Author: Christian Lopes
Date: 2011-06-13 11:58:25 -0700 (Mon, 13 Jun 2011)
New Revision: 25732
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/exportvizmap/
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/exportvizmap/ExportVizmapTaskFactory.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/VizmapWriter.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
Modified:
core3/core-task-impl/trunk/pom.xml
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Created vizmap export/import tasks.
Modified: core3/core-task-impl/trunk/pom.xml
===================================================================
--- core3/core-task-impl/trunk/pom.xml 2011-06-13 18:34:46 UTC (rev 25731)
+++ core3/core-task-impl/trunk/pom.xml 2011-06-13 18:58:25 UTC (rev 25732)
@@ -4,7 +4,7 @@
<parent>
<artifactId>parent</artifactId>
<groupId>org.cytoscape</groupId>
- <version>3.0.0-alpha7</version>
+ <version>3.0.0-alpha8-SNAPSHOT</version>
</parent>
<properties>
@@ -15,7 +15,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.cytoscape</groupId>
<artifactId>core-task-impl</artifactId>
- <version>3.0.0-alpha3-SNAPSHOT</version>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
<name>${bundle.symbolicName}</name>
@@ -107,17 +107,17 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha5-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>io-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha5-SNAPSHOT</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
@@ -129,12 +129,12 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>vizmap-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>default-mappings</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/exportvizmap/ExportVizmapTaskFactory.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/exportvizmap/ExportVizmapTaskFactory.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/exportvizmap/ExportVizmapTaskFactory.java
2011-06-13 18:58:25 UTC (rev 25732)
@@ -0,0 +1,23 @@
+package org.cytoscape.task.internal.exportvizmap;
+
+import org.cytoscape.io.write.VizmapWriterManager;
+import org.cytoscape.task.internal.io.VizmapWriter;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+public class ExportVizmapTaskFactory implements TaskFactory {
+
+ private final VizmapWriterManager writerManager;
+ private final VisualMappingManager vmMgr;
+
+ public ExportVizmapTaskFactory(VizmapWriterManager writerManager,
VisualMappingManager vmMgr) {
+ this.writerManager = writerManager;
+ this.vmMgr = vmMgr;
+ }
+
+ @Override
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new VizmapWriter(writerManager, vmMgr));
+ }
+}
\ No newline at end of file
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/VizmapWriter.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/VizmapWriter.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/io/VizmapWriter.java
2011-06-13 18:58:25 UTC (rev 25732)
@@ -0,0 +1,28 @@
+package org.cytoscape.task.internal.io;
+
+import java.io.File;
+import java.util.Set;
+
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.io.write.CyWriter;
+import org.cytoscape.io.write.VizmapWriterManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
+
+public class VizmapWriter extends TunableAbstractCyWriter<VizmapWriterManager>
{
+
+ private final VisualMappingManager vmMgr;
+
+ public VizmapWriter(VizmapWriterManager writerManager,
VisualMappingManager vmMgr) {
+ super(writerManager);
+ if (vmMgr == null) throw new
NullPointerException("VisualMappingManager is null");
+ this.vmMgr = vmMgr;
+ }
+
+ @Override
+ protected CyWriter getWriter(CyFileFilter filter, File file) throws
Exception {
+ Set<VisualStyle> styles = vmMgr.getAllVisualStyles();
+
+ return writerManager.getWriter(styles, filter, file);
+ }
+}
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTask.java
2011-06-13 18:58:25 UTC (rev 25732)
@@ -0,0 +1,76 @@
+package org.cytoscape.task.internal.loadvizmap;
+
+import java.io.File;
+import java.util.Set;
+
+import org.cytoscape.io.read.VizmapReader;
+import org.cytoscape.io.read.VizmapReaderManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+public class LoadVizmapFileTask extends AbstractTask {
+
+ @Tunable(description = "Vizmap file", params =
"fileCategory=vizmap;input=true")
+ public File file;
+
+ private final VisualMappingManager vmMgr;
+ private final VizmapReaderManager vizmapReaderMgr;
+
+ public LoadVizmapFileTask(VizmapReaderManager vizmapReaderMgr,
VisualMappingManager vmMgr) {
+ this.vizmapReaderMgr = vizmapReaderMgr;
+ this.vmMgr = vmMgr;
+ }
+
+ @Override
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ if (file == null) throw new NullPointerException("No file
specified!");
+
+ VizmapReader reader = vizmapReaderMgr.getReader(file.toURI(),
file.getName());
+
+ if (reader == null) throw new NullPointerException("Failed to
find appropriate reader for file: " + file);
+
+ insertTasksAfterCurrentTask(reader, new
AddVisualStylesTask(reader, vmMgr));
+ }
+}
+
+class AddVisualStylesTask extends AbstractTask {
+
+ private final VizmapReader reader;
+ private final VisualMappingManager vmMgr;
+
+ public AddVisualStylesTask(VizmapReader reader, VisualMappingManager
vmMgr) {
+ this.reader = reader;
+ this.vmMgr = vmMgr;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setTitle("Loading visual styles...");
+ final Set<VisualStyle> styles = reader.getVisualStyles();
+
+ if (styles != null) {
+ int count = 1;
+ int total = styles.size();
+
+ for (VisualStyle vs : styles) {
+ if (cancelled) break;
+ taskMonitor.setStatusMessage(count + " of " +
total + ": " + vs.getTitle());
+ vmMgr.addVisualStyle(vs);
+ taskMonitor.setProgress(count / total);
+ count++;
+ }
+
+ if (cancelled) {
+ // remove recently added styles
+ for (VisualStyle vs : styles) {
+ vmMgr.removeVisualStyle(vs);
+ }
+
+ taskMonitor.setProgress(1.0);
+ }
+ }
+ }
+}
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/loadvizmap/LoadVizmapFileTaskFactoryImpl.java
2011-06-13 18:58:25 UTC (rev 25732)
@@ -0,0 +1,24 @@
+package org.cytoscape.task.internal.loadvizmap;
+
+import org.cytoscape.io.read.VizmapReaderManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+
+public class LoadVizmapFileTaskFactoryImpl implements TaskFactory {
+
+ private final VizmapReaderManager vizmapReaderMgr;
+ private final VisualMappingManager vmMgr;
+
+ public LoadVizmapFileTaskFactoryImpl(VizmapReaderManager
vizmapReaderMgr, VisualMappingManager vmMgr) {
+ this.vizmapReaderMgr = vizmapReaderMgr;
+ this.vmMgr = vmMgr;
+ }
+
+ @Override
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new LoadVizmapFileTask(vizmapReaderMgr,
vmMgr));
+ }
+
+}
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-06-13 18:34:46 UTC (rev 25731)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-06-13 18:58:25 UTC (rev 25732)
@@ -27,6 +27,9 @@
<osgi:reference id="cyDataTableReaderManagerServiceRef"
interface="org.cytoscape.io.read.CyTableReaderManager" />
+
+ <osgi:reference id="vizmapReaderManagerServiceRef"
+ interface="org.cytoscape.io.read.VizmapReaderManager" />
<osgi:reference id="visualMappingManagerServiceRef"
interface="org.cytoscape.view.vizmap.VisualMappingManager" />
@@ -43,6 +46,9 @@
<osgi:reference id="networkViewWriterManagerServiceRef"
interface="org.cytoscape.io.write.CyNetworkViewWriterManager" />
+
+ <osgi:reference id="vizmapWriterManagerServiceRef"
+ interface="org.cytoscape.io.write.VizmapWriterManager" />
<osgi:reference id="sessionWriterManagerServiceRef"
interface="org.cytoscape.io.write.CySessionWriterManager" />
@@ -98,6 +104,15 @@
<entry key="accelerator" value="cmd shift l" />
</osgi:service-properties>
</osgi:service>
+
+ <osgi:service id="loadVizmapFileTaskFactoryService"
ref="loadVizmapFileTaskFactory"
+ interface="org.cytoscape.work.TaskFactory">
+ <osgi:service-properties>
+ <entry key="title" value="Vizmap File..." />
+ <entry key="preferredMenu" value="File.Import" />
+ <entry key="menuGravity" value="3.0" />
+ </osgi:service-properties>
+ </osgi:service>
<osgi:service id="loadAttrsFileTaskFactoryService"
ref="loadAttrsFileTaskFactory"
interface="org.cytoscape.work.TaskFactory">
@@ -545,6 +560,16 @@
</osgi:service-properties>
</osgi:service>
+ <osgi:service id="exportVizmapTaskFactoryService"
ref="exportVizmapTaskFactory"
+ interface="org.cytoscape.work.TaskFactory">
+ <osgi:service-properties>
+ <entry key="title" value="File..." />
+ <entry key="preferredMenu" value="File.Export.Vizmap" />
+ <entry key="enableFor" value="vizmap" />
+ <entry key="menuGravity" value="1.1" />
+ </osgi:service-properties>
+ </osgi:service>
+
<!-- consider removing -->
<!-- useful for command line, but not otherwise <osgi:service
id="setCurrentNetworkTaskFactoryService"
ref="setCurrentNetworkTaskFactory"
interface="org.cytoscape.work.TaskFactory"/> -->
Modified:
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-06-13 18:34:46 UTC (rev 25731)
+++
core3/core-task-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-06-13 18:58:25 UTC (rev 25732)
@@ -35,6 +35,12 @@
<constructor-arg ref="cyTableManagerServiceRef" />
</bean>
+ <bean id="loadVizmapFileTaskFactory"
+
class="org.cytoscape.task.internal.loadvizmap.LoadVizmapFileTaskFactoryImpl">
+ <constructor-arg ref="vizmapReaderManagerServiceRef" />
+ <constructor-arg ref="visualMappingManagerServiceRef" />
+ </bean>
+
<bean id="loadNetworkFileTaskFactory"
class="org.cytoscape.task.internal.loadnetwork.LoadNetworkFileTaskFactoryImpl">
<constructor-arg ref="cyNetworkReaderManagerServiceRef" />
@@ -330,6 +336,12 @@
class="org.cytoscape.task.internal.table.DeleteTableTaskFactory">
<constructor-arg ref="cyTableManagerServiceRef" />
</bean>
+
+ <bean id="exportVizmapTaskFactory"
+
class="org.cytoscape.task.internal.exportvizmap.ExportVizmapTaskFactory">
+ <constructor-arg ref="vizmapWriterManagerServiceRef" />
+ <constructor-arg ref="visualMappingManagerServiceRef" />
+ </bean>
<!-- Quick Start and Wizards -->
<bean id="quickStartTaskFactory"
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