[16/50] [abbrv] incubator-taverna-commandline git commit: taverna-commandline-launcher/

[st...@apache.org]

taverna-commandline-launcher/


Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/a8e6b3ed
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/a8e6b3ed
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/a8e6b3ed

Branch: refs/heads/master
Commit: a8e6b3edeb4682e71de34024376c51756de55474
Parents: e8f020f
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Sun Dec 28 01:44:56 2014 -0600
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Sun Dec 28 01:44:56 2014 -0600

----------------------------------------------------------------------
 .gitignore                                      |  24 -
 .project                                        |  23 -
 .travis.yml                                     |   1 -
 README.md                                       |   3 -
 pom.xml                                         |  96 ----
 .../commandline/CommandLineOptionsImpl.java     | 445 -------------------
 .../taverna/commandline/TavernaCommandLine.java | 139 ------
 src/main/resources/help.txt                     |  87 ----
 .../TestCommandLineOptionsHandler.java          | 267 -----------
 taverna-commandline-launcher/pom.xml            |  96 ++++
 .../commandline/CommandLineOptionsImpl.java     | 445 +++++++++++++++++++
 .../taverna/commandline/TavernaCommandLine.java | 139 ++++++
 .../src/main/resources/help.txt                 |  87 ++++
 .../TestCommandLineOptionsHandler.java          | 267 +++++++++++
 14 files changed, 1034 insertions(+), 1085 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.gitignore
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diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ebe0e5b..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,24 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.project
----------------------------------------------------------------------
diff --git a/.project b/.project
deleted file mode 100644
index 86e9dca..0000000
--- a/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>taverna-command-line</name>
-	<comment></comment>
-	<projects>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.m2e.core.maven2Builder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.m2e.core.maven2Nature</nature>
-	</natures>
-</projectDescription>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/README.md
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diff --git a/README.md b/README.md
deleted file mode 100644
index 31ac549..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Taverna 3 command line
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/command-line/
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index ad8330e..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,96 +0,0 @@
-<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/xsd/maven-4.0.0.xsd">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<groupId>net.sf.taverna</groupId>
-		<artifactId>taverna-parent</artifactId>
-		<version>3.0.1-SNAPSHOT</version>
-	</parent>
-	<groupId>uk.org.taverna.commandline</groupId>
-	<artifactId>taverna-command-line</artifactId>
-	<version>0.1.2-SNAPSHOT</version>
-	<build>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-jar-plugin</artifactId>
-				<version>2.4</version>
-				<configuration>
-					<archive>
-						<manifest>
-							<addClasspath>true</addClasspath>
-							<mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
-							<classpathLayoutType>custom</classpathLayoutType>
-							<customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
-						</manifest>
-					</archive>
-				</configuration>
-			</plugin>
-		</plugins>
-	</build>
-	<dependencies>
-		<dependency>
-			<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
-			<artifactId>taverna-commandline-api</artifactId>
-			<version>${t2.taverna-commandline.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>uk.org.taverna.osgi</groupId>
-			<artifactId>osgi-launcher</artifactId>
-			<version>${osgi.launcher.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>uk.org.taverna.configuration</groupId>
-			<artifactId>taverna-app-configuration-impl</artifactId>
-			<version>${taverna.configuration.version}</version>
-		</dependency>
-
- 		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>com.springsource.org.apache.commons.cli</artifactId>
-			<version>${commons.cli.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>commons-io</groupId>
-                        <artifactId>commons-io</artifactId>
-                        <version>${commons.io.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.log4j</groupId>
-			<artifactId>com.springsource.org.apache.log4j</artifactId>
-			<version>${log4j.version}</version>
-		</dependency>
-		<dependency>
-			<groupId>org.eclipse</groupId>
-			<artifactId>org.eclipse.osgi</artifactId>
-			<version>${osgi.equinox.version}</version>
-		</dependency>
-
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>${junit.version}</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-	<repositories>
-		<repository>
-			<releases />
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-			<id>mygrid-repository</id>
-			<name>myGrid Repository</name>
-			<url>http://www.mygrid.org.uk/maven/repository</url>
-		</repository>
-		<repository>
-			<releases>
-				<enabled>false</enabled>
-			</releases>
-			<snapshots />
-			<id>mygrid-snapshot-repository</id>
-			<name>myGrid Snapshot Repository</name>
-			<url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
-		</repository>
-	</repositories>
-</project>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
----------------------------------------------------------------------
diff --git a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
deleted file mode 100644
index b702e03..0000000
--- a/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
+++ /dev/null
@@ -1,445 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program 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 (at your option) any later version.
- *
- *  This program 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.  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 program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.commandline;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.GnuParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-/**
- * Handles the processing of command line arguments for enacting a workflow.
- * This class encapsulates all command line options, and exposes them through higher-level
- * accessors. Upon creation it checks the validity of the command line options and raises an
- * {@link InvalidOptionException} if they are invalid.
- *
- * @author Stuart Owen
- * @author David Withers
- */
-public class CommandLineOptionsImpl implements CommandLineOptions {
-
-	private static final String OUTPUTDIR = "outputdir";
-	private static final String BUNDLE = "bundle";
-	private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
-	private Options options;
-	private CommandLine commandLine;
-
-	public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
-		this.options = intitialiseOptions();
-		this.commandLine = processArgs(args);
-		checkForInvalid();
-	}
-
-	@Override
-	public boolean askedForHelp() {
-		return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
-	}
-
-	@Override
-	public boolean isProvenanceEnabled() {
-		return hasOption("provenance");
-	}
-
-	protected void checkForInvalid() throws InvalidOptionException {
-		if (askedForHelp()) return;
-		if (isProvenanceEnabled()
-				&& !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
-			throw new InvalidOptionException(
-					"You should be running with a database to use provenance");
-		if (isProvenanceEnabled() && hasOption("inmemory"))
-			throw new InvalidOptionException(
-					"You should be running with a database to use provenance");
-		if ((hasOption("inputfile") || hasOption("inputvalue"))
-				&& hasOption("inputdoc"))
-			throw new InvalidOptionException(
-					"You can't provide both -input and -inputdoc arguments");
-
-		if (hasOption("inputdelimiter") && hasOption("inputdoc"))
-			throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
-
-		if (getArgs().length == 0
-				&& !(hasOption("help") || hasOption("startdb")))
-			throw new InvalidOptionException("You must specify a workflow");
-
-		if (hasOption("inmemory") && hasOption("embedded"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-		if (hasOption("inmemory") && hasOption("clientserver"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-		if (hasOption("embedded") && hasOption("clientserver"))
-			throw new InvalidOptionException(
-					"The options -embedded, -clientserver and -inmemory cannot be used together");
-	}
-
-	@Override
-	public void displayHelp() {
-		boolean full = false;
-		if (hasOption("help")) full=true;
-		displayHelp(full);
-	}
-
-	@Override
-	public void displayHelp(boolean showFullText) {
-
-		HelpFormatter formatter = new HelpFormatter();
-		try {
-			formatter
-					.printHelp("executeworkflow [options] [workflow]", options);
-			if (showFullText) {
-				InputStream helpStream = CommandLineOptionsImpl.class
-						.getClassLoader().getResourceAsStream("help.txt");
-				String helpText = IOUtils.toString(helpStream);
-				System.out.println(helpText);
-			}
-
-		} catch (IOException e) {
-			logger.error("Failed to load the help document", e);
-			System.out.println("Failed to load the help document");
-			//System.exit(-1);
-		}
-	}
-
-	@Override
-	public String[] getArgs() {
-		return commandLine.getArgs();
-	}
-
-	/**
-	 *
-	 * @return the port that the database should run on
-	 */
-	@Override
-	public String getDatabasePort() {
-		return getOptionValue("port");
-	}
-
-	/**
-	 *
-	 * @return a path to a properties file that contains database configuration
-	 *         settings
-	 */
-	@Override
-	public String getDatabaseProperties() {
-		return getOptionValue("dbproperties");
-	}
-
-	/**
-	 * Returns an array that alternates between a portname and path to a file
-	 * containing the input values. Therefore the array will always contain an
-	 * even number of elements
-	 *
-	 * @return an array of portname and path to files containing individual
-	 *         inputs.
-	 */
-	@Override
-	public String[] getInputFiles() {
-		if (hasInputFiles()) {
-			return getOptionValues("inputfile");
-		} else {
-			return new String[] {};
-		}
-	}
-
-	@Override
-	public String[] getInputValues() {
-		if (hasInputValues()) {
-			return getOptionValues("inputvalue");
-		} else {
-			return new String[] {};
-		}
-	}
-
-	@Override
-	public String getLogFile() {
-		return getOptionValue("logfile");
-	}
-
-	public Option [] getOptions() {
-		return commandLine.getOptions();
-	}
-
-	private String getOptionValue(String opt) {
-		return commandLine.getOptionValue(opt);
-	}
-
-	private String[] getOptionValues(String arg0) {
-		return commandLine.getOptionValues(arg0);
-	}
-
-	/**
-	 *
-	 * @return the directory to write the results to
-	 */
-	@Override
-	public String getOutputDirectory() {
-		return getOptionValue(OUTPUTDIR);
-	}
-
-	@Override
-	public boolean getStartDatabase() {
-		return hasOption("startdb");
-	}
-
-	/**
-	 * @return the directory with Credential Manager's files
-	 */
-	@Override
-	public String getCredentialManagerDir() {
-		return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
-	}
-
-	@Override
-	public boolean getStartDatabaseOnly() throws InvalidOptionException {
-		return (getStartDatabase() && (getWorkflow() == null));
-	}
-
-	@Override
-	public String getWorkflow() throws InvalidOptionException {
-		if (getArgs().length == 0) {
-			return null;
-		} else if (getArgs().length != 1) {
-			throw new InvalidOptionException(
-					"You should only specify one workflow file");
-		} else {
-			return getArgs()[0];
-		}
-	}
-
-	@Override
-	public boolean hasDelimiterFor(String inputName) {
-		boolean result = false;
-		if (hasOption("inputdelimiter")) {
-			String [] values = getOptionValues("inputdelimiter");
-			for (int i=0;i<values.length;i+=2) {
-				if (values[i].equals(inputName))
-				{
-					result=true;
-					break;
-				}
-			}
-		}
-		return result;
-	}
-
-	@Override
-	public boolean hasInputFiles() {
-		return hasOption("inputfile");
-	}
-
-	@Override
-	public boolean hasInputValues() {
-		return hasOption("inputvalue");
-	}
-
-	@Override
-	public boolean hasLogFile() {
-		return hasOption("logfile");
-	}
-
-	@Override
-	public boolean hasOption(String option) {
-		return commandLine.hasOption(option);
-	}
-
-	@Override
-	public String inputDelimiter(String inputName) {
-		String result = null;
-		if (hasOption("inputdelimiter")) {
-			String [] values = getOptionValues("inputdelimiter");
-			for (int i=0;i<values.length;i+=2) {
-				if (values[i].equals(inputName))
-				{
-					result=values[i+1];
-					break;
-				}
-			}
-		}
-		return result;
-	}
-
-	@SuppressWarnings("static-access")
-	private Options intitialiseOptions() {
-		Option helpOption = new Option("help", "Display comprehensive help information.");
-
-		Option outputOption = OptionBuilder
-				.withArgName("directory")
-				.hasArg()
-				.withDescription(
-						"Save outputs as files in directory, default "
-								+ "is to make a new directory workflowName_output.")
-				.create(OUTPUTDIR);
-
-		Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
-				.withDescription("Save outputs to a new Workflow Run Bundle (zip).")
-				.create(BUNDLE);
-
-		Option logFileOption = OptionBuilder
-				.withArgName("filename")
-				.hasArg()
-				.withDescription(
-						"The logfile to which more verbose logging will be written to.")
-				.create("logfile");
-
-		Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
-				.withDescription("Load inputs from a Baclava document.").create(
-						"inputdoc");
-
-		Option inputFileOption = OptionBuilder
-				.withArgName("inputname filename").hasArgs(2)
-				.withValueSeparator(' ').withDescription(
-						"Load the named input from file or URL.").create(
-						"inputfile");
-
-		Option inputValueOption = OptionBuilder.withArgName("inputname value")
-				.hasArgs(2).withValueSeparator(' ').withDescription(
-						"Directly use the value for the named input.").create(
-						"inputvalue");
-
-		Option inputDelimiterOption = OptionBuilder
-				.withArgName("inputname delimiter")
-				.hasArgs(2)
-				.withValueSeparator(' ')
-				.withDescription(
-						"Cause an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list.")
-				.create("inputdelimiter");
-
-		Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
-				.withDescription(
-						"Load a properties file to configure the database.")
-				.create("dbproperties");
-
-		Option port = OptionBuilder
-				.withArgName("portnumber")
-				.hasArg()
-				.withDescription(
-						"The port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
-				.create("port");
-
-		Option embedded = new Option("embedded",
-				"Connect to an embedded Derby database. This can prevent mulitple invocations.");
-		Option clientserver = new Option("clientserver",
-				"Connect as a client to a derby server instance.");
-		Option inMemOption = new Option(
-				"inmemory",
-				"Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
-		Option startDB = new Option("startdb",
-				"Automatically start an internal Derby database server.");
-		Option provenance = new Option("provenance",
-				"Generate provenance information and store it in the database.");
-
-
-		Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
-		hasArg().withDescription(
-				"Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
-		.create(CREDENTIAL_MANAGER_DIR_OPTION);
-		Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
-
-		Options options = new Options();
-		options.addOption(helpOption);
-		options.addOption(inputFileOption);
-		options.addOption(inputValueOption);
-		options.addOption(inputDelimiterOption);
-		options.addOption(inputdocOption);
-		options.addOption(outputOption);
-		options.addOption(bundleOption);
-		options.addOption(inMemOption);
-		options.addOption(embedded);
-		options.addOption(clientserver);
-		options.addOption(dbProperties);
-		options.addOption(port);
-		options.addOption(startDB);
-		options.addOption(provenance);
-		options.addOption(logFileOption);
-		options.addOption(credentialManagerDirectory);
-		options.addOption(credentialManagerPassword);
-
-		return options;
-	}
-
-	@Override
-	public boolean isClientServer() {
-		return hasOption("clientserver");
-	}
-
-	@Override
-	public boolean isEmbedded() {
-		return hasOption("embedded");
-	}
-
-	@Override
-	public boolean isInMemory() {
-		return hasOption("inmemory");
-	}
-
-	private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
-		CommandLineParser parser = new GnuParser();
-		CommandLine line = null;
-		try {
-			// parse the command line arguments
-			line = parser.parse(options, args);
-		} catch (ParseException exp) {
-			// oops, something went wrong
-//			System.err.println("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
-//			System.exit(1);
-			throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
-		}
-		return line;
-	}
-
-	/**
-	 * Save the results to a directory if -outputdir has been explicitly defined,
-	 * or if -outputdoc has not been defined.
-	 *
-	 * @return boolean
-	 */
-	@Override
-	public boolean saveResultsToDirectory() {
-		return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
-	}
-
-	@Override
-	public String saveResultsToBundle() {
-		if (! hasSaveResultsToBundle()) { 
-			return null;
-		}
-		return getOptionValue(BUNDLE);
-	}
-
-	@Override
-	public boolean hasSaveResultsToBundle() {
-		return hasOption(BUNDLE);
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
deleted file mode 100644
index a462ba3..0000000
--- a/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
+++ /dev/null
@@ -1,139 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2012 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program 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 (at your option) any later version.
- *
- *  This program 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.  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 program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.commandline;
-
-import java.io.File;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.osgi.framework.BundleContext;
-import org.osgi.framework.BundleException;
-
-import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
-import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
-import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
-import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
-import uk.org.taverna.osgi.OsgiLauncher;
-
-/**
- * Main entry point for starting the Taverna Command Line Tool.
- *
- * @author David Withers
- */
-public class TavernaCommandLine {
-
-	private static final String COMMANDLINE_BUNDLE_NAME = "net.sf.taverna.t2.taverna-commandline.common";
-
-	private static File commandlineBundle;
-
-	private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
-
-	private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
-
-	/**
-	 * Starts the Taverna Command Line Tool.
-	 *
-	 * @param args
-	 *            Taverna Command Line arguments
-	 */
-	public static void main(final String[] args) {
-		try {
-			CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
-			if (commandLineOptions.askedForHelp()) {
-				commandLineOptions.displayHelp();
-			} else {
-				log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
-				log4jConfiguration.prepareLog4J();
-				setDerbyPaths();
-				OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
-				setFrameworkConfiguration(osgilauncher);
-				osgilauncher.start();
-				BundleContext context = osgilauncher.getContext();
-				context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
-						commandLineOptions, null);
-				osgilauncher.startServices(true);
-				osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
-			}
-		} catch (ArgumentsParsingException e) {
-			System.out.println(e.getMessage());
-		} catch (InvalidOptionException e) {
-			System.out.println(e.getMessage());
-		} catch (BundleException e) {
-			System.out.println(e.getMessage());
-		}
-	}
-
-	/**
-	 * Sets the OSGi Framework configuration.
-	 *
-	 * @param osgilauncher
-	 */
-	private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
-		ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
-		List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
-				.getFrameworkConfiguration();
-		if (!frameworkConfigurations.isEmpty()) {
-			Map<String, String> configurationMap = new HashMap<String, String>();
-			for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
-				configurationMap.put(frameworkConfiguration.getName(),
-						frameworkConfiguration.getValue());
-			}
-			osgilauncher.setFrameworkConfiguration(configurationMap);
-		}
-	}
-
-	private static List<URI> getBundleURIs() {
-		List<URI> bundleURIs = new ArrayList<URI>();
-		ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
-		File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
-		if (applicationProfile != null) {
-			for (BundleInfo bundle : applicationProfile.getBundle()) {
-				File bundleFile = new File(libDir, bundle.getFileName());
-				if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
-					commandlineBundle = bundleFile;
-				} else {
-					bundleURIs.add(bundleFile.toURI());
-				}
-			}
-		}
-		return bundleURIs;
-	}
-
-	private static File getAppDirectory() {
-		return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
-	}
-
-	private static void setDerbyPaths() {
-		System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
-		File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
-		System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/main/resources/help.txt
----------------------------------------------------------------------
diff --git a/src/main/resources/help.txt b/src/main/resources/help.txt
deleted file mode 100644
index fb082cc..0000000
--- a/src/main/resources/help.txt
+++ /dev/null
@@ -1,87 +0,0 @@
-By default, the workflow is executed using the -inmemory option, and the
-results are written out to a directory named after the workflow name.
-
-If this directory already exists then a new directory is created, and
-appended with _<n>, where n is incremented to the next available index.
-
-Results are written out to files named after the output port for that result.
-If a result is composed of lists, then a directory is created for the output
-port and individual list items are named after the list element index (with 1
-being the first index). The the output is the result of an error, the filename
-is appended with '.error'.
-
-You can provide your own output directory with the -outputdir option. There
-will be an error if the directory already exists.
-
-You can also record your results to a Baclava document using -outputdoc
-option. The document will be overwritten if it already exists.
-
-Inputs can be provided in three ways. Both -inputfile and -inputvalue options
-can be used together; -inputdoc option must be used on its own. -inputfile and
--inputvalue options both take two additional arguments, the name of the port
-for the input, and either a file containing the input data, or the input value
-itself respectively.
-
-If one of more of your workflow inputs is a list, you can create a list
-input by using the -inputdelimiter option, which may be used with either
--inputfile or -inputvalue. This option takes two parameters - an input name
-and the delimiter by which to split the input into a list.
-
-The delimiter may be a simple character, such as a comma or a new-line
-character, or a regular expression. The input string, or file, will then be
-converted into a list being split by the delimiter specified. Make sure to 
-put the delimiter character in quotes as it may be interpreted by the shell 
-as a special character, e.g. ;.
-
-If a list of greater depth (i.e. a list or lists or deeper) is required then
-you will need to use the -inputdoc option.  However, if you provide an input
-of lower depth to that required, then it will automatically be wrapped in one
-or more lists up to the required depth. Providing an input of greater depth
-than that required will result in an error.
-
-If a workflow has a high memory requirement, then it may be better to run it
-using a database to store data rather than storing it in memory, which is the
-default option. There are three options for using a database:
-
--embedded option, runs with an embedded database. This is slightly faster than
-the -clientserver option (below), but has the limitation that only one
-executeworkflow script may be executed simultaneously.
-
--clientserver option allows the workflow to be executed backed by the database
-running as a server. By default a database is not started for you, but may be
-started using -startdb option.
-
--startdb option starts a database. It may be used without providing a workflow
-to allow a database to be started separately, allowing multiple simultaneous
-executeworkflow script runs.
-
-More advanced database configurations can be specified using -dbproperties
-option, allowing you to take full control over the database used. This takes a
-second argument, the filename of the properties file, for which the following
-example contains the default settings:
-
-in_memory = true
-provenance = false
-connector = derby
-port = 1527
-dialect = org.hibernate.dialect.DerbyDialect
-start_derby = false
-driver = org.apache.derby.jdbc.EmbeddedDriver
-jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
-
-Note that when using -dbproperties together with other options, the other
-options take precedence.
-
--cmdir option lets you specify an absolute path to a directory where 
-Credential Manager's files (keystore and truststore - containing user's 
-credentials and trusted certificates for accessing secure services) are stored.
-If not specified and the workflow requires access to these files, Taverna will 
-try to find them in the default location in <TAVERNA_HOME>/security somewhere 
-inside user's home directory (depending on the platform).
-
--cmpassword option can be used to tell Taverna to expect the password for the 
-Credential Manager on standard input. If the password is not piped in, Taverna 
-will prompt you for it in the terminal and block until it is entered. Do not 
-enter your password in the command line! If -cmpassword option is not specified 
-and -cmdir option is used, Taverna will try to find the password in a special 
-file password.txt in the directory specified with -cmdir option.

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
----------------------------------------------------------------------
diff --git a/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
deleted file mode 100644
index 3e1d0f4..0000000
--- a/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
+++ /dev/null
@@ -1,267 +0,0 @@
-package uk.org.taverna.commandline;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
-import net.sf.taverna.t2.commandline.options.CommandLineOptions;
-
-import org.junit.Test;
-
-public class TestCommandLineOptionsHandler {
-
-	@Test
-	public void testWorkflowName() throws Exception {
-		CommandLineOptions handler = new CommandLineOptionsImpl(
-				new String[] { "myworkflow.t2flow" });
-		assertEquals("myworkflow.t2flow", handler.getWorkflow());
-	}
-
-	@Test
-	public void shouldShowHelp() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(
-				new String[] { "-help" });
-		assertTrue(options.askedForHelp());
-		options = new CommandLineOptionsImpl(
-				new String[] {});
-		assertTrue(options.askedForHelp());
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.askedForHelp());
-	}
-
-	@Test
-	public void getWorkflow() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(
-				new String[] { "-help" });
-		assertNull(options.getWorkflow());
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertEquals("myworkflow.t2flow", options.getWorkflow());
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void cannotProvideInputFileAndInputDoc() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
-				"-inputdoc", "myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void cannotProvideInputValueAndInputDoc() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
-				"-inputdoc", "myworkflow.t2flow" });
-	}
-
-	@Test
-	public void canProvideInputValueAndFileTogether() throws Exception {
-		//should not be an error
-		new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
-				"-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
-	}
-
-	@Test
-	public void getInputs() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
-		assertEquals(2, options.getInputFiles().length);
-		assertEquals("fred", options.getInputFiles()[0]);
-		assertEquals("fred.txt", options.getInputFiles()[1]);
-
-		options = new CommandLineOptionsImpl(new String[] { "-inputfile", "fred",
-				"fred.txt", "-inputfile", "fred2", "fred2.txt",
-				"myworkflow.t2flow" });
-		assertEquals(4, options.getInputFiles().length);
-		assertEquals("fred", options.getInputFiles()[0]);
-		assertEquals("fred.txt", options.getInputFiles()[1]);
-		assertEquals("fred2", options.getInputFiles()[2]);
-		assertEquals("fred2.txt", options.getInputFiles()[3]);
-
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertNotNull(options.getInputFiles());
-		assertEquals(0, options.getInputFiles().length);
-
-	}
-
-	@Test
-	public void hasInputValue() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
-		assertTrue(options.hasInputValues());
-
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.hasInputValues());
-	}
-
-	@Test
-	public void getInputValues() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
-		assertEquals(2, options.getInputValues().length);
-
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertNotNull(options.getInputValues());
-		assertEquals(0,options.getInputValues().length);
-	}
-
-	@Test
-	public void hasInputs() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
-		assertTrue(options.hasInputFiles());
-
-		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
-		assertFalse(options.hasInputFiles());
-	}
-
-	@Test
-	public void noWorkflowNameButStartDB() throws Exception {
-		// should not throw an error
-		CommandLineOptions options = new CommandLineOptionsImpl(
-				new String[] { "-startdb" });
-		assertTrue(options.getStartDatabase());
-		assertTrue(options.getStartDatabaseOnly());
-	}
-
-	@Test
-	public void workflowNameAndStartDB() throws Exception {
-		// should not throw an error
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-startdb", "myworkflow.t2flow" });
-		assertTrue(options.getStartDatabase());
-		assertFalse(options.getStartDatabaseOnly());
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void provenanceButNoDatabase() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-provenance",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void provenanceButNoDatabase2() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test
-	public void provenanceDatabase() throws Exception {
-		// should be no errors
-		new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
-				"myworkflow.t2flow" });
-		new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
-				"myworkflow.t2flow" });
-		new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
-				"dbproperties.properties", "myworkflow.t2flow" });
-	}
-
-	@Test
-	public void testHasInputDelimiter() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
-		assertTrue(options.hasDelimiterFor("in1"));
-		assertTrue(options.hasDelimiterFor("in2"));
-		assertFalse(options.hasDelimiterFor("in3"));
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInputDelimiterInvalidWithInputDoc() throws Exception {
-		new CommandLineOptionsImpl(new String[] {
-				"-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
-	}
-
-
-	@Test
-	public void testInputDelimiter() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
-		assertEquals(",",options.inputDelimiter("in1"));
-		assertEquals("!",options.inputDelimiter("in2"));
-		assertNull(options.inputDelimiter("in3"));
-	}
-
-	@Test
-	public void testInMemory() throws Exception {
-		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
-				"-inmemory", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("inmemory"));
-	}
-
-	@Test
-	public void testEmbedded() throws Exception {
-		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
-				"-embedded", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("embedded"));
-	}
-
-	@Test
-	public void testClientServer() throws Exception {
-		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
-				"-clientserver", "myworkflow.t2flow" });
-		assertTrue(handler.hasOption("clientserver"));
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidEmbeddedAndClientServer() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidEmbeddedAndMemory() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	public void testInvalidClientServerAndInMemory() throws Exception {
-		new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
-				"myworkflow.t2flow" });
-	}
-
-	@Test
-	public void isInMemory() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-inmemory", "myworkflow.t2flow" });
-
-		assertTrue(options.isInMemory());
-		assertFalse(options.isClientServer());
-		assertFalse(options.isEmbedded());
-	}
-
-	@Test
-	public void isClientServer() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-clientserver", "myworkflow.t2flow" });
-
-		assertTrue(options.isClientServer());
-		assertFalse(options.isInMemory());
-		assertFalse(options.isEmbedded());
-	}
-
-	@Test
-	public void hasLogFile() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-logfile","/tmp/logging", "myworkflow.t2flow" });
-
-		assertTrue(options.hasLogFile());
-		assertEquals("/tmp/logging", options.getLogFile());
-	}
-
-	@Test(expected = InvalidOptionException.class)
-	@SuppressWarnings("unused")
-	public void hasLogFileNotValidWithoutWorkflow() throws Exception{
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-logfile","/tmp/logging"});
-	}
-
-	@Test
-	public void isEmbedded() throws Exception {
-		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
-				"-embedded", "myworkflow.t2flow" });
-
-		assertTrue(options.isEmbedded());
-		assertFalse(options.isInMemory());
-		assertFalse(options.isClientServer());
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/pom.xml b/taverna-commandline-launcher/pom.xml
new file mode 100644
index 0000000..ad8330e
--- /dev/null
+++ b/taverna-commandline-launcher/pom.xml
@@ -0,0 +1,96 @@
+<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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>net.sf.taverna</groupId>
+		<artifactId>taverna-parent</artifactId>
+		<version>3.0.1-SNAPSHOT</version>
+	</parent>
+	<groupId>uk.org.taverna.commandline</groupId>
+	<artifactId>taverna-command-line</artifactId>
+	<version>0.1.2-SNAPSHOT</version>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<version>2.4</version>
+				<configuration>
+					<archive>
+						<manifest>
+							<addClasspath>true</addClasspath>
+							<mainClass>uk.org.taverna.commandline.TavernaCommandLine</mainClass>
+							<classpathLayoutType>custom</classpathLayoutType>
+							<customClasspathLayout>../${artifact.groupId}/${artifact.artifactId}-${artifact.baseVersion}${dashClassifier?}.${artifact.extension}</customClasspathLayout>
+						</manifest>
+					</archive>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+	<dependencies>
+		<dependency>
+			<groupId>net.sf.taverna.t2.taverna-commandline</groupId>
+			<artifactId>taverna-commandline-api</artifactId>
+			<version>${t2.taverna-commandline.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>uk.org.taverna.osgi</groupId>
+			<artifactId>osgi-launcher</artifactId>
+			<version>${osgi.launcher.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>uk.org.taverna.configuration</groupId>
+			<artifactId>taverna-app-configuration-impl</artifactId>
+			<version>${taverna.configuration.version}</version>
+		</dependency>
+
+ 		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>com.springsource.org.apache.commons.cli</artifactId>
+			<version>${commons.cli.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+                        <artifactId>commons-io</artifactId>
+                        <version>${commons.io.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.log4j</groupId>
+			<artifactId>com.springsource.org.apache.log4j</artifactId>
+			<version>${log4j.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.eclipse</groupId>
+			<artifactId>org.eclipse.osgi</artifactId>
+			<version>${osgi.equinox.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit.version}</version>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+	<repositories>
+		<repository>
+			<releases />
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<id>mygrid-repository</id>
+			<name>myGrid Repository</name>
+			<url>http://www.mygrid.org.uk/maven/repository</url>
+		</repository>
+		<repository>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
+			<snapshots />
+			<id>mygrid-snapshot-repository</id>
+			<name>myGrid Snapshot Repository</name>
+			<url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+		</repository>
+	</repositories>
+</project>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
new file mode 100644
index 0000000..b702e03
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/CommandLineOptionsImpl.java
@@ -0,0 +1,445 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ *  Modifications to the initial code base are copyright of their
+ *  respective authors, or their employers as appropriate.
+ *
+ *  This program 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 (at your option) any later version.
+ *
+ *  This program 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.  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 program; if not, write to the Free Software
+ *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package uk.org.taverna.commandline;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.GnuParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.OptionBuilder;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * Handles the processing of command line arguments for enacting a workflow.
+ * This class encapsulates all command line options, and exposes them through higher-level
+ * accessors. Upon creation it checks the validity of the command line options and raises an
+ * {@link InvalidOptionException} if they are invalid.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class CommandLineOptionsImpl implements CommandLineOptions {
+
+	private static final String OUTPUTDIR = "outputdir";
+	private static final String BUNDLE = "bundle";
+	private static final Logger logger = Logger.getLogger(CommandLineOptionsImpl.class);
+	private Options options;
+	private CommandLine commandLine;
+
+	public CommandLineOptionsImpl(String[] args) throws ArgumentsParsingException, InvalidOptionException {
+		this.options = intitialiseOptions();
+		this.commandLine = processArgs(args);
+		checkForInvalid();
+	}
+
+	@Override
+	public boolean askedForHelp() {
+		return hasOption("help") || (getArgs().length==0 && getOptions().length==0);
+	}
+
+	@Override
+	public boolean isProvenanceEnabled() {
+		return hasOption("provenance");
+	}
+
+	protected void checkForInvalid() throws InvalidOptionException {
+		if (askedForHelp()) return;
+		if (isProvenanceEnabled()
+				&& !(hasOption("embedded") || hasOption("clientserver") || hasOption("dbproperties")))
+			throw new InvalidOptionException(
+					"You should be running with a database to use provenance");
+		if (isProvenanceEnabled() && hasOption("inmemory"))
+			throw new InvalidOptionException(
+					"You should be running with a database to use provenance");
+		if ((hasOption("inputfile") || hasOption("inputvalue"))
+				&& hasOption("inputdoc"))
+			throw new InvalidOptionException(
+					"You can't provide both -input and -inputdoc arguments");
+
+		if (hasOption("inputdelimiter") && hasOption("inputdoc"))
+			throw new InvalidOptionException("You cannot combine the -inputdelimiter and -inputdoc arguments");
+
+		if (getArgs().length == 0
+				&& !(hasOption("help") || hasOption("startdb")))
+			throw new InvalidOptionException("You must specify a workflow");
+
+		if (hasOption("inmemory") && hasOption("embedded"))
+			throw new InvalidOptionException(
+					"The options -embedded, -clientserver and -inmemory cannot be used together");
+		if (hasOption("inmemory") && hasOption("clientserver"))
+			throw new InvalidOptionException(
+					"The options -embedded, -clientserver and -inmemory cannot be used together");
+		if (hasOption("embedded") && hasOption("clientserver"))
+			throw new InvalidOptionException(
+					"The options -embedded, -clientserver and -inmemory cannot be used together");
+	}
+
+	@Override
+	public void displayHelp() {
+		boolean full = false;
+		if (hasOption("help")) full=true;
+		displayHelp(full);
+	}
+
+	@Override
+	public void displayHelp(boolean showFullText) {
+
+		HelpFormatter formatter = new HelpFormatter();
+		try {
+			formatter
+					.printHelp("executeworkflow [options] [workflow]", options);
+			if (showFullText) {
+				InputStream helpStream = CommandLineOptionsImpl.class
+						.getClassLoader().getResourceAsStream("help.txt");
+				String helpText = IOUtils.toString(helpStream);
+				System.out.println(helpText);
+			}
+
+		} catch (IOException e) {
+			logger.error("Failed to load the help document", e);
+			System.out.println("Failed to load the help document");
+			//System.exit(-1);
+		}
+	}
+
+	@Override
+	public String[] getArgs() {
+		return commandLine.getArgs();
+	}
+
+	/**
+	 *
+	 * @return the port that the database should run on
+	 */
+	@Override
+	public String getDatabasePort() {
+		return getOptionValue("port");
+	}
+
+	/**
+	 *
+	 * @return a path to a properties file that contains database configuration
+	 *         settings
+	 */
+	@Override
+	public String getDatabaseProperties() {
+		return getOptionValue("dbproperties");
+	}
+
+	/**
+	 * Returns an array that alternates between a portname and path to a file
+	 * containing the input values. Therefore the array will always contain an
+	 * even number of elements
+	 *
+	 * @return an array of portname and path to files containing individual
+	 *         inputs.
+	 */
+	@Override
+	public String[] getInputFiles() {
+		if (hasInputFiles()) {
+			return getOptionValues("inputfile");
+		} else {
+			return new String[] {};
+		}
+	}
+
+	@Override
+	public String[] getInputValues() {
+		if (hasInputValues()) {
+			return getOptionValues("inputvalue");
+		} else {
+			return new String[] {};
+		}
+	}
+
+	@Override
+	public String getLogFile() {
+		return getOptionValue("logfile");
+	}
+
+	public Option [] getOptions() {
+		return commandLine.getOptions();
+	}
+
+	private String getOptionValue(String opt) {
+		return commandLine.getOptionValue(opt);
+	}
+
+	private String[] getOptionValues(String arg0) {
+		return commandLine.getOptionValues(arg0);
+	}
+
+	/**
+	 *
+	 * @return the directory to write the results to
+	 */
+	@Override
+	public String getOutputDirectory() {
+		return getOptionValue(OUTPUTDIR);
+	}
+
+	@Override
+	public boolean getStartDatabase() {
+		return hasOption("startdb");
+	}
+
+	/**
+	 * @return the directory with Credential Manager's files
+	 */
+	@Override
+	public String getCredentialManagerDir() {
+		return getOptionValue(CREDENTIAL_MANAGER_DIR_OPTION);
+	}
+
+	@Override
+	public boolean getStartDatabaseOnly() throws InvalidOptionException {
+		return (getStartDatabase() && (getWorkflow() == null));
+	}
+
+	@Override
+	public String getWorkflow() throws InvalidOptionException {
+		if (getArgs().length == 0) {
+			return null;
+		} else if (getArgs().length != 1) {
+			throw new InvalidOptionException(
+					"You should only specify one workflow file");
+		} else {
+			return getArgs()[0];
+		}
+	}
+
+	@Override
+	public boolean hasDelimiterFor(String inputName) {
+		boolean result = false;
+		if (hasOption("inputdelimiter")) {
+			String [] values = getOptionValues("inputdelimiter");
+			for (int i=0;i<values.length;i+=2) {
+				if (values[i].equals(inputName))
+				{
+					result=true;
+					break;
+				}
+			}
+		}
+		return result;
+	}
+
+	@Override
+	public boolean hasInputFiles() {
+		return hasOption("inputfile");
+	}
+
+	@Override
+	public boolean hasInputValues() {
+		return hasOption("inputvalue");
+	}
+
+	@Override
+	public boolean hasLogFile() {
+		return hasOption("logfile");
+	}
+
+	@Override
+	public boolean hasOption(String option) {
+		return commandLine.hasOption(option);
+	}
+
+	@Override
+	public String inputDelimiter(String inputName) {
+		String result = null;
+		if (hasOption("inputdelimiter")) {
+			String [] values = getOptionValues("inputdelimiter");
+			for (int i=0;i<values.length;i+=2) {
+				if (values[i].equals(inputName))
+				{
+					result=values[i+1];
+					break;
+				}
+			}
+		}
+		return result;
+	}
+
+	@SuppressWarnings("static-access")
+	private Options intitialiseOptions() {
+		Option helpOption = new Option("help", "Display comprehensive help information.");
+
+		Option outputOption = OptionBuilder
+				.withArgName("directory")
+				.hasArg()
+				.withDescription(
+						"Save outputs as files in directory, default "
+								+ "is to make a new directory workflowName_output.")
+				.create(OUTPUTDIR);
+
+		Option bundleOption = OptionBuilder.withArgName(BUNDLE).hasArg()
+				.withDescription("Save outputs to a new Workflow Run Bundle (zip).")
+				.create(BUNDLE);
+
+		Option logFileOption = OptionBuilder
+				.withArgName("filename")
+				.hasArg()
+				.withDescription(
+						"The logfile to which more verbose logging will be written to.")
+				.create("logfile");
+
+		Option inputdocOption = OptionBuilder.withArgName("document").hasArg()
+				.withDescription("Load inputs from a Baclava document.").create(
+						"inputdoc");
+
+		Option inputFileOption = OptionBuilder
+				.withArgName("inputname filename").hasArgs(2)
+				.withValueSeparator(' ').withDescription(
+						"Load the named input from file or URL.").create(
+						"inputfile");
+
+		Option inputValueOption = OptionBuilder.withArgName("inputname value")
+				.hasArgs(2).withValueSeparator(' ').withDescription(
+						"Directly use the value for the named input.").create(
+						"inputvalue");
+
+		Option inputDelimiterOption = OptionBuilder
+				.withArgName("inputname delimiter")
+				.hasArgs(2)
+				.withValueSeparator(' ')
+				.withDescription(
+						"Cause an inputvalue or inputfile to be split into a list according to the delimiter. The associated workflow input must be expected to receive a list.")
+				.create("inputdelimiter");
+
+		Option dbProperties = OptionBuilder.withArgName("filename").hasArg()
+				.withDescription(
+						"Load a properties file to configure the database.")
+				.create("dbproperties");
+
+		Option port = OptionBuilder
+				.withArgName("portnumber")
+				.hasArg()
+				.withDescription(
+						"The port that the database is running on. If set requested to start its own internal server, this is the start port that will be used.")
+				.create("port");
+
+		Option embedded = new Option("embedded",
+				"Connect to an embedded Derby database. This can prevent mulitple invocations.");
+		Option clientserver = new Option("clientserver",
+				"Connect as a client to a derby server instance.");
+		Option inMemOption = new Option(
+				"inmemory",
+				"Run the workflow with data stored in-memory rather than in a database (this is the default option). This can give performance inprovements, at the cost of overall memory usage.");
+		Option startDB = new Option("startdb",
+				"Automatically start an internal Derby database server.");
+		Option provenance = new Option("provenance",
+				"Generate provenance information and store it in the database.");
+
+
+		Option credentialManagerDirectory = OptionBuilder.withArgName("directory path").
+		hasArg().withDescription(
+				"Absolute path to a directory where Credential Manager's files (keystore and truststore) are located.")
+		.create(CREDENTIAL_MANAGER_DIR_OPTION);
+		Option credentialManagerPassword = new Option(CREDENTIAL_MANAGER_PASSWORD_OPTION, "Indicate that the master password for Credential Manager will be provided on standard input."); // optional password option, to be read from standard input
+
+		Options options = new Options();
+		options.addOption(helpOption);
+		options.addOption(inputFileOption);
+		options.addOption(inputValueOption);
+		options.addOption(inputDelimiterOption);
+		options.addOption(inputdocOption);
+		options.addOption(outputOption);
+		options.addOption(bundleOption);
+		options.addOption(inMemOption);
+		options.addOption(embedded);
+		options.addOption(clientserver);
+		options.addOption(dbProperties);
+		options.addOption(port);
+		options.addOption(startDB);
+		options.addOption(provenance);
+		options.addOption(logFileOption);
+		options.addOption(credentialManagerDirectory);
+		options.addOption(credentialManagerPassword);
+
+		return options;
+	}
+
+	@Override
+	public boolean isClientServer() {
+		return hasOption("clientserver");
+	}
+
+	@Override
+	public boolean isEmbedded() {
+		return hasOption("embedded");
+	}
+
+	@Override
+	public boolean isInMemory() {
+		return hasOption("inmemory");
+	}
+
+	private CommandLine processArgs(String[] args) throws ArgumentsParsingException {
+		CommandLineParser parser = new GnuParser();
+		CommandLine line = null;
+		try {
+			// parse the command line arguments
+			line = parser.parse(options, args);
+		} catch (ParseException exp) {
+			// oops, something went wrong
+//			System.err.println("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage());
+//			System.exit(1);
+			throw new ArgumentsParsingException("Taverna command line arguments' parsing failed. Reason: " + exp.getMessage(), exp);
+		}
+		return line;
+	}
+
+	/**
+	 * Save the results to a directory if -outputdir has been explicitly defined,
+	 * or if -outputdoc has not been defined.
+	 *
+	 * @return boolean
+	 */
+	@Override
+	public boolean saveResultsToDirectory() {
+		return (options.hasOption(OUTPUTDIR) || !hasSaveResultsToBundle());
+	}
+
+	@Override
+	public String saveResultsToBundle() {
+		if (! hasSaveResultsToBundle()) { 
+			return null;
+		}
+		return getOptionValue(BUNDLE);
+	}
+
+	@Override
+	public boolean hasSaveResultsToBundle() {
+		return hasOption(BUNDLE);
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
new file mode 100644
index 0000000..a462ba3
--- /dev/null
+++ b/taverna-commandline-launcher/src/main/java/uk/org/taverna/commandline/TavernaCommandLine.java
@@ -0,0 +1,139 @@
+/*******************************************************************************
+ * Copyright (C) 2012 The University of Manchester
+ *
+ *  Modifications to the initial code base are copyright of their
+ *  respective authors, or their employers as appropriate.
+ *
+ *  This program 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 (at your option) any later version.
+ *
+ *  This program 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.  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 program; if not, write to the Free Software
+ *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package uk.org.taverna.commandline;
+
+import java.io.File;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import net.sf.taverna.t2.commandline.exceptions.ArgumentsParsingException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.osgi.framework.BundleContext;
+import org.osgi.framework.BundleException;
+
+import uk.org.taverna.commons.profile.xml.jaxb.ApplicationProfile;
+import uk.org.taverna.commons.profile.xml.jaxb.BundleInfo;
+import uk.org.taverna.commons.profile.xml.jaxb.FrameworkConfiguration;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.configuration.app.impl.ApplicationConfigurationImpl;
+import uk.org.taverna.configuration.app.impl.Log4JConfiguration;
+import uk.org.taverna.osgi.OsgiLauncher;
+
+/**
+ * Main entry point for starting the Taverna Command Line Tool.
+ *
+ * @author David Withers
+ */
+public class TavernaCommandLine {
+
+	private static final String COMMANDLINE_BUNDLE_NAME = "net.sf.taverna.t2.taverna-commandline.common";
+
+	private static File commandlineBundle;
+
+	private static ApplicationConfiguration applicationConfiguration = new ApplicationConfigurationImpl();
+
+	private static Log4JConfiguration log4jConfiguration = new Log4JConfiguration();
+
+	/**
+	 * Starts the Taverna Command Line Tool.
+	 *
+	 * @param args
+	 *            Taverna Command Line arguments
+	 */
+	public static void main(final String[] args) {
+		try {
+			CommandLineOptions commandLineOptions = new CommandLineOptionsImpl(args);
+			if (commandLineOptions.askedForHelp()) {
+				commandLineOptions.displayHelp();
+			} else {
+				log4jConfiguration.setApplicationConfiguration(applicationConfiguration);
+				log4jConfiguration.prepareLog4J();
+				setDerbyPaths();
+				OsgiLauncher osgilauncher = new OsgiLauncher(getAppDirectory(), getBundleURIs());
+				setFrameworkConfiguration(osgilauncher);
+				osgilauncher.start();
+				BundleContext context = osgilauncher.getContext();
+				context.registerService("net.sf.taverna.t2.commandline.options.CommandLineOptions",
+						commandLineOptions, null);
+				osgilauncher.startServices(true);
+				osgilauncher.startBundle(osgilauncher.installBundle(commandlineBundle.toURI()));
+			}
+		} catch (ArgumentsParsingException e) {
+			System.out.println(e.getMessage());
+		} catch (InvalidOptionException e) {
+			System.out.println(e.getMessage());
+		} catch (BundleException e) {
+			System.out.println(e.getMessage());
+		}
+	}
+
+	/**
+	 * Sets the OSGi Framework configuration.
+	 *
+	 * @param osgilauncher
+	 */
+	private static void setFrameworkConfiguration(OsgiLauncher osgilauncher) {
+		ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+		List<FrameworkConfiguration> frameworkConfigurations = applicationProfile
+				.getFrameworkConfiguration();
+		if (!frameworkConfigurations.isEmpty()) {
+			Map<String, String> configurationMap = new HashMap<String, String>();
+			for (FrameworkConfiguration frameworkConfiguration : frameworkConfigurations) {
+				configurationMap.put(frameworkConfiguration.getName(),
+						frameworkConfiguration.getValue());
+			}
+			osgilauncher.setFrameworkConfiguration(configurationMap);
+		}
+	}
+
+	private static List<URI> getBundleURIs() {
+		List<URI> bundleURIs = new ArrayList<URI>();
+		ApplicationProfile applicationProfile = applicationConfiguration.getApplicationProfile();
+		File libDir = new File(applicationConfiguration.getStartupDir(), "lib");
+		if (applicationProfile != null) {
+			for (BundleInfo bundle : applicationProfile.getBundle()) {
+				File bundleFile = new File(libDir, bundle.getFileName());
+				if (bundle.getSymbolicName().equals(COMMANDLINE_BUNDLE_NAME)) {
+					commandlineBundle = bundleFile;
+				} else {
+					bundleURIs.add(bundleFile.toURI());
+				}
+			}
+		}
+		return bundleURIs;
+	}
+
+	private static File getAppDirectory() {
+		return new File(applicationConfiguration.getApplicationHomeDir().getAbsolutePath());
+	}
+
+	private static void setDerbyPaths() {
+		System.setProperty("derby.system.home", getAppDirectory().getAbsolutePath());
+		File logFile = new File(applicationConfiguration.getLogDir(), "derby.log");
+		System.setProperty("derby.stream.error.file", logFile.getAbsolutePath());
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/main/resources/help.txt
----------------------------------------------------------------------
diff --git a/taverna-commandline-launcher/src/main/resources/help.txt b/taverna-commandline-launcher/src/main/resources/help.txt
new file mode 100644
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--- /dev/null
+++ b/taverna-commandline-launcher/src/main/resources/help.txt
@@ -0,0 +1,87 @@
+By default, the workflow is executed using the -inmemory option, and the
+results are written out to a directory named after the workflow name.
+
+If this directory already exists then a new directory is created, and
+appended with _<n>, where n is incremented to the next available index.
+
+Results are written out to files named after the output port for that result.
+If a result is composed of lists, then a directory is created for the output
+port and individual list items are named after the list element index (with 1
+being the first index). The the output is the result of an error, the filename
+is appended with '.error'.
+
+You can provide your own output directory with the -outputdir option. There
+will be an error if the directory already exists.
+
+You can also record your results to a Baclava document using -outputdoc
+option. The document will be overwritten if it already exists.
+
+Inputs can be provided in three ways. Both -inputfile and -inputvalue options
+can be used together; -inputdoc option must be used on its own. -inputfile and
+-inputvalue options both take two additional arguments, the name of the port
+for the input, and either a file containing the input data, or the input value
+itself respectively.
+
+If one of more of your workflow inputs is a list, you can create a list
+input by using the -inputdelimiter option, which may be used with either
+-inputfile or -inputvalue. This option takes two parameters - an input name
+and the delimiter by which to split the input into a list.
+
+The delimiter may be a simple character, such as a comma or a new-line
+character, or a regular expression. The input string, or file, will then be
+converted into a list being split by the delimiter specified. Make sure to 
+put the delimiter character in quotes as it may be interpreted by the shell 
+as a special character, e.g. ;.
+
+If a list of greater depth (i.e. a list or lists or deeper) is required then
+you will need to use the -inputdoc option.  However, if you provide an input
+of lower depth to that required, then it will automatically be wrapped in one
+or more lists up to the required depth. Providing an input of greater depth
+than that required will result in an error.
+
+If a workflow has a high memory requirement, then it may be better to run it
+using a database to store data rather than storing it in memory, which is the
+default option. There are three options for using a database:
+
+-embedded option, runs with an embedded database. This is slightly faster than
+the -clientserver option (below), but has the limitation that only one
+executeworkflow script may be executed simultaneously.
+
+-clientserver option allows the workflow to be executed backed by the database
+running as a server. By default a database is not started for you, but may be
+started using -startdb option.
+
+-startdb option starts a database. It may be used without providing a workflow
+to allow a database to be started separately, allowing multiple simultaneous
+executeworkflow script runs.
+
+More advanced database configurations can be specified using -dbproperties
+option, allowing you to take full control over the database used. This takes a
+second argument, the filename of the properties file, for which the following
+example contains the default settings:
+
+in_memory = true
+provenance = false
+connector = derby
+port = 1527
+dialect = org.hibernate.dialect.DerbyDialect
+start_derby = false
+driver = org.apache.derby.jdbc.EmbeddedDriver
+jdbcuri = jdbc:derby:t2-database;create=true;upgrade=true
+
+Note that when using -dbproperties together with other options, the other
+options take precedence.
+
+-cmdir option lets you specify an absolute path to a directory where 
+Credential Manager's files (keystore and truststore - containing user's 
+credentials and trusted certificates for accessing secure services) are stored.
+If not specified and the workflow requires access to these files, Taverna will 
+try to find them in the default location in <TAVERNA_HOME>/security somewhere 
+inside user's home directory (depending on the platform).
+
+-cmpassword option can be used to tell Taverna to expect the password for the 
+Credential Manager on standard input. If the password is not piped in, Taverna 
+will prompt you for it in the terminal and block until it is entered. Do not 
+enter your password in the command line! If -cmpassword option is not specified 
+and -cmdir option is used, Taverna will try to find the password in a special 
+file password.txt in the directory specified with -cmdir option.

http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/a8e6b3ed/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
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diff --git a/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
new file mode 100644
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+++ b/taverna-commandline-launcher/src/test/java/uk/org/taverna/commandline/TestCommandLineOptionsHandler.java
@@ -0,0 +1,267 @@
+package uk.org.taverna.commandline;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.junit.Test;
+
+public class TestCommandLineOptionsHandler {
+
+	@Test
+	public void testWorkflowName() throws Exception {
+		CommandLineOptions handler = new CommandLineOptionsImpl(
+				new String[] { "myworkflow.t2flow" });
+		assertEquals("myworkflow.t2flow", handler.getWorkflow());
+	}
+
+	@Test
+	public void shouldShowHelp() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(
+				new String[] { "-help" });
+		assertTrue(options.askedForHelp());
+		options = new CommandLineOptionsImpl(
+				new String[] {});
+		assertTrue(options.askedForHelp());
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertFalse(options.askedForHelp());
+	}
+
+	@Test
+	public void getWorkflow() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(
+				new String[] { "-help" });
+		assertNull(options.getWorkflow());
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertEquals("myworkflow.t2flow", options.getWorkflow());
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void cannotProvideInputFileAndInputDoc() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-inputfile", "fred", "fred.txt",
+				"-inputdoc", "myworkflow.t2flow" });
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void cannotProvideInputValueAndInputDoc() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "fred.txt",
+				"-inputdoc", "myworkflow.t2flow" });
+	}
+
+	@Test
+	public void canProvideInputValueAndFileTogether() throws Exception {
+		//should not be an error
+		new CommandLineOptionsImpl(new String[] { "-inputvalue", "fred", "abc",
+				"-inputfile","fred2","fred2.txt","myworkflow.t2flow" });
+	}
+
+	@Test
+	public void getInputs() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
+		assertEquals(2, options.getInputFiles().length);
+		assertEquals("fred", options.getInputFiles()[0]);
+		assertEquals("fred.txt", options.getInputFiles()[1]);
+
+		options = new CommandLineOptionsImpl(new String[] { "-inputfile", "fred",
+				"fred.txt", "-inputfile", "fred2", "fred2.txt",
+				"myworkflow.t2flow" });
+		assertEquals(4, options.getInputFiles().length);
+		assertEquals("fred", options.getInputFiles()[0]);
+		assertEquals("fred.txt", options.getInputFiles()[1]);
+		assertEquals("fred2", options.getInputFiles()[2]);
+		assertEquals("fred2.txt", options.getInputFiles()[3]);
+
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertNotNull(options.getInputFiles());
+		assertEquals(0, options.getInputFiles().length);
+
+	}
+
+	@Test
+	public void hasInputValue() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+		assertTrue(options.hasInputValues());
+
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertFalse(options.hasInputValues());
+	}
+
+	@Test
+	public void getInputValues() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputvalue", "fred", "abc", "myworkflow.t2flow" });
+		assertEquals(2, options.getInputValues().length);
+
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertNotNull(options.getInputValues());
+		assertEquals(0,options.getInputValues().length);
+	}
+
+	@Test
+	public void hasInputs() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputfile", "fred", "fred.txt", "myworkflow.t2flow" });
+		assertTrue(options.hasInputFiles());
+
+		options = new CommandLineOptionsImpl(new String[] { "myworkflow.t2flow" });
+		assertFalse(options.hasInputFiles());
+	}
+
+	@Test
+	public void noWorkflowNameButStartDB() throws Exception {
+		// should not throw an error
+		CommandLineOptions options = new CommandLineOptionsImpl(
+				new String[] { "-startdb" });
+		assertTrue(options.getStartDatabase());
+		assertTrue(options.getStartDatabaseOnly());
+	}
+
+	@Test
+	public void workflowNameAndStartDB() throws Exception {
+		// should not throw an error
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-startdb", "myworkflow.t2flow" });
+		assertTrue(options.getStartDatabase());
+		assertFalse(options.getStartDatabaseOnly());
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void provenanceButNoDatabase() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-provenance",
+				"myworkflow.t2flow" });
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void provenanceButNoDatabase2() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-provenance", "-inmemory",
+				"myworkflow.t2flow" });
+	}
+
+	@Test
+	public void provenanceDatabase() throws Exception {
+		// should be no errors
+		new CommandLineOptionsImpl(new String[] { "-provenance", "-embedded",
+				"myworkflow.t2flow" });
+		new CommandLineOptionsImpl(new String[] { "-provenance", "-clientserver",
+				"myworkflow.t2flow" });
+		new CommandLineOptionsImpl(new String[] { "-provenance", "-dbproperties",
+				"dbproperties.properties", "myworkflow.t2flow" });
+	}
+
+	@Test
+	public void testHasInputDelimiter() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2",",","myworkflow.t2flow" });
+		assertTrue(options.hasDelimiterFor("in1"));
+		assertTrue(options.hasDelimiterFor("in2"));
+		assertFalse(options.hasDelimiterFor("in3"));
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void testInputDelimiterInvalidWithInputDoc() throws Exception {
+		new CommandLineOptionsImpl(new String[] {
+				"-inputdoc","doc.xml","-inputdelimiter","in1",",","myworkflow.t2flow" });
+	}
+
+
+	@Test
+	public void testInputDelimiter() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inputvalue","in1","1,2,3","-inputdelimiter","in1",",","-inputdelimiter","in2","!","myworkflow.t2flow" });
+		assertEquals(",",options.inputDelimiter("in1"));
+		assertEquals("!",options.inputDelimiter("in2"));
+		assertNull(options.inputDelimiter("in3"));
+	}
+
+	@Test
+	public void testInMemory() throws Exception {
+		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+				"-inmemory", "myworkflow.t2flow" });
+		assertTrue(handler.hasOption("inmemory"));
+	}
+
+	@Test
+	public void testEmbedded() throws Exception {
+		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+				"-embedded", "myworkflow.t2flow" });
+		assertTrue(handler.hasOption("embedded"));
+	}
+
+	@Test
+	public void testClientServer() throws Exception {
+		CommandLineOptions handler = new CommandLineOptionsImpl(new String[] {
+				"-clientserver", "myworkflow.t2flow" });
+		assertTrue(handler.hasOption("clientserver"));
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void testInvalidEmbeddedAndClientServer() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-clientserver", "-embedded",
+				"myworkflow.t2flow" });
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void testInvalidEmbeddedAndMemory() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-embedded", "-inmemory",
+				"myworkflow.t2flow" });
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	public void testInvalidClientServerAndInMemory() throws Exception {
+		new CommandLineOptionsImpl(new String[] { "-clientserver", "-inmemory",
+				"myworkflow.t2flow" });
+	}
+
+	@Test
+	public void isInMemory() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-inmemory", "myworkflow.t2flow" });
+
+		assertTrue(options.isInMemory());
+		assertFalse(options.isClientServer());
+		assertFalse(options.isEmbedded());
+	}
+
+	@Test
+	public void isClientServer() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-clientserver", "myworkflow.t2flow" });
+
+		assertTrue(options.isClientServer());
+		assertFalse(options.isInMemory());
+		assertFalse(options.isEmbedded());
+	}
+
+	@Test
+	public void hasLogFile() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-logfile","/tmp/logging", "myworkflow.t2flow" });
+
+		assertTrue(options.hasLogFile());
+		assertEquals("/tmp/logging", options.getLogFile());
+	}
+
+	@Test(expected = InvalidOptionException.class)
+	@SuppressWarnings("unused")
+	public void hasLogFileNotValidWithoutWorkflow() throws Exception{
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-logfile","/tmp/logging"});
+	}
+
+	@Test
+	public void isEmbedded() throws Exception {
+		CommandLineOptions options = new CommandLineOptionsImpl(new String[] {
+				"-embedded", "myworkflow.t2flow" });
+
+		assertTrue(options.isEmbedded());
+		assertFalse(options.isInMemory());
+		assertFalse(options.isClientServer());
+	}
+
+}