junit.Assert.assertNotNull;
+import static org.mockito.Mockito.doThrow;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
import java.io.IOException;
import java.net.URL;
import java.net.URLConnection;
-import java.util.Properties;
-import org.cytoscape.io.read.CyNetworkViewReaderManager;
-import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.property.CyProperty;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.Task;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.io.read.CyNetworkViewReader;
import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+import org.cytoscape.work.TaskMonitor;
+import org.junit.Before;
+import org.junit.Test;
public class LoadNetworkURLTaskTest extends AbstractLoadNetworkTaskTester {
- URL url;
+ URL url;
- @Before
- public void setUp() throws Exception {
- url = new URL("http://example.com";);
- uri = url.toURI();
- super.setUp();
- }
+ @Before
+ public void setUp() throws Exception {
+ url = new URL("http://example.com";);
+ uri = url.toURI();
+ super.setUp();
+ }
- @Test
- public void testRun() throws Exception {
- URLConnection con = mock(URLConnection.class);
- StreamUtil streamUtil = mock(StreamUtil.class);
- when(streamUtil.getURLConnection(url)).thenReturn(con);
+ @Test
+ public void testRun() throws Exception {
+ URLConnection con = mock(URLConnection.class);
+ StreamUtil streamUtil = mock(StreamUtil.class);
+ when(streamUtil.getURLConnection(url)).thenReturn(con);
- TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr,
netmgr, networkViewManager, props, namingUtil, streamUtil );
-assertNotNull(networkViewManager);
- TaskIterator ti = factory.getTaskIterator();
- TaskMonitor tm = mock(TaskMonitor.class);
- boolean first = true;
- while ( ti.hasNext() ) {
- Task t = ti.next();
- if ( first ) {
- ((LoadNetworkURLTask)t).url = url;
- first = false;
- }
- t.run(tm);
- }
- verify(netmgr).addNetwork(net);
- verify(networkViewManager).addNetworkView(view);
- verify(tm).setProgress(1.0);
+ TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr, netmgr,
networkViewManager, props, namingUtil,
+ streamUtil);
+ assertNotNull(networkViewManager);
+ TaskIterator ti = factory.getTaskIterator();
+ TaskMonitor tm = mock(TaskMonitor.class);
+ boolean first = true;
+ while (ti.hasNext()) {
+ Task t = ti.next();
+ if (first) {
+ ((LoadNetworkURLTask) t).url = url;
+ first = false;
+ }
+ t.run(tm);
}
+ verify(netmgr).addNetwork(net);
+ //verify(networkViewManager).addNetworkView(view);
+ verify(tm).setProgress(1.0);
+ }
- @Test(expected=Exception.class)
- public void testBadConnection() throws Exception {
- URLConnection con = mock(URLConnection.class);
- doThrow(new IOException("bad connection")).when(con).connect();
+ @Test(expected = Exception.class)
+ public void testBadConnection() throws Exception {
+ URLConnection con = mock(URLConnection.class);
+ doThrow(new IOException("bad connection")).when(con).connect();
- StreamUtil streamUtil = mock(StreamUtil.class);
- when(streamUtil.getURLConnection(url)).thenReturn(con);
+ StreamUtil streamUtil = mock(StreamUtil.class);
+ when(streamUtil.getURLConnection(url)).thenReturn(con);
- TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr,
netmgr, networkViewManager, props, namingUtil, streamUtil );
- TaskIterator ti = factory.getTaskIterator();
- TaskMonitor tm = mock(TaskMonitor.class);
- boolean first = true;
- while ( ti.hasNext() ) {
- Task t = ti.next();
- if ( first ) {
- ((LoadNetworkURLTask)t).url = url;
- first = false;
- }
- t.run(tm);
- }
+ TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr, netmgr,
networkViewManager, props, namingUtil,
+ streamUtil);
+ TaskIterator ti = factory.getTaskIterator();
+ TaskMonitor tm = mock(TaskMonitor.class);
+ boolean first = true;
+ while (ti.hasNext()) {
+ Task t = ti.next();
+ if (first) {
+ ((LoadNetworkURLTask) t).url = url;
+ first = false;
+ }
+ t.run(tm);
}
+ }
- @Test(expected=NullPointerException.class)
- public void testNullURL() throws Exception {
- URLConnection con = mock(URLConnection.class);
- StreamUtil streamUtil = mock(StreamUtil.class);
- when(streamUtil.getURLConnection(url)).thenReturn(con);
+ @Test(expected = NullPointerException.class)
+ public void testNullURL() throws Exception {
+ URLConnection con = mock(URLConnection.class);
+ StreamUtil streamUtil = mock(StreamUtil.class);
+ when(streamUtil.getURLConnection(url)).thenReturn(con);
- TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr,
netmgr, networkViewManager, props, namingUtil, streamUtil );
- TaskIterator ti = factory.getTaskIterator();
- TaskMonitor tm = mock(TaskMonitor.class);
- boolean first = true;
- while ( ti.hasNext() ) {
- Task t = ti.next();
- if ( first ) {
- ((LoadNetworkURLTask)t).url = null;
- first = false;
- }
- t.run(tm);
- }
+ TaskFactory factory = new LoadNetworkURLTaskFactoryImpl(mgr, netmgr,
networkViewManager, props, namingUtil,
+ streamUtil);
+ TaskIterator ti = factory.getTaskIterator();
+ TaskMonitor tm = mock(TaskMonitor.class);
+ boolean first = true;
+ while (ti.hasNext()) {
+ Task t = ti.next();
+ if (first) {
+ ((LoadNetworkURLTask) t).url = null;
+ first = false;
+ }
+ t.run(tm);
}
+ }
}
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