taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.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.data;

 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.util.HashMap;
 import java.util.Map;

 import net.sf.taverna.t2.commandline.CommandLineResultListener;
 import net.sf.taverna.t2.invocation.InvocationContext;
 import net.sf.taverna.t2.invocation.WorkflowDataToken;
 import net.sf.taverna.t2.reference.ErrorDocument;
 import net.sf.taverna.t2.reference.ExternalReferenceSPI;
 import net.sf.taverna.t2.reference.Identified;
 import net.sf.taverna.t2.reference.IdentifiedList;
 import net.sf.taverna.t2.reference.ReferenceSet;
 import net.sf.taverna.t2.reference.T2Reference;
 import net.sf.taverna.t2.reference.T2ReferenceType;

 import org.apache.log4j.Logger;

 /**
  * Handles all recording of results as they are received by the {@link CommandLineResultListener}
  * or when the workflow enactment has completed.
  * This includes saving as a Baclava Document, or storing individual results.
  *
  * @author Stuart Owen
  * @see BaclavaDocumentHandler
  * @see CommandLineResultListener
  *
  */
 public class SaveResultsHandler {

 	private final Map<String, Integer> portsAndDepth;
 	private HashMap<String, Integer> depthSeen;
 	private final File rootDirectory;
 	private static Logger logger = Logger
 			.getLogger(CommandLineResultListener.class);
 	private final File outputDocumentFile;

 	public SaveResultsHandler(Map<String, Integer> portsAndDepth,
 			File rootDirectory, File outputDocumentFile) {

 		this.portsAndDepth = portsAndDepth;
 		this.rootDirectory = rootDirectory;
 		this.outputDocumentFile = outputDocumentFile;

 		depthSeen = new HashMap<String, Integer>();
 		for (String portName : portsAndDepth.keySet()) {
 			depthSeen.put(portName, -1);
 		}
 	}

 	public void tokenReceived(WorkflowDataToken token, String portName) {
 		if (rootDirectory != null) { //only save individual results if a directory is specified
 			if (portsAndDepth.containsKey(portName)) {
 				int[] index = token.getIndex();
 				if (depthSeen.get(portName) == -1)
 					depthSeen.put(portName, index.length);
 				if (index.length >= depthSeen.get(portName)) {
 					storeToken(token, portName);
 				}
 			} else {
 				logger
 						.error("Result recieved for unexpected Port: "
 								+ portName);
 			}
 		}
 	}

 	public void saveOutputDocument(Map<String,WorkflowDataToken> allResults) throws Exception {
 		if (outputDocumentFile!=null) {
 			new BaclavaDocumentHandler().storeDocument(allResults, outputDocumentFile);
 		}
 	}

 	protected void storeToken(WorkflowDataToken token, String portName) {

 		if (token.getData().getReferenceType() == T2ReferenceType.IdentifiedList) {
 			saveList(token, portName);
 		} else {
 			File dataDirectory = rootDirectory;
 			File dataFile = null;

 			if (token.getIndex().length > 0) {
 				dataDirectory = new File(rootDirectory, portName);
 				for (int i = 0; i < token.getIndex().length - 1; i++) {
 					dataDirectory = new File(dataDirectory, String
 							.valueOf(token.getIndex()[i] + 1));
 				}
 				dataFile = new File(dataDirectory, String.valueOf(token
 						.getIndex()[token.getIndex().length - 1] + 1));
 			} else {
 				dataFile = new File(dataDirectory, portName);
 			}

 			if (!dataDirectory.exists()) {
 				dataDirectory.mkdirs();
 			}

 			if (dataFile.exists()) {
 				System.err.println("There is already data saved to: "
 						+ dataFile.getAbsolutePath());
 				System.exit(-1);
 			}

 			saveIndividualDataFile(token.getData(), dataFile, token
 					.getContext());
 		}
 	}

 	private void saveList(WorkflowDataToken token, String portName) {
 		File dataDirectory = null;
 		int[] index = token.getIndex();

 		if (index.length > 0) {
 			dataDirectory = new File(rootDirectory, portName);
 			for (int i = 0; i < index.length - 1; i++) {
 				dataDirectory = new File(dataDirectory, String.valueOf(token
 						.getIndex()[i] + 1));
 			}
 			dataDirectory = new File(dataDirectory, String.valueOf(token
 					.getIndex()[index.length - 1]+ 1));
 		} else {
 			dataDirectory = new File(rootDirectory, portName);
 		}

 		T2Reference reference = token.getData();
 		IdentifiedList<T2Reference> list = token.getContext()
 				.getReferenceService().getListService().getList(reference);
 		saveListItems(token.getContext(), dataDirectory,  list);
 	}

 	private void saveListItems(InvocationContext context, File dataDirectory,IdentifiedList<T2Reference> list) {
 		int c = 0;
 		if (!dataDirectory.exists()) {
 			dataDirectory.mkdirs();
 		}
 		for (T2Reference id : list) {
 			File dataFile = new File(dataDirectory, String.valueOf(c+1));
 			if (id.getReferenceType() ==  T2ReferenceType.IdentifiedList) {
 				IdentifiedList<T2Reference> innerList = context
 				.getReferenceService().getListService().getList(id);
 				saveListItems(context, dataFile, innerList);
 			}
 			else {
 				saveIndividualDataFile(id, dataFile, context);
 			}
 			c++;
 		}
 	}

 	protected void saveIndividualDataFile(T2Reference reference, File dataFile,
 			InvocationContext context) {

 		if (dataFile.exists()) {
 			System.err.println("There is already data saved to: "
 					+ dataFile.getAbsolutePath());
 			System.exit(-1);
 		}

 		Object data = null;
 		if (reference.containsErrors()) {
 			ErrorDocument errorDoc = context.getReferenceService()
 			.getErrorDocumentService().getError(reference);
 			data = ErrorDocumentHandler.buildErrorDocumentString(errorDoc, context);
 			dataFile = new File(dataFile.getAbsolutePath()+".error");
 		} else {
 			// FIXME: this really should be done using a stream rather
 			// than an instance of the object in memory

 			Identified identified = context.getReferenceService().resolveIdentifier(reference, null, context);
 			ReferenceSet referenceSet = (ReferenceSet) identified;

 			if (referenceSet.getExternalReferences().isEmpty()) {
 				data = context.getReferenceService().renderIdentifier(reference,
 						Object.class, context);
 			}
 			else {
 				ExternalReferenceSPI externalReference = referenceSet.getExternalReferences().iterator().next();
 				data = externalReference.openStream(context);
 			}
 		}

 		FileOutputStream fos;
 		try {
 			fos = new FileOutputStream(dataFile);
 			if (data instanceof InputStream) {
 				InputStream inStream = (InputStream)data;
 				int c;
 				while ( ( c = inStream.read() ) != -1  ) {
 					fos.write( (char) c);
 				}
 				fos.flush();
 				fos.close();
 			}
 			if (data instanceof byte[]) {
 				fos.write((byte[]) data);
 				fos.flush();
 				fos.close();
 			} else {
 				PrintWriter out = new PrintWriter(new OutputStreamWriter(fos));
 				out.print(data.toString());
 				out.flush();
 				out.close();
 			}
 		} catch (FileNotFoundException e) {
 			logger.error("Unable to find the file: '"
 					+ dataFile.getAbsolutePath() + "' for writing results", e);
 		} catch (IOException e) {
 			logger.error("IO Error writing resuts to: '"
 					+ dataFile.getAbsolutePath(), e);
 		}
 	}


 }
	/*******************************************************************************
	* 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.data;

	import java.io.File;
	import java.io.FileNotFoundException;
	import java.io.FileOutputStream;
	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStreamWriter;
	import java.io.PrintWriter;
	import java.util.HashMap;
	import java.util.Map;

	import net.sf.taverna.t2.commandline.CommandLineResultListener;
	import net.sf.taverna.t2.invocation.InvocationContext;
	import net.sf.taverna.t2.invocation.WorkflowDataToken;
	import net.sf.taverna.t2.reference.ErrorDocument;
	import net.sf.taverna.t2.reference.ExternalReferenceSPI;
	import net.sf.taverna.t2.reference.Identified;
	import net.sf.taverna.t2.reference.IdentifiedList;
	import net.sf.taverna.t2.reference.ReferenceSet;
	import net.sf.taverna.t2.reference.T2Reference;
	import net.sf.taverna.t2.reference.T2ReferenceType;

	import org.apache.log4j.Logger;

	/**
	* Handles all recording of results as they are received by the {@link CommandLineResultListener}
	* or when the workflow enactment has completed.
	* This includes saving as a Baclava Document, or storing individual results.
	*
	* @author Stuart Owen
	* @see BaclavaDocumentHandler
	* @see CommandLineResultListener
	*
	*/
	public class SaveResultsHandler {

	private final Map<String, Integer> portsAndDepth;
	private HashMap<String, Integer> depthSeen;
	private final File rootDirectory;
	private static Logger logger = Logger
	.getLogger(CommandLineResultListener.class);
	private final File outputDocumentFile;

	public SaveResultsHandler(Map<String, Integer> portsAndDepth,
	File rootDirectory, File outputDocumentFile) {

	this.portsAndDepth = portsAndDepth;
	this.rootDirectory = rootDirectory;
	this.outputDocumentFile = outputDocumentFile;

	depthSeen = new HashMap<String, Integer>();
	for (String portName : portsAndDepth.keySet()) {
	depthSeen.put(portName, -1);
	}
	}

	public void tokenReceived(WorkflowDataToken token, String portName) {
	if (rootDirectory != null) { //only save individual results if a directory is specified
	if (portsAndDepth.containsKey(portName)) {
	int[] index = token.getIndex();
	if (depthSeen.get(portName) == -1)
	depthSeen.put(portName, index.length);
	if (index.length >= depthSeen.get(portName)) {
	storeToken(token, portName);
	}
	} else {
	logger
	.error("Result recieved for unexpected Port: "
	+ portName);
	}
	}
	}

	public void saveOutputDocument(Map<String,WorkflowDataToken> allResults) throws Exception {
	if (outputDocumentFile!=null) {
	new BaclavaDocumentHandler().storeDocument(allResults, outputDocumentFile);
	}
	}

	protected void storeToken(WorkflowDataToken token, String portName) {

	if (token.getData().getReferenceType() == T2ReferenceType.IdentifiedList) {
	saveList(token, portName);
	} else {
	File dataDirectory = rootDirectory;
	File dataFile = null;

	if (token.getIndex().length > 0) {
	dataDirectory = new File(rootDirectory, portName);
	for (int i = 0; i < token.getIndex().length - 1; i++) {
	dataDirectory = new File(dataDirectory, String
	.valueOf(token.getIndex()[i] + 1));
	}
	dataFile = new File(dataDirectory, String.valueOf(token
	.getIndex()[token.getIndex().length - 1] + 1));
	} else {
	dataFile = new File(dataDirectory, portName);
	}

	if (!dataDirectory.exists()) {
	dataDirectory.mkdirs();
	}

	if (dataFile.exists()) {
	System.err.println("There is already data saved to: "
	+ dataFile.getAbsolutePath());
	System.exit(-1);
	}

	saveIndividualDataFile(token.getData(), dataFile, token
	.getContext());
	}
	}

	private void saveList(WorkflowDataToken token, String portName) {
	File dataDirectory = null;
	int[] index = token.getIndex();

	if (index.length > 0) {
	dataDirectory = new File(rootDirectory, portName);
	for (int i = 0; i < index.length - 1; i++) {
	dataDirectory = new File(dataDirectory, String.valueOf(token
	.getIndex()[i] + 1));
	}
	dataDirectory = new File(dataDirectory, String.valueOf(token
	.getIndex()[index.length - 1]+ 1));
	} else {
	dataDirectory = new File(rootDirectory, portName);
	}

	T2Reference reference = token.getData();
	IdentifiedList<T2Reference> list = token.getContext()
	.getReferenceService().getListService().getList(reference);
	saveListItems(token.getContext(), dataDirectory, list);
	}

	private void saveListItems(InvocationContext context, File dataDirectory,IdentifiedList<T2Reference> list) {
	int c = 0;
	if (!dataDirectory.exists()) {
	dataDirectory.mkdirs();
	}
	for (T2Reference id : list) {
	File dataFile = new File(dataDirectory, String.valueOf(c+1));
	if (id.getReferenceType() == T2ReferenceType.IdentifiedList) {
	IdentifiedList<T2Reference> innerList = context
	.getReferenceService().getListService().getList(id);
	saveListItems(context, dataFile, innerList);
	}
	else {
	saveIndividualDataFile(id, dataFile, context);
	}
	c++;
	}
	}

	protected void saveIndividualDataFile(T2Reference reference, File dataFile,
	InvocationContext context) {

	if (dataFile.exists()) {
	System.err.println("There is already data saved to: "
	+ dataFile.getAbsolutePath());
	System.exit(-1);
	}

	Object data = null;
	if (reference.containsErrors()) {
	ErrorDocument errorDoc = context.getReferenceService()
	.getErrorDocumentService().getError(reference);
	data = ErrorDocumentHandler.buildErrorDocumentString(errorDoc, context);
	dataFile = new File(dataFile.getAbsolutePath()+".error");
	} else {
	// FIXME: this really should be done using a stream rather
	// than an instance of the object in memory

	Identified identified = context.getReferenceService().resolveIdentifier(reference, null, context);
	ReferenceSet referenceSet = (ReferenceSet) identified;

	if (referenceSet.getExternalReferences().isEmpty()) {
	data = context.getReferenceService().renderIdentifier(reference,
	Object.class, context);
	}
	else {
	ExternalReferenceSPI externalReference = referenceSet.getExternalReferences().iterator().next();
	data = externalReference.openStream(context);
	}
	}

	FileOutputStream fos;
	try {
	fos = new FileOutputStream(dataFile);
	if (data instanceof InputStream) {
	InputStream inStream = (InputStream)data;
	int c;
	while ( ( c = inStream.read() ) != -1 ) {
	fos.write( (char) c);
	}
	fos.flush();
	fos.close();
	}
	if (data instanceof byte[]) {
	fos.write((byte[]) data);
	fos.flush();
	fos.close();
	} else {
	PrintWriter out = new PrintWriter(new OutputStreamWriter(fos));
	out.print(data.toString());
	out.flush();
	out.close();
	}
	} catch (FileNotFoundException e) {
	logger.error("Unable to find the file: '"
	+ dataFile.getAbsolutePath() + "' for writing results", e);
	} catch (IOException e) {
	logger.error("IO Error writing resuts to: '"
	+ dataFile.getAbsolutePath(), e);
	}
	}


	}