Author: mes
Date: 2012-03-13 14:41:05 -0700 (Tue, 13 Mar 2012)
New Revision: 28522
Added:
core3/impl/trunk/gui-cmdline-parser-impl/
core3/impl/trunk/gui-cmdline-parser-impl/pom.xml
core3/impl/trunk/gui-cmdline-parser-impl/src/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/Parser.java
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java
Modified:
core3/gui-distribution/trunk/features/src/main/resources/features.xml
core3/impl/trunk/welcome-impl/src/main/java/org/cytoscape/welcome/internal/WelcomeScreenAction.java
Log:
added a command line parser for the gui application
Modified: core3/gui-distribution/trunk/features/src/main/resources/features.xml
===================================================================
--- core3/gui-distribution/trunk/features/src/main/resources/features.xml
2012-03-13 20:57:09 UTC (rev 28521)
+++ core3/gui-distribution/trunk/features/src/main/resources/features.xml
2012-03-13 21:41:05 UTC (rev 28522)
@@ -11,7 +11,7 @@
<bundle
start-level="102">mvn:cytoscape-temp/l2fprod-common-sheet/7.3</bundle>
<bundle
start-level="103">mvn:com.lowagie.text/com.springsource.com.lowagie.text/2.0.8</bundle>
- <bundle
start-level="103">mvn:org.cytoscape.wrappers/org.swinglabs.swingx/1.6.1</bundle>
+ <bundle
start-level="103">mvn:cytoscape-temp/org.swinglabs.swingx/1.6.1</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/l2fprod-common-shared/7.3</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/l2fprod-common-fontchooser/7.3</bundle>
<bundle start-level="103">wrap:mvn:net.sf.opencsv/opencsv/2.1</bundle>
@@ -19,9 +19,9 @@
<bundle
start-level="103">mvn:org.apache.commons/com.springsource.org.apache.commons.collections/3.2.1</bundle>
<bundle start-level="103">mvn:cytoscape-temp/colt/1.2.0</bundle>
<bundle start-level="103">mvn:cytoscape-temp/prefuse/20071021</bundle>
- <bundle
start-level="103">mvn:org.cytoscape.wrappers/org.apache.lucene/3.0.2</bundle>
+ <bundle
start-level="103">mvn:cytoscape-temp/org.apache.lucene/3.0.2</bundle>
<bundle
start-level="103">mvn:org.jdom/com.springsource.org.jdom/1.1.0</bundle>
- <bundle
start-level="103">mvn:org.cytoscape.wrappers/org.swinglabs.swing-layout/1.0.3</bundle>
+ <bundle
start-level="103">mvn:cytoscape-temp/org.swinglabs.swing-layout/1.0.3</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/freehep-graphicsio/2.1.3</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/freehep-graphicsio-svg/2.1.3</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/freehep-graphics2d/2.1.3</bundle>
@@ -35,8 +35,6 @@
<bundle
start-level="103">mvn:org.dom4j/com.springsource.org.dom4j/1.6.1</bundle>
<bundle start-level="103">mvn:cytoscape-temp/violinstrings/1.0.2</bundle>
<bundle start-level="103">mvn:cytoscape-temp/jsbml/0.8-b1</bundle>
-
-
<bundle start-level="103">mvn:cytoscape-temp/jigsaw/2.2.6</bundle>
<bundle start-level="103">mvn:cytoscape-temp/stax2-api/3.0.1</bundle>
<bundle start-level="103">mvn:cytoscape-temp/staxmate/2.0.0</bundle>
@@ -49,6 +47,7 @@
<bundle start-level="103">mvn:cytoscape-temp/paxtools-core/4.1.1</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/biopax-converter/4.1.1</bundle>
<bundle
start-level="103">mvn:com.googlecode.guava-osgi/guava-osgi/9.0.0</bundle>
+ <bundle
start-level="103">mvn:org.cytoscape/cy-commons-cli/${cytoscape.support.version}</bundle>
<bundle
start-level="103">mvn:org.apache.commons/com.springsource.org.apache.commons.io/1.4.0</bundle>
<bundle start-level="103">mvn:psidev.psi.tools/xxindex/0.11</bundle>
@@ -148,7 +147,8 @@
<bundle
start-level="180">mvn:org.cytoscape/scripting-impl/${cytoscape.impl.version}</bundle>
- <bundle
start-level="185">mvn:org.cytoscape/welcome-impl/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="185">mvn:org.cytoscape/gui-cmdline-parser-impl/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="190">mvn:org.cytoscape/welcome-impl/${cytoscape.impl.version}</bundle>
</feature>
</features>
Added: core3/impl/trunk/gui-cmdline-parser-impl/pom.xml
===================================================================
--- core3/impl/trunk/gui-cmdline-parser-impl/pom.xml
(rev 0)
+++ core3/impl/trunk/gui-cmdline-parser-impl/pom.xml 2012-03-13 21:41:05 UTC
(rev 28522)
@@ -0,0 +1,116 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+
+ <parent>
+ <artifactId>impl-parent</artifactId>
+ <groupId>org.cytoscape</groupId>
+ <version>3.0.0-alpha8-SNAPSHOT</version>
+ </parent>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.gui-cmdline-parser-impl</bundle.symbolicName>
+
<bundle.namespace>org.cytoscape.cmdline.gui.internal</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>gui-cmdline-parser-impl</artifactId>
+
+ <name>${bundle.symbolicName} [${bundle.namespace}]</name>
+
+ <packaging>bundle</packaging>
+
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-jar-plugin</artifactId>
+ <version>${maven-jar-plugin.version}</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>test-jar</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+
<version>${maven-surefire-plugin.version}</version>
+ <configuration>
+
<redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+
<version>${maven-bundle-plugin.version}</version>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+
<Export-Package>!${bundle.namespace}.*</Export-Package>
+
<Private-Package>${bundle.namespace}.*</Private-Package>
+
<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ <enabled>true</enabled>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+ <dependencies>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>property-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>application-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>service-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>io-api</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>cy-commons-cli</artifactId>
+ <version>${cytoscape.support.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>cmdline</artifactId>
+ <version>${cytoscape.support.version}</version>
+ </dependency>
+ </dependencies>
+
+</project>
Added:
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java
(rev 0)
+++
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/CyActivator.java
2012-03-13 21:41:05 UTC (rev 28522)
@@ -0,0 +1,32 @@
+package org.cytoscape.cmdline.gui.internal;
+
+import org.cytoscape.cmdline.CommandLineArgs;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.application.CyVersion;
+import org.cytoscape.application.CyShutdown;
+import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.service.util.AbstractCyActivator;
+import java.util.Properties;
+
+import org.osgi.framework.BundleContext;
+
+public class CyActivator extends AbstractCyActivator {
+ public CyActivator() {
+ super();
+ }
+
+ public void start(BundleContext bc) {
+ CommandLineArgs args = getService(bc,CommandLineArgs.class);
+ CyVersion cyVersion = getService(bc,CyVersion.class);
+ CyShutdown cyShutdown = getService(bc,CyShutdown.class);
+ StreamUtil streamUtil = getService(bc,StreamUtil.class);
+
+ CyProperty<Properties> props =
(CyProperty<Properties>)getService(bc, CyProperty.class,
"(cyPropertyName=cytoscape3.props)");
+
+ StartupConfig sc = new
StartupConfig(props.getProperties(),streamUtil);
+
+
+ Parser p = new Parser(args.getArgs(), cyShutdown, cyVersion,
sc,props.getProperties());
+ sc.start();
+ }
+}
Added:
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/Parser.java
===================================================================
---
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/Parser.java
(rev 0)
+++
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/Parser.java
2012-03-13 21:41:05 UTC (rev 28522)
@@ -0,0 +1,214 @@
+/*
+ File: Parser.java
+
+ Copyright (c) 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.cmdline.gui.internal;
+
+import org.cytoscape.application.CyShutdown;
+import org.cytoscape.application.CyVersion;
+
+import java.util.Properties;
+
+import java.awt.Dimension;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class Parser {
+ private static final Logger logger =
LoggerFactory.getLogger(Parser.class);
+
+ private final String[] args;
+ private final Options options;
+ private final CyShutdown shutdown;
+ private final CyVersion version;
+ private final StartupConfig startupConfig;
+ private final Properties props;
+
+ public Parser(String[] args, CyShutdown shutdown, CyVersion version,
StartupConfig startupConfig, Properties props) {
+ this.args = args;
+ this.shutdown = shutdown;
+ this.version = version;
+ this.startupConfig = startupConfig;
+ this.props = props;
+ options = initOptions();
+ parseCommandLine(args);
+ }
+
+ private Options initOptions() {
+ Options opt = new Options();
+
+ opt.addOption("h", "help", false, "Print this message.");
+ opt.addOption("v", "version", false, "Print the version
number.");
+
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("session")
+ .withDescription("Load a cytoscape session (.cys)
file.")
+
.withValueSeparator('\0').withArgName("file").hasArg() // only allow one
session!!!
+ .create("s"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("network")
+ .withDescription( "Load a network file (any
format).")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("N"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("edge-table")
+ .withDescription("Load an edge attributes table
file (any table format).")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("e"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("node-table")
+ .withDescription("Load a node attributes table
file (any table format).")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("n"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("global-table")
+ .withDescription("Load a global attributes table
file (any table format).")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("g"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("plugin")
+ .withDescription("Load a SIMPLIFIED plugin jar
file/URL.")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("p"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("bundle")
+ .withDescription("Load a BUNDLE plugin jar file
or URL.")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("b"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("props")
+ .withDescription(
+ "Load cytoscape properties file (Java properties
format) or individual property: -P name=value.")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("P"));
+
+ opt.addOption(OptionBuilder
+ .withLongOpt("vizmap")
+ .withDescription("Load vizmap properties file
(Cytoscape VizMap format).")
+
.withValueSeparator('\0').withArgName("file").hasArgs()
+ .create("V"));
+
+ return opt;
+ }
+
+ private void parseCommandLine(String[] args) {
+
+ // try to parse the cmd line
+ CommandLineParser parser = new PosixParser();
+ CommandLine line = null;
+
+ // first load the simple exit options
+ try {
+ line = parser.parse(options, args);
+ } catch (ParseException e) {
+ logger.error("Parsing command line failed: " +
e.getMessage());
+ printHelp();
+ props.setProperty("tempHideWelcomeScreen","true");
+ shutdown.exit(1);
+ return;
+ }
+
+ if (line.hasOption("h")) {
+ printHelp();
+ shutdown.exit(0);
+ props.setProperty("tempHideWelcomeScreen","true");
+ return;
+ }
+
+ if (line.hasOption("v")) {
+ logger.info("Cytoscape version: " +
version.getVersion());
+ System.out.println("Cytoscape version: " +
version.getVersion());
+ props.setProperty("tempHideWelcomeScreen","true");
+ shutdown.exit(0);
+ return;
+ }
+
+ // always load any properties specified
+ if (line.hasOption("P"))
+ startupConfig.setProperties(line.getOptionValues("P"));
+
+ // always load any plugins specified
+ if (line.hasOption("p"))
+
startupConfig.setSimplifiedPlugins(line.getOptionValues("p"));
+
+ // always load any bundle plugins specified
+ if (line.hasOption("b"))
+
startupConfig.setBundlePlugins(line.getOptionValues("b"));
+
+ // Either load the session ...
+ if (line.hasOption("s")) {
+ startupConfig.setSession(line.getOptionValue("s"));
+
+ // ... or all the rest.
+ } else {
+ if (line.hasOption("N"))
+
startupConfig.setNetworks(line.getOptionValues("N"));
+
+ if (line.hasOption("V"))
+
startupConfig.setVizMapProps(line.getOptionValues("V"));
+
+ if (line.hasOption("n"))
+
startupConfig.setNodeTables(line.getOptionValues("n"));
+
+ if (line.hasOption("e"))
+
startupConfig.setEdgeTables(line.getOptionValues("e"));
+
+ if (line.hasOption("g"))
+
startupConfig.setGlobalTables(line.getOptionValues("g"));
+ }
+ }
+
+ private void printHelp() {
+ HelpFormatter formatter = new HelpFormatter();
+ formatter.printHelp("cytoscape.{sh|bat} [OPTIONS]", options);
+ }
+}
Added:
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java
===================================================================
---
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java
(rev 0)
+++
core3/impl/trunk/gui-cmdline-parser-impl/src/main/java/org/cytoscape/cmdline/gui/internal/StartupConfig.java
2012-03-13 21:41:05 UTC (rev 28522)
@@ -0,0 +1,175 @@
+/*
+ File: StartupConfig.java
+
+ Copyright (c) 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.cmdline.gui.internal;
+
+import org.cytoscape.application.CyShutdown;
+import org.cytoscape.application.CyVersion;
+import org.cytoscape.io.util.StreamUtil;
+
+import java.util.Properties;
+
+import java.awt.Dimension;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class StartupConfig {
+ private static final Logger logger =
LoggerFactory.getLogger(StartupConfig.class);
+
+ private final Properties globalProps;
+ private final Properties localProps = new Properties();
+ private final StreamUtil streamUtil;
+ private boolean taskStart = false;
+
+ public StartupConfig(Properties globalProps, StreamUtil streamUtil) {
+ this.globalProps = globalProps;
+ this.streamUtil = streamUtil;
+ }
+
+ public void setProperties(String[] potentialProps) {
+ Properties argProps = new Properties();
+
+ Matcher propPattern =
Pattern.compile("^((\\w+\\.*)+)\\=(.+)$").matcher("");
+
+ for ( String potential : potentialProps ) {
+ propPattern.reset(potential);
+
+ // check to see if the string is a key value pair
+ if (propPattern.matches()) {
+ argProps.setProperty(propPattern.group(1),
propPattern.group(3));
+
+ // otherwise assume it's a file/url
+ } else {
+ try {
+ InputStream in = null;
+
+ try {
+ in =
streamUtil.getInputStream(potential);
+ if (in != null)
+ localProps.load(in);
+ else
+ logger.info("Couldn't load property: " +
potential);
+ } finally {
+ if (in != null) {
+ in.close();
+ }
+ }
+ } catch (IOException e) {
+ logger.warn("Couldn't load property '"+
potential + "' from file: "+e.getMessage(), e);
+ }
+ }
+ }
+
+ // Transfer argument properties into the full properties.
+ // We do this so that anything specified on the command line
+ // overrides anything specified in a file.
+ localProps.putAll(argProps);
+ }
+
+ public void setSimplifiedPlugins(String[] args){
+ taskStart = true;
+ }
+
+ public void setBundlePlugins(String[] args){
+ taskStart = true;
+ }
+
+ public void setSession(String args){
+ taskStart = true;
+ }
+
+ public void setNetworks(String[] args){
+ taskStart = true;
+ }
+
+ public void setVizMapProps(String[] args){
+ taskStart = true;
+ }
+
+ public void setNodeTables(String[] args){
+ taskStart = true;
+ }
+
+ public void setEdgeTables(String[] args){
+ taskStart = true;
+ }
+
+ public void setGlobalTables(String[] args){
+ taskStart = true;
+ }
+
+ public void start() {
+ // set the properties
+ // no need to do this in a task since it's so fast
+ globalProps.putAll(localProps);
+
+ // Only proceed if we've specified tasks for execution
+ // on the command line.
+ if ( !taskStart )
+ return;
+
+ // Since we've set command line args we presumably
+ // don't want to see the welcome screen, so we
+ // disable it here.
+ globalProps.setProperty("tempHideWelcomeScreen","true");
+
+ /*
+
+ taskIterator.append( pluginManager.loadSimplifiedPlugins() );
+ taskIterator.append( pluginManager.loadBundlePlugins() );
+
+ if ( sessionName != null ) {
+ taskIterator.append( sessionTaskFactory.loadSession(
sessionName ) );
+
+ } else {
+ for ( String network : networkNames )
+ taskIterator.append( loadNetwork.loadNetwork(
network ) );
+ for ( String nodeTable : nodeTables )
+ taskIterator.append( loadTable.loadTable(
nodeTable, CyNode.class ) );
+ for ( String edgeTable : edgeTables )
+ taskIterator.append( loadTable.loadTable(
edgeTable, CyEdge.class ) );
+ for ( String globalTable : globalTables )
+ taskIterator.append( loadTable.loadTable(
globalTable, null ) );
+ for ( String vizmap : vizmapProps )
+ taskIterator.append( vizmapLoader.loadVizmap(
vizmap ) );
+ }
+
+ taskManager.execute(taskIterator);
+ */
+ }
+}
Modified:
core3/impl/trunk/welcome-impl/src/main/java/org/cytoscape/welcome/internal/WelcomeScreenAction.java
===================================================================
---
core3/impl/trunk/welcome-impl/src/main/java/org/cytoscape/welcome/internal/WelcomeScreenAction.java
2012-03-13 20:57:09 UTC (rev 28521)
+++
core3/impl/trunk/welcome-impl/src/main/java/org/cytoscape/welcome/internal/WelcomeScreenAction.java
2012-03-13 21:41:05 UTC (rev 28522)
@@ -2,6 +2,7 @@
import java.awt.event.ActionEvent;
import java.util.Properties;
+import javax.swing.SwingUtilities;
import org.cytoscape.application.CyApplicationConfiguration;
import org.cytoscape.application.events.CyStartEvent;
@@ -21,7 +22,8 @@
private static final long serialVersionUID = 2584201062371825221L;
- public static final String DO_NOT_DISPLAY_PROP_NAME =
"hideWelcomScreen";
+ public static final String DO_NOT_DISPLAY_PROP_NAME =
"hideWelcomeScreen";
+ public static final String TEMP_DO_NOT_DISPLAY_PROP_NAME =
"tempHideWelcomeScreen";
private static final String MENU_NAME = "Show Welcome Screen...";
private static final String PARENT_NAME = "Help";
@@ -65,7 +67,11 @@
this.bc = bc;
// Show it if necessary
- startup();
+ SwingUtilities.invokeLater( new Runnable() {
+ public void run() {
+ startup();
+ }
+ });
}
@Override
@@ -79,20 +85,36 @@
}
public void startup() {
- // Simply displays the dialog after startup.
+
+ // Displays the dialog after startup based on whether
+ // the specified property has been set.
final String hideString =
this.cyProps.getProperties().getProperty(DO_NOT_DISPLAY_PROP_NAME);
+ hide = parseBoolean(hideString);
+
+ if (!hide) {
+ final String tempHideString =
this.cyProps.getProperties().getProperty(TEMP_DO_NOT_DISPLAY_PROP_NAME);
+ hide = parseBoolean(tempHideString);
+ }
+ // remove this property regardless!
+
this.cyProps.getProperties().remove(TEMP_DO_NOT_DISPLAY_PROP_NAME);
+
+ if(!hide)
+ actionPerformed(null);
+ }
+
+ private boolean parseBoolean(String hideString) {
+ boolean lhide = false;
if (hideString == null)
- hide = false;
+ lhide = false;
else {
try {
- hide = Boolean.parseBoolean(hideString);
+ // might make it true!
+ lhide = Boolean.parseBoolean(hideString);
} catch (Exception ex) {
- hide = false;
+ lhide = false;
}
}
-
- if(hide == false)
- actionPerformed(null);
+ return lhide;
}
}
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