taverna-commandline-1.2/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.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.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;

 import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
 import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
 import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
 import net.sf.taverna.t2.commandline.options.CommandLineOptions;
 import net.sf.taverna.t2.invocation.InvocationContext;
 import net.sf.taverna.t2.invocation.WorkflowDataToken;
 import net.sf.taverna.t2.reference.T2Reference;
 import net.sf.taverna.t2.workflowmodel.DataflowInputPort;

 import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
 import org.embl.ebi.escience.baclava.DataThing;

 /**
  *
  * Handles the reading, or processing, or input values according to arguments provided to the commandline.
  * The may be either as direct values, from a file, or from a Baclava document.
  *
  * Also handles registering the input values with the Reference Service, ready to initiate
  * the workflow run.
  *
  * @author Stuart Owen
  *
  */
 public class InputsHandler {

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


 	public void checkProvidedInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options) throws InputMismatchException  {
 		//we dont check for the document
 		if (options.getInputDocument()==null) {
 			Set<String> providedInputNames = new HashSet<String>();
 			for (int i=0;i<options.getInputFiles().length;i+=2) {
 				providedInputNames.add(options.getInputFiles()[i]);
 			}

 			for (int i=0;i<options.getInputValues().length;i+=2) {
 				providedInputNames.add(options.getInputValues()[i]);
 			}

 			if (portMap.size()*2 != (options.getInputFiles().length + options.getInputValues().length)) {
 				throw new InputMismatchException("The number of inputs provided does not match the number of input ports.",portMap.keySet(),providedInputNames);
 			}

 			for (String portName : portMap.keySet()) {
 				if (!providedInputNames.contains(portName)) {
 					throw new InputMismatchException("The provided inputs does not contain an input for the port '"+portName+"'",portMap.keySet(),providedInputNames);
 				}
 			}
 		}
 	}


 	public Map<String, WorkflowDataToken> registerInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options,
 			InvocationContext context) throws InvalidOptionException, ReadInputException  {
 		Map<String,WorkflowDataToken> inputs = new HashMap<String, WorkflowDataToken>();
 		URL url;
 		try {
 			url = new URL("file:");
 		} catch (MalformedURLException e1) {
 			//Should never happen, but just incase:
 			throw new ReadInputException("The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",e1);
 		}

 		if (options.hasInputFiles()) {
 			String[] inputParams = options.getInputFiles();
 			for (int i = 0; i < inputParams.length; i = i + 2) {
 				String inputName = inputParams[i];
 				try {
 					URL inputURL = new URL(url, inputParams[i + 1]);
 					DataflowInputPort port = portMap.get(inputName);

 					if (port==null) {
 						throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
 					}

 					T2Reference entityId=null;

 					if (options.hasDelimiterFor(inputName)) {
 						String delimiter=options.inputDelimiter(inputName);
 						Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);

 						value=checkForDepthMismatch(1, port.getDepth(), inputName, value);
 						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
 					}
 					else
 					{
 						Object value = IOUtils.toByteArray(inputURL.openStream());
 						value=checkForDepthMismatch(0, port.getDepth(), inputName, value);
 						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
 					}

 					WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
 					inputs.put(inputName, token);

 				} catch (IndexOutOfBoundsException e) {
 					throw new InvalidOptionException("Missing input filename for input "+ inputName);
 				} catch (IOException e) {
 					throw new InvalidOptionException("Could not read input " + inputName + ": " + e.getMessage());
 				}
 			}
 		}

 		if (options.hasInputValues()) {
 			String[] inputParams = options.getInputValues();
 			for (int i = 0; i < inputParams.length; i = i + 2) {
 				String inputName = inputParams[i];
 				try {
 					String inputValue = inputParams[i + 1];
 					DataflowInputPort port = portMap.get(inputName);

 					if (port==null) {
 						throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
 					}

 					T2Reference entityId=null;
 					if (options.hasDelimiterFor(inputName)) {
 						String delimiter=options.inputDelimiter(inputName);
 						Object value=checkForDepthMismatch(1, port.getDepth(), inputName, inputValue.split(delimiter));
 						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
 					}
 					else
 					{
 						Object value=checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
 						entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
 					}

 					WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
 					inputs.put(inputName, token);

 				} catch (IndexOutOfBoundsException e) {
 					throw new InvalidOptionException("Missing input value for input "+ inputName);
 				}
 			}

 		}

 		if (options.getInputDocument()!=null) {
 			String inputDocPath = options.getInputDocument();
 			Map<String, DataThing> things = new BaclavaDocumentHandler().readInputDocument(inputDocPath);
 			for (String inputName : things.keySet()) {
 				DataThing thing = things.get(inputName);
 				Object object = thing.getDataObject();
 				T2Reference entityId=context.getReferenceService().register(object,getObjectDepth(object), true, context);
 				WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
 				inputs.put(inputName, token);
 			}
 		}

 		return inputs;
 	}

 	private Object checkForDepthMismatch(int inputDepth,int portDepth,String inputName,Object inputValue) throws InvalidOptionException {
 		if (inputDepth!=portDepth) {
 			if (inputDepth<portDepth) {
 				logger.warn("Wrapping input for '" + inputName + "' from a depth of "+inputDepth+" to the required depth of "+portDepth);
 				while (inputDepth<portDepth) {
 					List<Object> l=new ArrayList<Object>();
 					l.add(inputValue);
 					inputValue=l;
 					inputDepth++;
 				}
 			}
 			else {
 				String msg="There is a mismatch between depth of the list for the input port '"+inputName+"' and the data presented. The input port requires a "+depthToString(portDepth)+" and the data presented is a "+depthToString(inputDepth);
 				throw new InvalidOptionException(msg);
 			}
 		}

 		return inputValue;
 	}

 	private String depthToString(int depth) {
 		switch (depth) {
 		case 0:
 			return "single item";
 		case 1:
 			return "list";
 		case 2:
 			return "list of lists";
 		default:
 			return "list of depth "+depth;
 		}
 	}


 	@SuppressWarnings("unchecked")
 	private int getObjectDepth(Object o) {
 		int result = 0;
 		if (o instanceof Iterable) {
 			result++;
 			Iterator i = ((Iterable) o).iterator();

 			if (i.hasNext()) {
 				Object child = i.next();
 				result = result + getObjectDepth(child);
 			}
 		}
 		return result;
 	}
 }
	/*******************************************************************************
	* 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.IOException;
	import java.net.MalformedURLException;
	import java.net.URL;
	import java.util.ArrayList;
	import java.util.HashMap;
	import java.util.HashSet;
	import java.util.Iterator;
	import java.util.List;
	import java.util.Map;
	import java.util.Set;

	import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
	import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
	import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
	import net.sf.taverna.t2.commandline.options.CommandLineOptions;
	import net.sf.taverna.t2.invocation.InvocationContext;
	import net.sf.taverna.t2.invocation.WorkflowDataToken;
	import net.sf.taverna.t2.reference.T2Reference;
	import net.sf.taverna.t2.workflowmodel.DataflowInputPort;

	import org.apache.commons.io.IOUtils;
	import org.apache.log4j.Logger;
	import org.embl.ebi.escience.baclava.DataThing;

	/**
	*
	* Handles the reading, or processing, or input values according to arguments provided to the commandline.
	* The may be either as direct values, from a file, or from a Baclava document.
	*
	* Also handles registering the input values with the Reference Service, ready to initiate
	* the workflow run.
	*
	* @author Stuart Owen
	*
	*/
	public class InputsHandler {

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


	public void checkProvidedInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options) throws InputMismatchException {
	//we dont check for the document
	if (options.getInputDocument()==null) {
	Set<String> providedInputNames = new HashSet<String>();
	for (int i=0;i<options.getInputFiles().length;i+=2) {
	providedInputNames.add(options.getInputFiles()[i]);
	}

	for (int i=0;i<options.getInputValues().length;i+=2) {
	providedInputNames.add(options.getInputValues()[i]);
	}

	if (portMap.size()*2 != (options.getInputFiles().length + options.getInputValues().length)) {
	throw new InputMismatchException("The number of inputs provided does not match the number of input ports.",portMap.keySet(),providedInputNames);
	}

	for (String portName : portMap.keySet()) {
	if (!providedInputNames.contains(portName)) {
	throw new InputMismatchException("The provided inputs does not contain an input for the port '"+portName+"'",portMap.keySet(),providedInputNames);
	}
	}
	}
	}


	public Map<String, WorkflowDataToken> registerInputs(Map<String, DataflowInputPort> portMap, CommandLineOptions options,
	InvocationContext context) throws InvalidOptionException, ReadInputException {
	Map<String,WorkflowDataToken> inputs = new HashMap<String, WorkflowDataToken>();
	URL url;
	try {
	url = new URL("file:");
	} catch (MalformedURLException e1) {
	//Should never happen, but just incase:
	throw new ReadInputException("The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",e1);
	}

	if (options.hasInputFiles()) {
	String[] inputParams = options.getInputFiles();
	for (int i = 0; i < inputParams.length; i = i + 2) {
	String inputName = inputParams[i];
	try {
	URL inputURL = new URL(url, inputParams[i + 1]);
	DataflowInputPort port = portMap.get(inputName);

	if (port==null) {
	throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
	}

	T2Reference entityId=null;

	if (options.hasDelimiterFor(inputName)) {
	String delimiter=options.inputDelimiter(inputName);
	Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);

	value=checkForDepthMismatch(1, port.getDepth(), inputName, value);
	entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
	}
	else
	{
	Object value = IOUtils.toByteArray(inputURL.openStream());
	value=checkForDepthMismatch(0, port.getDepth(), inputName, value);
	entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
	}

	WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
	inputs.put(inputName, token);

	} catch (IndexOutOfBoundsException e) {
	throw new InvalidOptionException("Missing input filename for input "+ inputName);
	} catch (IOException e) {
	throw new InvalidOptionException("Could not read input " + inputName + ": " + e.getMessage());
	}
	}
	}

	if (options.hasInputValues()) {
	String[] inputParams = options.getInputValues();
	for (int i = 0; i < inputParams.length; i = i + 2) {
	String inputName = inputParams[i];
	try {
	String inputValue = inputParams[i + 1];
	DataflowInputPort port = portMap.get(inputName);

	if (port==null) {
	throw new InvalidOptionException("Cannot find an input port named '"+inputName+"'");
	}

	T2Reference entityId=null;
	if (options.hasDelimiterFor(inputName)) {
	String delimiter=options.inputDelimiter(inputName);
	Object value=checkForDepthMismatch(1, port.getDepth(), inputName, inputValue.split(delimiter));
	entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
	}
	else
	{
	Object value=checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
	entityId=context.getReferenceService().register(value, port.getDepth(), true, context);
	}

	WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
	inputs.put(inputName, token);

	} catch (IndexOutOfBoundsException e) {
	throw new InvalidOptionException("Missing input value for input "+ inputName);
	}
	}

	}

	if (options.getInputDocument()!=null) {
	String inputDocPath = options.getInputDocument();
	Map<String, DataThing> things = new BaclavaDocumentHandler().readInputDocument(inputDocPath);
	for (String inputName : things.keySet()) {
	DataThing thing = things.get(inputName);
	Object object = thing.getDataObject();
	T2Reference entityId=context.getReferenceService().register(object,getObjectDepth(object), true, context);
	WorkflowDataToken token = new WorkflowDataToken("",new int[]{}, entityId, context);
	inputs.put(inputName, token);
	}
	}

	return inputs;
	}

	private Object checkForDepthMismatch(int inputDepth,int portDepth,String inputName,Object inputValue) throws InvalidOptionException {
	if (inputDepth!=portDepth) {
	if (inputDepth<portDepth) {
	logger.warn("Wrapping input for '" + inputName + "' from a depth of "+inputDepth+" to the required depth of "+portDepth);
	while (inputDepth<portDepth) {
	List<Object> l=new ArrayList<Object>();
	l.add(inputValue);
	inputValue=l;
	inputDepth++;
	}
	}
	else {
	String msg="There is a mismatch between depth of the list for the input port '"+inputName+"' and the data presented. The input port requires a "+depthToString(portDepth)+" and the data presented is a "+depthToString(inputDepth);
	throw new InvalidOptionException(msg);
	}
	}

	return inputValue;
	}

	private String depthToString(int depth) {
	switch (depth) {
	case 0:
	return "single item";
	case 1:
	return "list";
	case 2:
	return "list of lists";
	default:
	return "list of depth "+depth;
	}
	}


	@SuppressWarnings("unchecked")
	private int getObjectDepth(Object o) {
	int result = 0;
	if (o instanceof Iterable) {
	result++;
	Iterator i = ((Iterable) o).iterator();

	if (i.hasNext()) {
	Object child = i.next();
	result = result + getObjectDepth(child);
	}
	}
	return result;
	}
	}