taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineLauncher.java - incubator-taverna-commandline - Git at Google

 /*******************************************************************************
  * 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 net.sf.taverna.t2.commandline;

 import java.io.BufferedReader;
 import java.io.Console;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.Authenticator;
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;

 import javax.naming.NamingException;

 import net.sf.taverna.platform.spring.RavenAwareClassPathXmlApplicationContext;
 import net.sf.taverna.raven.launcher.Launchable;
 import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
 import net.sf.taverna.t2.commandline.data.InputsHandler;
 import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
 import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
 import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
 import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
 import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
 import net.sf.taverna.t2.commandline.options.CommandLineOptions;
 import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
 import net.sf.taverna.t2.facade.WorkflowInstanceFacade.State;
 import net.sf.taverna.t2.invocation.InvocationContext;
 import net.sf.taverna.t2.invocation.TokenOrderException;
 import net.sf.taverna.t2.invocation.WorkflowDataToken;
 import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory;
 import net.sf.taverna.t2.provenance.ProvenanceConnectorFactoryRegistry;
 import net.sf.taverna.t2.provenance.connector.ProvenanceConnector;
 import net.sf.taverna.t2.reference.ReferenceService;
 import net.sf.taverna.t2.security.credentialmanager.CMException;
 import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
 import net.sf.taverna.t2.security.credentialmanager.CredentialManagerAuthenticator;
 import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
 import net.sf.taverna.t2.workflowmodel.Dataflow;
 import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
 import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
 import net.sf.taverna.t2.workflowmodel.DataflowValidationReport;
 import net.sf.taverna.t2.workflowmodel.EditException;
 import net.sf.taverna.t2.workflowmodel.Edits;
 import net.sf.taverna.t2.workflowmodel.EditsRegistry;
 import net.sf.taverna.t2.workflowmodel.InvalidDataflowException;
 import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;
 import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializer;
 import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerRegistry;

 import org.apache.log4j.Level;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PatternLayout;
 import org.apache.log4j.PropertyConfigurator;
 import org.apache.log4j.RollingFileAppender;
 import org.jdom.Element;
 import org.jdom.JDOMException;
 import org.jdom.input.SAXBuilder;
 import org.springframework.context.ApplicationContext;

 /**
  * A utility class that wraps the process of executing a workflow, allowing
  * workflows to be easily executed independently of the GUI.
  *
  * @author Stuart Owen
  */

 public class CommandLineLauncher implements Launchable {

 	private static Logger logger = Logger.getLogger(CommandLineLauncher.class);

 	/**
 	 * Main method, purely for development and debugging purposes. Full
 	 * execution of workflows will not work through this method.
 	 *
 	 * @param args
 	 * @throws Exception
 	 */
 	public static void main(String[] args) {
 		new CommandLineLauncher().launch(args);
 	}

 	public int launch(String[] args) {

 		try {
 			CommandLineOptions options = new CommandLineOptions(args);
 			initialiseLogging(options);
 			int result = setupAndExecute(args,options);
 			System.exit(result);
 			return result;
 		} catch (EditException e) {
 			error("There was an error opening the workflow: " + e.getMessage());
 		} catch (DeserializationException e) {
 			error("There was an error opening the workflow: " + e.getMessage());
 		} catch (InvalidDataflowException e) {
 			error("There was an error validating the workflow: "
 					+ e.getMessage());
 		} catch (TokenOrderException e) {
 			error("There was an error starting the workflow execution: "
 					+ e.getMessage());
 		} catch (InvalidOptionException e) {
 			error(e.getMessage());
 		} catch (ReadInputException e) {
 			error(e.getMessage());
 		} catch (OpenDataflowException e) {
 			error(e.getMessage());
 		} catch (DatabaseConfigurationException e) {
 			error(e.getMessage());
 		}
 		catch (CMException e) {
 			error("There was an error instantiating Credential Manager: " + e.getMessage());
 		}
 		// Should be unreachable
 		System.exit(-1);
 		return -1;
 	}

 	private void initialiseLogging(CommandLineOptions options) {
 		LogManager.resetConfiguration();

 		if (System.getProperty("log4j.configuration") == null) {
 			try {
 				PropertyConfigurator.configure(CommandLineLauncher.class
 						.getClassLoader().getResource("cl-log4j.properties")
 						.toURI().toURL());
 			} catch (MalformedURLException e) {
 				logger
 						.error(
 								"There was a serious error reading the default logging configuration",
 								e);
 			} catch (URISyntaxException e) {
 				logger
 						.error(
 								"There was a serious error reading the default logging configuration",
 								e);
 			}

 		} else {
 			PropertyConfigurator.configure(System
 					.getProperty("log4j.configuration"));
 		}

 		if (options.hasLogFile()) {
 			RollingFileAppender appender;
 			try {

 				PatternLayout layout = new PatternLayout(
 						"%-5p %d{ISO8601} (%c:%L) - %m%n");
 				appender = new RollingFileAppender(layout, options.getLogFile());
 				appender.setMaxFileSize("1MB");
 				appender.setEncoding("UTF-8");
 				appender.setMaxBackupIndex(4);
 				// Let root logger decide level
 				appender.setThreshold(Level.ALL);
 				LogManager.getRootLogger().addAppender(appender);
 			} catch (IOException e) {
 				System.err.println("Could not log to " + options.getLogFile());
 			}
 		}
 	}

 	public int setupAndExecute(String[] args,CommandLineOptions options) throws InvalidOptionException,
 			EditException, DeserializationException, InvalidDataflowException,
 			TokenOrderException, ReadInputException, OpenDataflowException,
 			DatabaseConfigurationException, CMException {


 		if (!options.askedForHelp()) {
 			Authenticator.setDefault(new CredentialManagerAuthenticator());
 			setupDatabase(options);

 			if (options.getWorkflow() != null) {

 				// Initialise Credential Manager and SSL stuff quite early as parsing and
 				// validating the workflow might require its services
 				String credentialManagerDirPath = options.getCredentialManagerDir();
 				String credentialManagerPassword = null;
 				if (options.hasOption(CommandLineOptions.CREDENTIAL_MANAGER_PASSWORD_OPTION)){ // if this parameter was used when launching the command line tool
 					// Try to read the password from stdin (terminal or pipe)
 					credentialManagerPassword = getCredentialManagerPasswordFromStdin();
 				}
 				else{
 					// Try to read the password from a special file located in
 					// Credential Manager directory (if the dir was not null)
 					credentialManagerPassword = getCredentialManagerPasswordFromFile(options.getCredentialManagerDir());
 				}
 				if (credentialManagerPassword != null){
 					// Initialise Credential Manager (Taverna's Keystore and Truststore) and
 					// SSL stuff - set the SSLSocketFactory to use Taverna's Keystore and Truststore.

 					// If credentialManagerDirPath is null - initialize from the default location in <TAVERNA_HOME>/security somewhere
 					// inside user's home directory. This should not be used when running command
 					// line tool on a server and the Credential Manager dir path should always be
 					// passed in as we do not want to store the security files in user's home directory
 					// on the server (we do not even know which user the command line tool will be running as).

 					//if (credentialManagerDirPath != null){
 						CredentialManager.initialiseSSL(credentialManagerDirPath, credentialManagerPassword); // this can now handle situations when credentialManagerDirPath is null
 					//}
 					//else{
 						// Initialize from the default location in <TAVERNA_HOME>/security somewhere
 						// inside user's home directory. This should not be used when running command
 						// line tool on a server and the Credential Manager dir path should always be
 						// passed in as we do not want to store the security files in user's home directory
 						// on the server (we do not even know which user the command line tool will be running as).
 					//	CredentialManager.initialiseSSL(credentialManagerPassword);
 					//}
 				}
 				else{
 					logger.warn("No master password provided for Credential Manager.");
 				}

 				URL workflowURL = readWorkflowURL(options.getWorkflow());

 				Dataflow dataflow = openDataflow(workflowURL);
 				validateDataflow(dataflow);

 				InvocationContext context = createInvocationContext();

 				WorkflowInstanceFacade facade = compileFacade(dataflow, context);
 				InputsHandler inputsHandler = new InputsHandler();
 				Map<String, DataflowInputPort> portMap = new HashMap<String, DataflowInputPort>();

 				for (DataflowInputPort port : dataflow.getInputPorts()) {
 					portMap.put(port.getName(), port);
 				}
 				inputsHandler.checkProvidedInputs(portMap, options);
 				Map<String, WorkflowDataToken> inputs = inputsHandler
 						.registerInputs(portMap, options, context);

 				CommandLineResultListener resultListener = addResultListener(
 						facade, context, dataflow, options);

 				executeWorkflow(facade, inputs, resultListener);
 			}
 		} else {
 			options.displayHelp();
 		}

 		// wait until user hits CTRL-C before exiting
 		if (options.getStartDatabaseOnly()) {
 			// FIXME: need to do this more gracefully.
 			while (true) {
 				try {
 					Thread.sleep(500);
 				} catch (InterruptedException e) {
 					return 0;
 				}
 			}
 		}

 		return 0;
 	}

 	protected void validateDataflow(Dataflow dataflow)
 			throws InvalidDataflowException {
 		// FIXME: this needs expanding upon to give more details info back to
 		// the user
 		// FIXME: added a getMessage to InvalidDataflowException may be good
 		// place to do this.
 		DataflowValidationReport report = dataflow.checkValidity();
 		if (!report.isValid()) {
 			throw new InvalidDataflowException(dataflow, report);
 		}
 	}

 	protected void executeWorkflow(WorkflowInstanceFacade facade,
 			Map<String, WorkflowDataToken> inputs,
 			CommandLineResultListener resultListener)
 			throws TokenOrderException {
 		facade.fire();
 		for (String inputName : inputs.keySet()) {
 			WorkflowDataToken token = inputs.get(inputName);
 			facade.pushData(token, inputName);
 		}
 		while (facade.getState().compareTo(State.completed) < 0) {
 			try {
 				Thread.sleep(100);
 			} catch (InterruptedException e) {
 				logger
 						.warn(
 								"Thread Interuption Exception whilst waiting for dataflow completion",
 								e);
 			}
 		}
 		resultListener.saveProvenance();
 		resultListener.saveOutputDocument();
 	}

 	private void setupDatabase(CommandLineOptions options)
 			throws DatabaseConfigurationException {
 		DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
 				options);
 		dbHandler.configureDatabase();
 		if (!options.isInMemory()) {
 			try {
 				dbHandler.testDatabaseConnection();
 			} catch (NamingException e) {
 				throw new DatabaseConfigurationException(
 						"There was an error trying to setup the database datasource: "
 								+ e.getMessage(), e);
 			} catch (SQLException e) {
 				if (options.isClientServer()) {
 					throw new DatabaseConfigurationException(
 							"There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
 							e);
 				}
 				if (options.isEmbedded()) {
 					throw new DatabaseConfigurationException(
 							"There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
 							e);
 				}
 			}
 		}

 	}

 	private InvocationContext createInvocationContext() {
 		ReferenceService referenceService = createReferenceServiceBean();
 		ProvenanceConnector connector = null;
 		DataManagementConfiguration dbConfig = DataManagementConfiguration
 				.getInstance();
 		if (dbConfig.isProvenanceEnabled()) {
 			String connectorType = dbConfig.getConnectorType();

 			for (ProvenanceConnectorFactory factory : ProvenanceConnectorFactoryRegistry
 					.getInstance().getInstances()) {
 				if (connectorType.equalsIgnoreCase(factory.getConnectorType())) {
 					connector = factory.getProvenanceConnector();
 				}

 			}
 			if (connector != null) {
 				connector.init();
 			} else {
 				error("Unable to initialise the provenance - the ProvenanceConnector cannot be found.");
 			}
 		}
 		InvocationContext context = new CommandLineInvocationContext(
 				referenceService, connector);
 		if (connector != null){
 			connector.setInvocationContext(context);
 		}
 		return context;
 	}

 	private File determineOutputDir(CommandLineOptions options,
 			String dataflowName) {
 		File result = null;
 		if (options.getOutputDirectory() != null) {
 			result = new File(options.getOutputDirectory());
 			if (result.exists()) {
 				error("The specified output directory '"
 						+ options.getOutputDirectory() + "' already exists");
 			}
 		} else if (options.getOutputDocument() == null) {
 			result = new File(dataflowName + "_output");
 			int x = 1;
 			while (result.exists()) {
 				result = new File(dataflowName + "_output_" + x);
 				x++;
 			}
 		}
 		if (result != null) {
 			System.out.println("Outputs will be saved to the directory: "
 					+ result.getAbsolutePath());
 		}
 		return result;
 	}

 	protected void error(String msg) {
 		System.err.println(msg);
 		System.exit(-1);
 	}

 	private URL readWorkflowURL(String workflowOption)
 			throws OpenDataflowException {
 		URL url;
 		try {
 			url = new URL("file:");
 			return new URL(url, workflowOption);
 		} catch (MalformedURLException e) {
 			throw new OpenDataflowException(
 					"The was an error processing the URL to the workflow: "
 							+ e.getMessage(), e);
 		}
 	}

 	/**
 	 *
 	 * @param cmDir
 	 * @return Password for Credential Manager.
 	 * @throws CMException
 	 */
 	private String getCredentialManagerPasswordFromFile(String cmDir) throws CMException{

 		if (cmDir == null){
 			return null;
 		}
 		File passwordFile = new File(cmDir, "password.txt");
 		String password = null;
 		BufferedReader buffReader = null;
 		try {
 			buffReader = new BufferedReader(new FileReader(passwordFile));
 			password = buffReader.readLine();
 		} catch (IOException ioe) {
 			// For some reason the error of the exception thrown
 			// does not get printed from the Launcher so print it here as
 			// well as it gives more clue as to what is going wrong.
 			logger.error("There was an error reading the Credential Manager password from "
 					+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
 			throw new CMException(
 					"There was an error reading the Credential Manager password from "
 							+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
 		} finally {
 			try {
 				buffReader.close();
 			} catch (Exception ioe1) {
 				// Ignore
 			}
 		}
 		return password;
 	}

 	private String getCredentialManagerPasswordFromStdin() throws CMException{

 		String password = null;

 		Console console = System.console();

 		if (console == null) { // password is being piped in, not entered in the terminal by user
 			BufferedReader buffReader = null;
     		try {
     			buffReader = new BufferedReader(new InputStreamReader(System.in));
     			password = buffReader.readLine();
     		}
     		catch (IOException ex) {
     			// For some reason the error of the exception thrown
     			// does not get printed from the Launcher so print it here as
     			// well as it gives more clue as to what is going wrong.
     			logger.error("An error occured while trying to read Credential Manager's password the user piped in: "
 						+ ex.getMessage(), ex);
     			throw new CMException(
 						"An error occured while trying to read Credential Manager's password the user piped in: "
 								+ ex.getMessage(), ex);
 				}
     		finally {
     			try {
     				buffReader.close();
     			} catch (Exception ioe1) {
     				// Ignore
     			}
     		}
 		}
 		else{ // read the password from the terminal as entered by the user
 			try {
 				// Block until user enters password
 				char passwordArray[] = console
 						.readPassword("Password for Credential Manager: ");
 				if (passwordArray != null) { // user did not abort input
 					password = new String(passwordArray);
 				} // else password will be null

 			} catch (Exception ex) {
     			// For some reason the error of the exception thrown
     			// does not get printed from the Launcher so print it here as
     			// well as it gives more clue as to what is going wrong.
 				logger.error("An error occured while trying to read Credential Manager's password from the terminal: "
 								+ ex.getMessage(), ex);
 				throw new CMException(
 						"An error occured while trying to read Credential Manager's password from the terminal: "
 								+ ex.getMessage(), ex);
 			}
 		}
         return password;
 	}

 	private CommandLineResultListener addResultListener(
 			WorkflowInstanceFacade facade, InvocationContext context,
 			Dataflow dataflow, CommandLineOptions options) {
 		File outputDir = null;
 		File baclavaDoc = null;
 		File janus = null;
 		File janusDir = null;
 		File opm = null;

 		if (options.saveResultsToDirectory()) {
 			outputDir = determineOutputDir(options, dataflow.getLocalName());
 			janusDir = outputDir;
 		}
 		if (options.getOutputDocument() != null) {
 			baclavaDoc = new File(options.getOutputDocument());
 		}
 		if (options.isJanus()) {
 			if (options.getJanus() == null) {
 				if (janusDir == null) {
 					janusDir = determineOutputDir(options, dataflow.getLocalName());
 				}
 				janus = new File(janusDir, "provenance-janus.rdf");
 			} else {
 				janus = new File(options.getJanus());
 			}
 		}
 		if (options.isOPM()) {
 			if (options.getOPM() == null) {
 				if (janusDir == null) {
 					janusDir = determineOutputDir(options, dataflow.getLocalName());
 				}
 				opm = new File(janusDir, "provenance-opm.rdf");
 			} else {
 				opm = new File(options.getOPM());
 			}
 		}

 		Map<String, Integer> outputPortNamesAndDepth = new HashMap<String, Integer>();
 		for (DataflowOutputPort port : dataflow.getOutputPorts()) {
 			outputPortNamesAndDepth.put(port.getName(), port.getDepth());
 		}
 		SaveResultsHandler resultsHandler = new SaveResultsHandler(
 				outputPortNamesAndDepth, outputDir, baclavaDoc, janus, opm);
 		CommandLineResultListener listener = new CommandLineResultListener(
 				outputPortNamesAndDepth.size(), resultsHandler,
 				outputDir != null, baclavaDoc != null, opm != null, janus != null, facade.getWorkflowRunId());
 		facade.addResultListener(listener);
 		return listener;

 	}

 	protected ReferenceService createReferenceServiceBean() {
 		ApplicationContext appContext = new RavenAwareClassPathXmlApplicationContext(
 				DataManagementConfiguration.getInstance().getDatabaseContext());
 		return (ReferenceService) appContext
 				.getBean("t2reference.service.referenceService");
 	}

 	protected WorkflowInstanceFacade compileFacade(Dataflow dataflow,
 			InvocationContext context) throws InvalidDataflowException {
 		Edits edits = EditsRegistry.getEdits();
 		return edits.createWorkflowInstanceFacade(dataflow, context, "");
 	}

 	protected Dataflow openDataflow(URL workflowURL)
 			throws DeserializationException, EditException,
 			OpenDataflowException {
 		XMLDeserializer deserializer = XMLDeserializerRegistry.getInstance()
 				.getDeserializer();
 		SAXBuilder builder = new SAXBuilder();
 		Element el;
 		try {
 			InputStream stream = workflowURL.openStream();
 			el = builder.build(stream).detachRootElement();
 		} catch (JDOMException e) {
 			throw new OpenDataflowException(
 					"There was a problem processing the workflow XML: "
 							+ e.getMessage(), e);
 		} catch (IOException e) {
 			throw new OpenDataflowException(
 					"There was a problem reading the workflow file: "
 							+ e.getMessage(), e);
 		}
 		return deserializer.deserializeDataflow(el);
 	}

 }
	/*******************************************************************************
	* 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 net.sf.taverna.t2.commandline;

	import java.io.BufferedReader;
	import java.io.Console;
	import java.io.File;
	import java.io.FileReader;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.InputStreamReader;
	import java.net.Authenticator;
	import java.net.MalformedURLException;
	import java.net.URISyntaxException;
	import java.net.URL;
	import java.sql.SQLException;
	import java.util.HashMap;
	import java.util.Map;

	import javax.naming.NamingException;

	import net.sf.taverna.platform.spring.RavenAwareClassPathXmlApplicationContext;
	import net.sf.taverna.raven.launcher.Launchable;
	import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
	import net.sf.taverna.t2.commandline.data.InputsHandler;
	import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
	import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
	import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
	import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
	import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
	import net.sf.taverna.t2.commandline.options.CommandLineOptions;
	import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
	import net.sf.taverna.t2.facade.WorkflowInstanceFacade.State;
	import net.sf.taverna.t2.invocation.InvocationContext;
	import net.sf.taverna.t2.invocation.TokenOrderException;
	import net.sf.taverna.t2.invocation.WorkflowDataToken;
	import net.sf.taverna.t2.provenance.ProvenanceConnectorFactory;
	import net.sf.taverna.t2.provenance.ProvenanceConnectorFactoryRegistry;
	import net.sf.taverna.t2.provenance.connector.ProvenanceConnector;
	import net.sf.taverna.t2.reference.ReferenceService;
	import net.sf.taverna.t2.security.credentialmanager.CMException;
	import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
	import net.sf.taverna.t2.security.credentialmanager.CredentialManagerAuthenticator;
	import net.sf.taverna.t2.workbench.reference.config.DataManagementConfiguration;
	import net.sf.taverna.t2.workflowmodel.Dataflow;
	import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
	import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
	import net.sf.taverna.t2.workflowmodel.DataflowValidationReport;
	import net.sf.taverna.t2.workflowmodel.EditException;
	import net.sf.taverna.t2.workflowmodel.Edits;
	import net.sf.taverna.t2.workflowmodel.EditsRegistry;
	import net.sf.taverna.t2.workflowmodel.InvalidDataflowException;
	import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;
	import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializer;
	import net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerRegistry;

	import org.apache.log4j.Level;
	import org.apache.log4j.LogManager;
	import org.apache.log4j.Logger;
	import org.apache.log4j.PatternLayout;
	import org.apache.log4j.PropertyConfigurator;
	import org.apache.log4j.RollingFileAppender;
	import org.jdom.Element;
	import org.jdom.JDOMException;
	import org.jdom.input.SAXBuilder;
	import org.springframework.context.ApplicationContext;

	/**
	* A utility class that wraps the process of executing a workflow, allowing
	* workflows to be easily executed independently of the GUI.
	*
	* @author Stuart Owen
	*/

	public class CommandLineLauncher implements Launchable {

	private static Logger logger = Logger.getLogger(CommandLineLauncher.class);

	/**
	* Main method, purely for development and debugging purposes. Full
	* execution of workflows will not work through this method.
	*
	* @param args
	* @throws Exception
	*/
	public static void main(String[] args) {
	new CommandLineLauncher().launch(args);
	}

	public int launch(String[] args) {

	try {
	CommandLineOptions options = new CommandLineOptions(args);
	initialiseLogging(options);
	int result = setupAndExecute(args,options);
	System.exit(result);
	return result;
	} catch (EditException e) {
	error("There was an error opening the workflow: " + e.getMessage());
	} catch (DeserializationException e) {
	error("There was an error opening the workflow: " + e.getMessage());
	} catch (InvalidDataflowException e) {
	error("There was an error validating the workflow: "
	+ e.getMessage());
	} catch (TokenOrderException e) {
	error("There was an error starting the workflow execution: "
	+ e.getMessage());
	} catch (InvalidOptionException e) {
	error(e.getMessage());
	} catch (ReadInputException e) {
	error(e.getMessage());
	} catch (OpenDataflowException e) {
	error(e.getMessage());
	} catch (DatabaseConfigurationException e) {
	error(e.getMessage());
	}
	catch (CMException e) {
	error("There was an error instantiating Credential Manager: " + e.getMessage());
	}
	// Should be unreachable
	System.exit(-1);
	return -1;
	}

	private void initialiseLogging(CommandLineOptions options) {
	LogManager.resetConfiguration();

	if (System.getProperty("log4j.configuration") == null) {
	try {
	PropertyConfigurator.configure(CommandLineLauncher.class
	.getClassLoader().getResource("cl-log4j.properties")
	.toURI().toURL());
	} catch (MalformedURLException e) {
	logger
	.error(
	"There was a serious error reading the default logging configuration",
	e);
	} catch (URISyntaxException e) {
	logger
	.error(
	"There was a serious error reading the default logging configuration",
	e);
	}

	} else {
	PropertyConfigurator.configure(System
	.getProperty("log4j.configuration"));
	}

	if (options.hasLogFile()) {
	RollingFileAppender appender;
	try {

	PatternLayout layout = new PatternLayout(
	"%-5p %d{ISO8601} (%c:%L) - %m%n");
	appender = new RollingFileAppender(layout, options.getLogFile());
	appender.setMaxFileSize("1MB");
	appender.setEncoding("UTF-8");
	appender.setMaxBackupIndex(4);
	// Let root logger decide level
	appender.setThreshold(Level.ALL);
	LogManager.getRootLogger().addAppender(appender);
	} catch (IOException e) {
	System.err.println("Could not log to " + options.getLogFile());
	}
	}
	}

	public int setupAndExecute(String[] args,CommandLineOptions options) throws InvalidOptionException,
	EditException, DeserializationException, InvalidDataflowException,
	TokenOrderException, ReadInputException, OpenDataflowException,
	DatabaseConfigurationException, CMException {


	if (!options.askedForHelp()) {
	Authenticator.setDefault(new CredentialManagerAuthenticator());
	setupDatabase(options);

	if (options.getWorkflow() != null) {

	// Initialise Credential Manager and SSL stuff quite early as parsing and
	// validating the workflow might require its services
	String credentialManagerDirPath = options.getCredentialManagerDir();
	String credentialManagerPassword = null;
	if (options.hasOption(CommandLineOptions.CREDENTIAL_MANAGER_PASSWORD_OPTION)){ // if this parameter was used when launching the command line tool
	// Try to read the password from stdin (terminal or pipe)
	credentialManagerPassword = getCredentialManagerPasswordFromStdin();
	}
	else{
	// Try to read the password from a special file located in
	// Credential Manager directory (if the dir was not null)
	credentialManagerPassword = getCredentialManagerPasswordFromFile(options.getCredentialManagerDir());
	}
	if (credentialManagerPassword != null){
	// Initialise Credential Manager (Taverna's Keystore and Truststore) and
	// SSL stuff - set the SSLSocketFactory to use Taverna's Keystore and Truststore.

	// If credentialManagerDirPath is null - initialize from the default location in <TAVERNA_HOME>/security somewhere
	// inside user's home directory. This should not be used when running command
	// line tool on a server and the Credential Manager dir path should always be
	// passed in as we do not want to store the security files in user's home directory
	// on the server (we do not even know which user the command line tool will be running as).

	//if (credentialManagerDirPath != null){
	CredentialManager.initialiseSSL(credentialManagerDirPath, credentialManagerPassword); // this can now handle situations when credentialManagerDirPath is null
	//}
	//else{
	// Initialize from the default location in <TAVERNA_HOME>/security somewhere
	// inside user's home directory. This should not be used when running command
	// line tool on a server and the Credential Manager dir path should always be
	// passed in as we do not want to store the security files in user's home directory
	// on the server (we do not even know which user the command line tool will be running as).
	// CredentialManager.initialiseSSL(credentialManagerPassword);
	//}
	}
	else{
	logger.warn("No master password provided for Credential Manager.");
	}

	URL workflowURL = readWorkflowURL(options.getWorkflow());

	Dataflow dataflow = openDataflow(workflowURL);
	validateDataflow(dataflow);

	InvocationContext context = createInvocationContext();

	WorkflowInstanceFacade facade = compileFacade(dataflow, context);
	InputsHandler inputsHandler = new InputsHandler();
	Map<String, DataflowInputPort> portMap = new HashMap<String, DataflowInputPort>();

	for (DataflowInputPort port : dataflow.getInputPorts()) {
	portMap.put(port.getName(), port);
	}
	inputsHandler.checkProvidedInputs(portMap, options);
	Map<String, WorkflowDataToken> inputs = inputsHandler
	.registerInputs(portMap, options, context);

	CommandLineResultListener resultListener = addResultListener(
	facade, context, dataflow, options);

	executeWorkflow(facade, inputs, resultListener);
	}
	} else {
	options.displayHelp();
	}

	// wait until user hits CTRL-C before exiting
	if (options.getStartDatabaseOnly()) {
	// FIXME: need to do this more gracefully.
	while (true) {
	try {
	Thread.sleep(500);
	} catch (InterruptedException e) {
	return 0;
	}
	}
	}

	return 0;
	}

	protected void validateDataflow(Dataflow dataflow)
	throws InvalidDataflowException {
	// FIXME: this needs expanding upon to give more details info back to
	// the user
	// FIXME: added a getMessage to InvalidDataflowException may be good
	// place to do this.
	DataflowValidationReport report = dataflow.checkValidity();
	if (!report.isValid()) {
	throw new InvalidDataflowException(dataflow, report);
	}
	}

	protected void executeWorkflow(WorkflowInstanceFacade facade,
	Map<String, WorkflowDataToken> inputs,
	CommandLineResultListener resultListener)
	throws TokenOrderException {
	facade.fire();
	for (String inputName : inputs.keySet()) {
	WorkflowDataToken token = inputs.get(inputName);
	facade.pushData(token, inputName);
	}
	while (facade.getState().compareTo(State.completed) < 0) {
	try {
	Thread.sleep(100);
	} catch (InterruptedException e) {
	logger
	.warn(
	"Thread Interuption Exception whilst waiting for dataflow completion",
	e);
	}
	}
	resultListener.saveProvenance();
	resultListener.saveOutputDocument();
	}

	private void setupDatabase(CommandLineOptions options)
	throws DatabaseConfigurationException {
	DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
	options);
	dbHandler.configureDatabase();
	if (!options.isInMemory()) {
	try {
	dbHandler.testDatabaseConnection();
	} catch (NamingException e) {
	throw new DatabaseConfigurationException(
	"There was an error trying to setup the database datasource: "
	+ e.getMessage(), e);
	} catch (SQLException e) {
	if (options.isClientServer()) {
	throw new DatabaseConfigurationException(
	"There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
	e);
	}
	if (options.isEmbedded()) {
	throw new DatabaseConfigurationException(
	"There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
	e);
	}
	}
	}

	}

	private InvocationContext createInvocationContext() {
	ReferenceService referenceService = createReferenceServiceBean();
	ProvenanceConnector connector = null;
	DataManagementConfiguration dbConfig = DataManagementConfiguration
	.getInstance();
	if (dbConfig.isProvenanceEnabled()) {
	String connectorType = dbConfig.getConnectorType();

	for (ProvenanceConnectorFactory factory : ProvenanceConnectorFactoryRegistry
	.getInstance().getInstances()) {
	if (connectorType.equalsIgnoreCase(factory.getConnectorType())) {
	connector = factory.getProvenanceConnector();
	}

	}
	if (connector != null) {
	connector.init();
	} else {
	error("Unable to initialise the provenance - the ProvenanceConnector cannot be found.");
	}
	}
	InvocationContext context = new CommandLineInvocationContext(
	referenceService, connector);
	if (connector != null){
	connector.setInvocationContext(context);
	}
	return context;
	}

	private File determineOutputDir(CommandLineOptions options,
	String dataflowName) {
	File result = null;
	if (options.getOutputDirectory() != null) {
	result = new File(options.getOutputDirectory());
	if (result.exists()) {
	error("The specified output directory '"
	+ options.getOutputDirectory() + "' already exists");
	}
	} else if (options.getOutputDocument() == null) {
	result = new File(dataflowName + "_output");
	int x = 1;
	while (result.exists()) {
	result = new File(dataflowName + "_output_" + x);
	x++;
	}
	}
	if (result != null) {
	System.out.println("Outputs will be saved to the directory: "
	+ result.getAbsolutePath());
	}
	return result;
	}

	protected void error(String msg) {
	System.err.println(msg);
	System.exit(-1);
	}

	private URL readWorkflowURL(String workflowOption)
	throws OpenDataflowException {
	URL url;
	try {
	url = new URL("file:");
	return new URL(url, workflowOption);
	} catch (MalformedURLException e) {
	throw new OpenDataflowException(
	"The was an error processing the URL to the workflow: "
	+ e.getMessage(), e);
	}
	}

	/**
	*
	* @param cmDir
	* @return Password for Credential Manager.
	* @throws CMException
	*/
	private String getCredentialManagerPasswordFromFile(String cmDir) throws CMException{

	if (cmDir == null){
	return null;
	}
	File passwordFile = new File(cmDir, "password.txt");
	String password = null;
	BufferedReader buffReader = null;
	try {
	buffReader = new BufferedReader(new FileReader(passwordFile));
	password = buffReader.readLine();
	} catch (IOException ioe) {
	// For some reason the error of the exception thrown
	// does not get printed from the Launcher so print it here as
	// well as it gives more clue as to what is going wrong.
	logger.error("There was an error reading the Credential Manager password from "
	+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
	throw new CMException(
	"There was an error reading the Credential Manager password from "
	+ passwordFile.toString() + ": " + ioe.getMessage(), ioe);
	} finally {
	try {
	buffReader.close();
	} catch (Exception ioe1) {
	// Ignore
	}
	}
	return password;
	}

	private String getCredentialManagerPasswordFromStdin() throws CMException{

	String password = null;

	Console console = System.console();

	if (console == null) { // password is being piped in, not entered in the terminal by user
	BufferedReader buffReader = null;
	try {
	buffReader = new BufferedReader(new InputStreamReader(System.in));
	password = buffReader.readLine();
	}
	catch (IOException ex) {
	// For some reason the error of the exception thrown
	// does not get printed from the Launcher so print it here as
	// well as it gives more clue as to what is going wrong.
	logger.error("An error occured while trying to read Credential Manager's password the user piped in: "
	+ ex.getMessage(), ex);
	throw new CMException(
	"An error occured while trying to read Credential Manager's password the user piped in: "
	+ ex.getMessage(), ex);
	}
	finally {
	try {
	buffReader.close();
	} catch (Exception ioe1) {
	// Ignore
	}
	}
	}
	else{ // read the password from the terminal as entered by the user
	try {
	// Block until user enters password
	char passwordArray[] = console
	.readPassword("Password for Credential Manager: ");
	if (passwordArray != null) { // user did not abort input
	password = new String(passwordArray);
	} // else password will be null

	} catch (Exception ex) {
	// For some reason the error of the exception thrown
	// does not get printed from the Launcher so print it here as
	// well as it gives more clue as to what is going wrong.
	logger.error("An error occured while trying to read Credential Manager's password from the terminal: "
	+ ex.getMessage(), ex);
	throw new CMException(
	"An error occured while trying to read Credential Manager's password from the terminal: "
	+ ex.getMessage(), ex);
	}
	}
	return password;
	}

	private CommandLineResultListener addResultListener(
	WorkflowInstanceFacade facade, InvocationContext context,
	Dataflow dataflow, CommandLineOptions options) {
	File outputDir = null;
	File baclavaDoc = null;
	File janus = null;
	File janusDir = null;
	File opm = null;

	if (options.saveResultsToDirectory()) {
	outputDir = determineOutputDir(options, dataflow.getLocalName());
	janusDir = outputDir;
	}
	if (options.getOutputDocument() != null) {
	baclavaDoc = new File(options.getOutputDocument());
	}
	if (options.isJanus()) {
	if (options.getJanus() == null) {
	if (janusDir == null) {
	janusDir = determineOutputDir(options, dataflow.getLocalName());
	}
	janus = new File(janusDir, "provenance-janus.rdf");
	} else {
	janus = new File(options.getJanus());
	}
	}
	if (options.isOPM()) {
	if (options.getOPM() == null) {
	if (janusDir == null) {
	janusDir = determineOutputDir(options, dataflow.getLocalName());
	}
	opm = new File(janusDir, "provenance-opm.rdf");
	} else {
	opm = new File(options.getOPM());
	}
	}

	Map<String, Integer> outputPortNamesAndDepth = new HashMap<String, Integer>();
	for (DataflowOutputPort port : dataflow.getOutputPorts()) {
	outputPortNamesAndDepth.put(port.getName(), port.getDepth());
	}
	SaveResultsHandler resultsHandler = new SaveResultsHandler(
	outputPortNamesAndDepth, outputDir, baclavaDoc, janus, opm);
	CommandLineResultListener listener = new CommandLineResultListener(
	outputPortNamesAndDepth.size(), resultsHandler,
	outputDir != null, baclavaDoc != null, opm != null, janus != null, facade.getWorkflowRunId());
	facade.addResultListener(listener);
	return listener;

	}

	protected ReferenceService createReferenceServiceBean() {
	ApplicationContext appContext = new RavenAwareClassPathXmlApplicationContext(
	DataManagementConfiguration.getInstance().getDatabaseContext());
	return (ReferenceService) appContext
	.getBean("t2reference.service.referenceService");
	}

	protected WorkflowInstanceFacade compileFacade(Dataflow dataflow,
	InvocationContext context) throws InvalidDataflowException {
	Edits edits = EditsRegistry.getEdits();
	return edits.createWorkflowInstanceFacade(dataflow, context, "");
	}

	protected Dataflow openDataflow(URL workflowURL)
	throws DeserializationException, EditException,
	OpenDataflowException {
	XMLDeserializer deserializer = XMLDeserializerRegistry.getInstance()
	.getDeserializer();
	SAXBuilder builder = new SAXBuilder();
	Element el;
	try {
	InputStream stream = workflowURL.openStream();
	el = builder.build(stream).detachRootElement();
	} catch (JDOMException e) {
	throw new OpenDataflowException(
	"There was a problem processing the workflow XML: "
	+ e.getMessage(), e);
	} catch (IOException e) {
	throw new OpenDataflowException(
	"There was a problem reading the workflow file: "
	+ e.getMessage(), e);
	}
	return deserializer.deserializeDataflow(el);
	}

	}