Author: mes
Date: 2011-03-11 11:50:25 -0800 (Fri, 11 Mar 2011)
New Revision: 24410
Added:
core3/command-executor-impl/trunk/
core3/command-executor-impl/trunk/osgi.bnd
core3/command-executor-impl/trunk/pom.xml
core3/command-executor-impl/trunk/src/
core3/command-executor-impl/trunk/src/main/
core3/command-executor-impl/trunk/src/main/java/
core3/command-executor-impl/trunk/src/main/java/org/
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorImpl.java
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTask.java
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTaskFactory.java
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/Executor.java
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/NTFExecutor.java
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/TFExecutor.java
core3/command-executor-impl/trunk/src/main/resources/
core3/command-executor-impl/trunk/src/main/resources/META-INF/
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
initial creation
Added: core3/command-executor-impl/trunk/osgi.bnd
===================================================================
--- core3/command-executor-impl/trunk/osgi.bnd (rev 0)
+++ core3/command-executor-impl/trunk/osgi.bnd 2011-03-11 19:50:25 UTC (rev
24410)
@@ -0,0 +1,5 @@
+#-----------------------------------------------------------------
+# Use this file to add customized Bnd instructions for the bundle
+#-----------------------------------------------------------------
+
+Private-Package: ${bundle.namespace}.*
Added: core3/command-executor-impl/trunk/pom.xml
===================================================================
--- core3/command-executor-impl/trunk/pom.xml (rev 0)
+++ core3/command-executor-impl/trunk/pom.xml 2011-03-11 19:50:25 UTC (rev
24410)
@@ -0,0 +1,88 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
+ </parent>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.command-executor-impl</bundle.symbolicName>
+
<bundle.namespace>org.cytoscape.command.internal</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>command-executor-impl</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+
+ <name>Command Executor</name>
+
+ <packaging>bundle</packaging>
+
+ <scm>
+
<connection>scm:svn:http://chianti.ucsd.edu/svn/core3/command-executor-impl/trunk</connection>
+
<developerConnection>scm:svn:svn+ssh://grenache.ucsd.edu/cellar/common/svn/core3/command-executor-impl/trunk</developerConnection>
+
<url>http://chianti.ucsd.edu/svn/core3/command-executor-impl/trunk</url>
+ </scm>
+
+ <repositories>
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM
snapshots -->
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <!-- bootstrap for cytoscape dependencies, namely the parent POM
releases -->
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.ops4j</groupId>
+ <artifactId>maven-pax-plugin</artifactId>
+ <version>${maven-pax-plugin.version}</version>
+ <extensions>true</extensions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+
<version>${maven-bundle-plugin.version}</version>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+
+ </plugins>
+ </build>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>core-task-api</artifactId>
+ <version>3.0.0-alpha2</version>
+ </dependency>
+ </dependencies>
+
+</project>
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorImpl.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorImpl.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorImpl.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,70 @@
+package org.cytoscape.command.internal;
+
+
+import java.util.Properties;
+import java.util.Map;
+import java.util.HashMap;
+import java.util.List;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.task.NetworkTaskFactory;
+
+public class CommandExecutorImpl {
+
+ private final Map<String,Executor> commandExecutorMap = new
HashMap<String,Executor>();
+ private final static Logger logger =
LoggerFactory.getLogger(CommandExecutorImpl.class);
+
+ public void addTaskFactory(TaskFactory tf, Map props) {
+ String commandName = (String)props.get("commandName");
+ if ( commandName != null )
+ commandExecutorMap.put(commandName, new TFExecutor(tf));
+ }
+
+ public void removeTaskFactory(TaskFactory tf, Map props) {
+ String commandName = (String)props.get("commandName");
+ if ( commandName != null )
+ commandExecutorMap.remove(commandName);
+ }
+
+ public void addNetworkTaskFactory(NetworkTaskFactory tf, Map props) {
+ String commandName = (String)props.get("commandName");
+ if ( commandName != null )
+ commandExecutorMap.put(commandName, new
NTFExecutor(tf));
+ }
+
+ public void removeNetworkTaskFactory(NetworkTaskFactory tf, Map props) {
+ String commandName = (String)props.get("commandName");
+ if ( commandName != null )
+ commandExecutorMap.remove(commandName);
+ }
+
+ public void executeList(List<String> commandLines) {
+ try {
+ for ( String line : commandLines ) {
+ System.out.println("begin parsing line: '" +
line + "'");
+ for ( String command :
commandExecutorMap.keySet() ) {
+ System.out.println("testing command: '"
+ command + "'");
+ if ( line.length() < command.length() )
+ continue;
+ final String comm =
line.substring(0,command.length());
+ final String args =
line.substring(command.length(),line.length());
+ System.out.println("comm: '" + comm +
"'");
+ System.out.println("args: '" + args +
"'");
+ if ( comm.equals(command) ) {
+ System.out.println(" --
executing");
+ Executor e =
commandExecutorMap.get(command);
+ e.execute(args);
+ break;
+ } else {
+ System.out.println(" -- trying
next");
+ }
+ }
+ }
+ } catch (Exception e) {
+ logger.error("Command parsing error: ", e);
+ }
+ }
+}
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTask.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTask.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTask.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,90 @@
+
+/*
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ 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.command.internal;
+
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+
+
+import java.util.List;
+import java.util.ArrayList;
+
+
+public class CommandExecutorTask extends AbstractTask {
+
+ @Tunable(description="Select the command file:", params="input=true")
+ public File file;
+
+ private final CommandExecutorImpl cei;
+
+ public CommandExecutorTask(CommandExecutorImpl cei) {
+ super();
+ this.cei = cei;
+ }
+
+ public void run(TaskMonitor e) throws Exception {
+ if (file == null)
+ throw new NullPointerException("You must specify a non-null
command file to load!");
+
+ FileReader fin = null;
+ BufferedReader bin = null;
+
+ try {
+
+ fin = new FileReader(file);
+ bin = new BufferedReader(fin);
+ List<String> lines = new ArrayList<String>();
+ String s;
+
+ while ((s = bin.readLine()) != null)
+ lines.add( s.trim() );
+
+ cei.executeList(lines);
+
+ } finally {
+ if ( bin != null )
+ bin.close();
+ if ( fin != null )
+ fin.close();
+ }
+ }
+}
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTaskFactory.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTaskFactory.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/CommandExecutorTaskFactory.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,47 @@
+
+/*
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ 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.command.internal;
+
+
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskIterator;
+
+
+public class CommandExecutorTaskFactory implements TaskFactory {
+
+ private final CommandExecutorImpl cei;
+
+ public CommandExecutorTaskFactory(CommandExecutorImpl cei) {
+ this.cei = cei;
+ }
+
+ public TaskIterator getTaskIterator() {
+ return new TaskIterator(new CommandExecutorTask(cei));
+ }
+}
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/Executor.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/Executor.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/Executor.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,8 @@
+
+package org.cytoscape.command.internal;
+
+
+
+interface Executor {
+ void execute(String args);
+}
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/NTFExecutor.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/NTFExecutor.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/NTFExecutor.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,19 @@
+
+
+package org.cytoscape.command.internal;
+
+import org.cytoscape.task.NetworkTaskFactory;
+
+class NTFExecutor extends TFExecutor {
+ private final NetworkTaskFactory ntf;
+
+ public NTFExecutor(NetworkTaskFactory ntf) {
+ super(ntf);
+ this.ntf = ntf;
+ }
+
+ public void execute(String args) {
+ System.out.println("set current network!");
+ super.execute(args);
+ }
+}
Added:
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/TFExecutor.java
===================================================================
---
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/TFExecutor.java
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/java/org/cytoscape/command/internal/TFExecutor.java
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,16 @@
+
+package org.cytoscape.command.internal;
+
+import org.cytoscape.work.TaskFactory;
+
+class TFExecutor implements Executor {
+ private final TaskFactory tf;
+
+ public TFExecutor(TaskFactory tf) {
+ this.tf = tf;
+ }
+
+ public void execute(String args) {
+ System.out.println("executing: " + tf + " with args: '" +
args + "'");
+ }
+}
Added:
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+
+ <osgi:service id="commandExecutorTaskFactoryService"
ref="commandExecutorTaskFactory"
+ interface="org.cytoscape.work.TaskFactory">
+ <osgi:service-properties>
+ <entry key="title" value="Load Command File" />
+ <entry key="preferredMenu" value="Plugins" />
+ </osgi:service-properties>
+ </osgi:service>
+
+ <osgi:set id="taskFactorySet"
+ interface="org.cytoscape.work.TaskFactory"
+ cardinality="0..N" >
+ <osgi:listener bind-method="addTaskFactory"
+ unbind-method="removeTaskFactory"
+ ref="commandExecutorImpl" />
+ </osgi:set>
+
+ <osgi:set id="networkTaskFactorySet"
+ interface="org.cytoscape.task.NetworkTaskFactory"
+ cardinality="0..N" >
+ <osgi:listener bind-method="addNetworkTaskFactory"
+ unbind-method="removeNetworkTaskFactory"
+ ref="commandExecutorImpl" />
+ </osgi:set>
+
+</beans>
Added:
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
(rev 0)
+++
core3/command-executor-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-03-11 19:50:25 UTC (rev 24410)
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:context="http://www.springframework.org/schema/context";
+ xmlns:util="http://www.springframework.org/schema/util";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/aop
+ http://www.springframework.org/schema/aop/spring-aop-2.5.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-2.5.xsd
+ http://www.springframework.org/schema/util
+ http://www.springframework.org/schema/util/spring-util-2.5.xsd
+ http://www.springframework.org/schema/lang
+ http://www.springframework.org/schema/lang/spring-lang-2.5.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+ <!--
+ regular spring configuration file defining the beans for this
bundle.
+ We've kept the osgi definitions in a separate configuration
file so
+ that this file can easily be used for integration testing
outside of
+ an OSGi environment
+ -->
+
+ <context:annotation-config />
+
+ <bean id="commandExecutorImpl"
class="org.cytoscape.command.internal.CommandExecutorImpl">
+ </bean>
+
+ <bean id="commandExecutorTaskFactory"
+ class="org.cytoscape.command.internal.CommandExecutorTaskFactory">
+ <constructor-arg ref="commandExecutorImpl" />
+ </bean>
+</beans>
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