taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivity.java - incubator-taverna-common-activities - Git at Google

 /*******************************************************************************
  * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
  *
  *  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.activities.externaltool;

 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

 import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroup;
 import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
 import net.sf.taverna.t2.annotation.Annotated;
 import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
 import net.sf.taverna.t2.reference.ExternalReferenceSPI;
 import net.sf.taverna.t2.reference.ReferenceService;
 import net.sf.taverna.t2.reference.T2Reference;
 import net.sf.taverna.t2.reference.WorkflowRunIdEntity;
 import net.sf.taverna.t2.workflowmodel.EditException;
 import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
 import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
 import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
 import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
 import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;

 import org.apache.log4j.Logger;

 import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
 import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
 import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
 import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
 import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
 import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;

 /**
  * This is the main class of the use case activity plugin. Here we store the
  * configuration and the description of a use case activity, configure the input
  * and output port and provide use case activity invocation
  *
  * @author Hajo Nils Krabbenhoeft
  */
 public class ExternalToolActivity extends AbstractAsynchronousActivity<ExternalToolActivityConfigurationBean> {

 	public static final String URI = "http://ns.taverna.org.uk/2010/activity/tool";

 	private static final String STDERR = "STDERR";

 	private static final String STDOUT = "STDOUT";

 	private static final String STDIN = "STDIN";

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

 	private ExternalToolActivityConfigurationBean configurationBean;
 	private UseCaseDescription mydesc;

 	private List<InvocationCreator> invocationCreators;

 	/**
 	 * Add the given MIME types to the given input/output port.
 	 *
 	 * @param annotated
 	 *            The port to which to add the MIME types.
 	 * @param mimeTypes
 	 *            A list of Strings specifying the MIME types to add.
 	 */
 	private void addMimeTypes(Annotated<?> annotated, List<String> mimeTypes) {
 		for (String mimeType : mimeTypes) {
 			MimeType mimeTypeAnnotation = new MimeType();
 			mimeTypeAnnotation.setText(mimeType);
 			try {
 				getEdits().getAddAnnotationChainEdit(annotated, mimeTypeAnnotation).doEdit();
 			} catch (EditException e) {
 				Logger.getLogger(ExternalToolActivity.class).error(e);
 			}
 		}
 	}

 	/**
 	 * Create a new input port with the given name, depth, element class and
 	 * MIME types.
 	 *
 	 * @param portName
 	 *            Name of the new port
 	 * @param portDepth
 	 *            Depth of the new port
 	 * @param translatedElementClass
 	 *            Which class of elements would this port like?
 	 * @param mimeTypes
 	 *            Accepted mime types for this port
 	 */
 	private void addInputWithMime(String portName, int portDepth, Class<?> translatedElementClass, List<String> mimeTypes) {
 		List<Class<? extends ExternalReferenceSPI>> handledReferenceSchemes = Collections.emptyList();
 		ActivityInputPort inputPort = getEdits().createActivityInputPort(portName, portDepth, true, handledReferenceSchemes,
 				translatedElementClass);
 		inputPorts.add(inputPort);
 		if (mimeTypes != null) {
 			addMimeTypes(inputPort, mimeTypes);
 		}
 	}

 	/**
 	 * Create a new output port with the given MIME types
 	 *
 	 * @param portName
 	 *            Name of the new port
 	 * @param portDepth
 	 *            Depth of the new port
 	 * @param mimeTypes
 	 *            Accepted mime types for this port
 	 */
 	private void addOutputWithMime(String portName, int portDepth, List<String> mimeTypes) {
 		ActivityOutputPort outputPort = getEdits().createActivityOutputPort(portName, portDepth, portDepth);
 		outputPorts.add(outputPort);
 		addMimeTypes(outputPort, mimeTypes);
 	}

 	@Override
 	public void configure(ExternalToolActivityConfigurationBean bean) throws ActivityConfigurationException {
 		this.configurationBean = bean;

 		try {
 			mydesc = bean.getUseCaseDescription();

 			inputPorts.clear();
 			outputPorts.clear();

 			if (mydesc != null) {

 			// loop through all script inputs and add them as taverna activity
 			// input ports
 			for (Map.Entry<String, ScriptInput> cur : mydesc.getInputs().entrySet()) {
 				ScriptInputUser scriptInputUser = (ScriptInputUser) cur.getValue();
 				// if the input port is a list, depth is 1 otherwise it is a
 				// single element, therefore depth 0
 				// if the input port is binary, we would like byte arrays,
 				// otherwise we require strings
 				addInputWithMime(cur.getKey(), scriptInputUser.isList() ? 1 : 0, cur.getValue().isBinary() ? byte[].class : String.class, scriptInputUser.getMime());

 			}
 			// loop through all script outputs and add them to taverna
 			for (Map.Entry<String, ScriptOutput> cur : mydesc.getOutputs().entrySet()) {
 				addOutputWithMime(cur.getKey(), 0, cur.getValue().getMime());
 			}
 			}

 			if (mydesc.isIncludeStdIn()) {
 				addInputWithMime(STDIN, 0, byte[].class, null);
 			}
 			if (mydesc.isIncludeStdOut()) {
 				addOutput(STDOUT, 0);
 			}
 			if (mydesc.isIncludeStdErr()) {
 				addOutput(STDERR, 0);
 			}
 		} catch (Exception e) {
 			throw new ActivityConfigurationException("Couldn't create ExternalTool Activity", e);
 		}
 	}

 	@Override
 	public ExternalToolActivityConfigurationBean getConfiguration() {
 		if (configurationBean != null) {
 			InvocationGroup invocationGroup = configurationBean.getInvocationGroup();
 			if (invocationGroup == null) {
 				if (configurationBean.getMechanism() != null) {
 					configurationBean.convertMechanismToDetails();
 				}
 			} else {
 				if (invocationGroup.getMechanism() != null) {
 					invocationGroup.convertMechanismToDetails();
 				}
 			}
 		}
 		return configurationBean;
 	}

 	public ExternalToolActivityConfigurationBean getConfigurationNoConversion() {
 		return configurationBean;
 	}

 	public InvocationMechanism recreateMechanism() {
 		if (configurationBean.getInvocationGroup() != null) {
 			if (configurationBean.getInvocationGroup().getMechanism() == null) {
 				configurationBean.getInvocationGroup().convertDetailsToMechanism();
 			}
 			return configurationBean.getInvocationGroup().getMechanism();
 		} else {
 			if (configurationBean.getMechanism() == null) {
 				configurationBean.convertDetailsToMechanism();
 			}
 			return configurationBean.getMechanism();
 		}
 	}

 	@Override
 	public void executeAsynch(final Map<String, T2Reference> data, final AsynchronousActivityCallback callback) {

 		callback.requestRun(new Runnable() {

 			public void run() {
 				ReferenceService referenceService = callback.getContext().getReferenceService();
 				UseCaseInvocation invoke = null;

 				/**
 				 * Note that retrying needs to be either done via Taverna's retry mechanism or as part of the specific invocation
 				 */
 				try {

 					invoke = getInvocation(recreateMechanism(),
 							configurationBean.getUseCaseDescription(), data, referenceService);
 					if (invoke == null) {
 						logger.error("Invoke is null");
 						callback.fail("No invocation mechanism found");
 					}
 					String runId = callback.getContext()
 							.getEntities(WorkflowRunIdEntity.class).get(0)
 							.getWorkflowRunId();
 					logger.info("Run id is " + runId);
 					invoke.rememberRun(runId);

 					invoke.setContext(callback.getContext());

 					// look at every use dynamic case input
 					for (String cur : invoke.getInputs()) {
 						if (!cur.equals(STDIN)) {
 							invoke.setInput(cur, referenceService,
 									data.get(cur));
 						}
 					}

 					if (mydesc.isIncludeStdIn() && (data.get(STDIN) != null)) {
 						invoke.setStdIn(referenceService, data.get(STDIN));
 					}

 					// submit the use case to its invocation mechanism
 					invoke.submit_generate_job(referenceService);

 					// retrieve the result.
 					Map<String, Object> downloads = invoke
 							.submit_wait_fetch_results(referenceService);
 					Map<String, T2Reference> result = new HashMap<String, T2Reference>();
 					for (Map.Entry<String, Object> cur : downloads.entrySet()) {
 						Object value = cur.getValue();

 						// register the result value with taverna
 						T2Reference reference = referenceService.register(
 								value, 0, true, callback.getContext());

 						// store the reference into the activity result
 						// set
 						result.put(cur.getKey(), reference);
 					}
 					callback.receiveResult(result, new int[0]);
 				} catch (InvocationException e) {
 					callback.fail(e.getMessage(), e);
 				}
 			}

 		});

 	}

 	public void setInvocationCreators(List<InvocationCreator> invocationCreators) {
 		this.invocationCreators = invocationCreators;
 	}

 	private UseCaseInvocation getInvocation(InvocationMechanism mechanism, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) {
 		UseCaseInvocation result = null;
 		InvocationCreator creator = null;
 		for (InvocationCreator c : invocationCreators) {
 			if (c.canHandle(mechanism.getType())) {
 				creator = c;
 				break;
 			}
 		}
 		if (creator != null) {
 			result = creator.convert(mechanism, description, data, referenceService);
 		}
 		return result;
 	}

 }
	/*******************************************************************************
	* Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
	*
	* 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.activities.externaltool;

	import java.util.Collections;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Map;

	import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroup;
	import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
	import net.sf.taverna.t2.annotation.Annotated;
	import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
	import net.sf.taverna.t2.reference.ExternalReferenceSPI;
	import net.sf.taverna.t2.reference.ReferenceService;
	import net.sf.taverna.t2.reference.T2Reference;
	import net.sf.taverna.t2.reference.WorkflowRunIdEntity;
	import net.sf.taverna.t2.workflowmodel.EditException;
	import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
	import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
	import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
	import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
	import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;

	import org.apache.log4j.Logger;

	import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
	import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
	import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
	import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
	import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
	import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;

	/**
	* This is the main class of the use case activity plugin. Here we store the
	* configuration and the description of a use case activity, configure the input
	* and output port and provide use case activity invocation
	*
	* @author Hajo Nils Krabbenhoeft
	*/
	public class ExternalToolActivity extends AbstractAsynchronousActivity<ExternalToolActivityConfigurationBean> {

	public static final String URI = "http://ns.taverna.org.uk/2010/activity/tool";

	private static final String STDERR = "STDERR";

	private static final String STDOUT = "STDOUT";

	private static final String STDIN = "STDIN";

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

	private ExternalToolActivityConfigurationBean configurationBean;
	private UseCaseDescription mydesc;

	private List<InvocationCreator> invocationCreators;

	/**
	* Add the given MIME types to the given input/output port.
	*
	* @param annotated
	* The port to which to add the MIME types.
	* @param mimeTypes
	* A list of Strings specifying the MIME types to add.
	*/
	private void addMimeTypes(Annotated<?> annotated, List<String> mimeTypes) {
	for (String mimeType : mimeTypes) {
	MimeType mimeTypeAnnotation = new MimeType();
	mimeTypeAnnotation.setText(mimeType);
	try {
	getEdits().getAddAnnotationChainEdit(annotated, mimeTypeAnnotation).doEdit();
	} catch (EditException e) {
	Logger.getLogger(ExternalToolActivity.class).error(e);
	}
	}
	}

	/**
	* Create a new input port with the given name, depth, element class and
	* MIME types.
	*
	* @param portName
	* Name of the new port
	* @param portDepth
	* Depth of the new port
	* @param translatedElementClass
	* Which class of elements would this port like?
	* @param mimeTypes
	* Accepted mime types for this port
	*/
	private void addInputWithMime(String portName, int portDepth, Class<?> translatedElementClass, List<String> mimeTypes) {
	List<Class<? extends ExternalReferenceSPI>> handledReferenceSchemes = Collections.emptyList();
	ActivityInputPort inputPort = getEdits().createActivityInputPort(portName, portDepth, true, handledReferenceSchemes,
	translatedElementClass);
	inputPorts.add(inputPort);
	if (mimeTypes != null) {
	addMimeTypes(inputPort, mimeTypes);
	}
	}

	/**
	* Create a new output port with the given MIME types
	*
	* @param portName
	* Name of the new port
	* @param portDepth
	* Depth of the new port
	* @param mimeTypes
	* Accepted mime types for this port
	*/
	private void addOutputWithMime(String portName, int portDepth, List<String> mimeTypes) {
	ActivityOutputPort outputPort = getEdits().createActivityOutputPort(portName, portDepth, portDepth);
	outputPorts.add(outputPort);
	addMimeTypes(outputPort, mimeTypes);
	}

	@Override
	public void configure(ExternalToolActivityConfigurationBean bean) throws ActivityConfigurationException {
	this.configurationBean = bean;

	try {
	mydesc = bean.getUseCaseDescription();

	inputPorts.clear();
	outputPorts.clear();

	if (mydesc != null) {

	// loop through all script inputs and add them as taverna activity
	// input ports
	for (Map.Entry<String, ScriptInput> cur : mydesc.getInputs().entrySet()) {
	ScriptInputUser scriptInputUser = (ScriptInputUser) cur.getValue();
	// if the input port is a list, depth is 1 otherwise it is a
	// single element, therefore depth 0
	// if the input port is binary, we would like byte arrays,
	// otherwise we require strings
	addInputWithMime(cur.getKey(), scriptInputUser.isList() ? 1 : 0, cur.getValue().isBinary() ? byte[].class : String.class, scriptInputUser.getMime());

	}
	// loop through all script outputs and add them to taverna
	for (Map.Entry<String, ScriptOutput> cur : mydesc.getOutputs().entrySet()) {
	addOutputWithMime(cur.getKey(), 0, cur.getValue().getMime());
	}
	}

	if (mydesc.isIncludeStdIn()) {
	addInputWithMime(STDIN, 0, byte[].class, null);
	}
	if (mydesc.isIncludeStdOut()) {
	addOutput(STDOUT, 0);
	}
	if (mydesc.isIncludeStdErr()) {
	addOutput(STDERR, 0);
	}
	} catch (Exception e) {
	throw new ActivityConfigurationException("Couldn't create ExternalTool Activity", e);
	}
	}

	@Override
	public ExternalToolActivityConfigurationBean getConfiguration() {
	if (configurationBean != null) {
	InvocationGroup invocationGroup = configurationBean.getInvocationGroup();
	if (invocationGroup == null) {
	if (configurationBean.getMechanism() != null) {
	configurationBean.convertMechanismToDetails();
	}
	} else {
	if (invocationGroup.getMechanism() != null) {
	invocationGroup.convertMechanismToDetails();
	}
	}
	}
	return configurationBean;
	}

	public ExternalToolActivityConfigurationBean getConfigurationNoConversion() {
	return configurationBean;
	}

	public InvocationMechanism recreateMechanism() {
	if (configurationBean.getInvocationGroup() != null) {
	if (configurationBean.getInvocationGroup().getMechanism() == null) {
	configurationBean.getInvocationGroup().convertDetailsToMechanism();
	}
	return configurationBean.getInvocationGroup().getMechanism();
	} else {
	if (configurationBean.getMechanism() == null) {
	configurationBean.convertDetailsToMechanism();
	}
	return configurationBean.getMechanism();
	}
	}

	@Override
	public void executeAsynch(final Map<String, T2Reference> data, final AsynchronousActivityCallback callback) {

	callback.requestRun(new Runnable() {

	public void run() {
	ReferenceService referenceService = callback.getContext().getReferenceService();
	UseCaseInvocation invoke = null;

	/**
	* Note that retrying needs to be either done via Taverna's retry mechanism or as part of the specific invocation
	*/
	try {

	invoke = getInvocation(recreateMechanism(),
	configurationBean.getUseCaseDescription(), data, referenceService);
	if (invoke == null) {
	logger.error("Invoke is null");
	callback.fail("No invocation mechanism found");
	}
	String runId = callback.getContext()
	.getEntities(WorkflowRunIdEntity.class).get(0)
	.getWorkflowRunId();
	logger.info("Run id is " + runId);
	invoke.rememberRun(runId);

	invoke.setContext(callback.getContext());

	// look at every use dynamic case input
	for (String cur : invoke.getInputs()) {
	if (!cur.equals(STDIN)) {
	invoke.setInput(cur, referenceService,
	data.get(cur));
	}
	}

	if (mydesc.isIncludeStdIn() && (data.get(STDIN) != null)) {
	invoke.setStdIn(referenceService, data.get(STDIN));
	}

	// submit the use case to its invocation mechanism
	invoke.submit_generate_job(referenceService);

	// retrieve the result.
	Map<String, Object> downloads = invoke
	.submit_wait_fetch_results(referenceService);
	Map<String, T2Reference> result = new HashMap<String, T2Reference>();
	for (Map.Entry<String, Object> cur : downloads.entrySet()) {
	Object value = cur.getValue();

	// register the result value with taverna
	T2Reference reference = referenceService.register(
	value, 0, true, callback.getContext());

	// store the reference into the activity result
	// set
	result.put(cur.getKey(), reference);
	}
	callback.receiveResult(result, new int[0]);
	} catch (InvocationException e) {
	callback.fail(e.getMessage(), e);
	}
	}

	});

	}

	public void setInvocationCreators(List<InvocationCreator> invocationCreators) {
	this.invocationCreators = invocationCreators;
	}

	private UseCaseInvocation getInvocation(InvocationMechanism mechanism, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) {
	UseCaseInvocation result = null;
	InvocationCreator creator = null;
	for (InvocationCreator c : invocationCreators) {
	if (c.canHandle(mechanism.getType())) {
	creator = c;
	break;
	}
	}
	if (creator != null) {
	result = creator.convert(mechanism, description, data, referenceService);
	}
	return result;
	}

	}