taverna-scufl2-t2flow/src/test/java/org/apache/taverna/scufl2/translator/t2flow/TestBeanshellActivityParser.java - incubator-taverna-language - Git at Google

 package org.apache.taverna.scufl2.translator.t2flow;
 /*
  *
  * Licensed to the Apache Software Foundation (ASF) under one
  * or more contributor license agreements.  See the NOTICE file
  * distributed with this work for additional information
  * regarding copyright ownership.  The ASF licenses this file
  * to you under the Apache License, Version 2.0 (the
  * "License"); you may not use this file except in compliance
  * with the License.  You may obtain a copy of the License at
  *
  *   http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing,
  * software distributed under the License is distributed on an
  * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
  * KIND, either express or implied.  See the License for the
  * specific language governing permissions and limitations
  * under the License.
  *
 */


 import static org.apache.taverna.scufl2.translator.t2flow.defaultactivities.BeanshellActivityParser.ACTIVITY_URI;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;

 import java.net.URL;
 import java.util.Arrays;
 import java.util.HashSet;
 import java.util.Set;

 import org.apache.taverna.scufl2.api.activity.Activity;
 import org.apache.taverna.scufl2.api.common.Scufl2Tools;
 import org.apache.taverna.scufl2.api.configurations.Configuration;
 import org.apache.taverna.scufl2.api.container.WorkflowBundle;
 import org.apache.taverna.scufl2.api.core.Processor;
 import org.apache.taverna.scufl2.api.port.InputActivityPort;
 import org.apache.taverna.scufl2.api.profiles.Profile;
 import org.apache.taverna.scufl2.translator.t2flow.T2FlowParser;
 import org.junit.Test;


 import com.fasterxml.jackson.databind.node.ObjectNode;

 public class TestBeanshellActivityParser {

 	private static final String WF_AS = "/as.t2flow";
 	private static final String WF_BEANSHELL_DEPS = "/beanshell-deps.t2flow";

 	private static Scufl2Tools scufl2Tools = new Scufl2Tools();

 	@Test
 	public void parseBeanshellScript() throws Exception {
 		URL wfResource = getClass().getResource(WF_AS);
 		assertNotNull("Could not find workflow " + WF_AS, wfResource);
 		T2FlowParser parser = new T2FlowParser();
 		parser.setValidating(true);
 		parser.setStrict(true);
 		WorkflowBundle researchObj = parser
 				.parseT2Flow(wfResource.openStream());
 		// System.out.println(researchObj.getProfiles().iterator().next()
 		// .getConfigurations());
 		Profile profile = researchObj.getProfiles().getByName("taverna-2.1.0");
 		// Processors: [Workflow19, Echo_List, Concatenate_two_strings,
 		// Concatenate_two_strings_2, Concatenate_two_strings_3,
 		// Concatenate_two_strings_4, Create_Lots_Of_Strings, String_constant]
 		Processor concat = researchObj.getMainWorkflow().getProcessors()
 				.getByName("Concatenate_two_strings");

 		Configuration concatConfig = scufl2Tools
 				.configurationForActivityBoundToProcessor(concat, profile);
 		Activity concatAct = (Activity) concatConfig.getConfigures();
 		assertEquals(ACTIVITY_URI,
 				concatAct.getType());

 		ObjectNode configResource = concatConfig.getJsonAsObjectNode();
 		assertEquals(ACTIVITY_URI.resolve("#Config"), concatConfig.getType());

 		assertEquals("http://ns.taverna.org.uk/2010/activity/localworker/org.embl.ebi.escience.scuflworkers.java.StringConcat",
 				configResource.get("derivedFrom").asText());

 		String script = configResource.get("script").asText();
 		assertEquals("output = string1 + string2;", script);

 		assertFalse(configResource.has("classLoader"));
 		assertFalse(configResource.has("dependency"));


 		Set<String> expectedInputs = new HashSet<String>(Arrays.asList(
 				"string1", "string2"));
 		assertEquals(expectedInputs, concatAct.getInputPorts().getNames());
 		InputActivityPort s1 = concatAct.getInputPorts().getByName("string1");
 		assertEquals(0, s1.getDepth().intValue());
 		InputActivityPort s2 = concatAct.getInputPorts().getByName("string2");
 		assertEquals(0, s2.getDepth().intValue());

 		/** TODO: Update tests
 		Set<PropertyResource> inputDef = configResource
 				.getPropertiesAsResources(
 						PORT_DEFINITION.resolve("#inputPortDefinition"));
 		assertEquals(2, inputDef.size());

 		Set<URI> expectedPortUris = new HashSet<URI>();
 		for (InputActivityPort inPort : concatAct.getInputPorts()) {
 			expectedPortUris.add(new URITools().relativeUriForBean(inPort,
 					concatConfig));
 		}
 		assertEquals(2, expectedPortUris.size());
 		assertEquals(2, inputDef.size());
 		for (PropertyResource portDef : inputDef) {
 			assertEquals(PORT_DEFINITION.resolve("#InputPortDefinition"),
 					portDef.getTypeURI());
 			assertNull(portDef.getResourceURI());
 			URI dataType = portDef.getPropertyAsResourceURI(PORT_DEFINITION
 					.resolve("#dataType"));

 			assertEquals("java", dataType.getScheme());
 			assertEquals("java.lang.String", dataType
 					.getSchemeSpecificPart());

 			URI portURI = portDef.getPropertyAsResourceURI(PORT_DEFINITION
 					.resolve("#definesInputPort"));
 			assertTrue("Unknown port " + portURI,
 					expectedPortUris.contains(portURI));

 		}

 		// TODO: Is java class here OK? It's a beanshell script after all..

 		Set<String> expectedOutputs = new HashSet<String>(
 				Arrays.asList("output"));
 		assertEquals(expectedOutputs, concatAct.getOutputPorts().getNames());
 		OutputActivityPort out = concatAct.getOutputPorts().getByName("output");
 		assertEquals(0, out.getDepth().intValue());

 		Set<PropertyResource> outputDef = configResource
 				.getPropertiesAsResources(
 						PORT_DEFINITION.resolve("#outputPortDefinition"));
 		assertEquals(1, outputDef.size());
 		PropertyResource out1Def = outputDef.iterator().next();
 		assertEquals(PORT_DEFINITION.resolve("#OutputPortDefinition"),
 				out1Def.getTypeURI());

 		Set<URI> mimeTypes = out1Def.getPropertiesAsResourceURIs(PORT_DEFINITION
 				.resolve("#expectedMimeType"));
 		assertEquals(1, mimeTypes.size());

 		assertEquals(URI.create("http://purl.org/NET/mediatypes/text/plain"),
 				mimeTypes.iterator().next());

 		 */

 		Processor echoList = researchObj.getMainWorkflow().getProcessors()
 				.getByName("Echo_List");
 		Configuration echoConfig = scufl2Tools
 				.configurationForActivityBoundToProcessor(echoList, profile);
 		Activity echoAct = (Activity) echoConfig.getConfigures();

 		expectedInputs = new HashSet<String>(Arrays.asList("inputlist"));
 		assertEquals(expectedInputs, echoAct.getInputPorts().getNames());
 		InputActivityPort inputList = echoAct.getInputPorts().getByName(
 				"inputlist");
 		assertEquals(1, inputList.getDepth().intValue());
 		/* TODO: Update tests
 		expectedOutputs = new HashSet<String>(Arrays.asList("outputlist"));
 		assertEquals(expectedOutputs, echoAct.getOutputPorts().getNames());
 		OutputActivityPort outputList = echoAct.getOutputPorts().getByName(
 				"outputlist");
 		assertEquals(1, outputList.getDepth().intValue());
 		*/
 	}


 	@Test
 	public void beanshellDependencies() throws Exception {
 		URL wfResource = getClass().getResource(WF_BEANSHELL_DEPS);
 		assertNotNull("Could not find workflow " + WF_BEANSHELL_DEPS, wfResource);
 		T2FlowParser parser = new T2FlowParser();
 		parser.setValidating(true);
 		parser.setStrict(true);
 		WorkflowBundle wfBundle = parser
 				.parseT2Flow(wfResource.openStream());

 		Profile profile = wfBundle.getMainProfile();
 		// Processors: [Workflow19, Echo_List, Concatenate_two_strings,
 		// Concatenate_two_strings_2, Concatenate_two_strings_3,
 		// Concatenate_two_strings_4, Create_Lots_Of_Strings, String_constant]
 		Processor a_c_workflow = wfBundle.getMainWorkflow().getProcessors()
 				.getByName("A_C_workflow");
 		Configuration a_c_config = scufl2Tools
 				.configurationForActivityBoundToProcessor(a_c_workflow, profile);
 		assertNotNull(a_c_config);
 		Configuration c2 = a_c_workflow.getActivityConfiguration(profile);
 		assertEquals(a_c_config,c2);
 /* TODO: Update tests
 		PropertyResource a_c_configResource = a_c_config.getJson();

 		assertFalse(a_c_configResource.hasProperty(ACTIVITY_URI.resolve("#derivedFrom")));
 		SortedSet<PropertyResource> deps = a_c_configResource.getPropertiesAsResources(DEPENDENCY_URI.resolve("#dependency"));
 		Set<String> jars = new HashSet<String>();
 		for (PropertyResource dep : deps) {
 			assertEquals(DEPENDENCY_URI.resolve("#LocalJarDependency"), dep.getTypeURI());
 			jars.add(dep.getPropertyAsString(DEPENDENCY_URI.resolve("#jarFile")));
 		}
 		assertEquals(new HashSet<String>(Arrays.asList("libraryA.jar", "libraryC.jar")),
 				jars);
 		assertFalse(a_c_configResource.hasProperty(DEPENDENCY_URI.resolve("#classLoader")));


 		Processor b_system = wfBundle.getMainWorkflow().getProcessors()
 				.getByName("B_system");
 		Configuration b_config = scufl2Tools
 				.configurationForActivityBoundToProcessor(b_system, profile);

 		PropertyResource b_configResource = b_config.getJson();

 		deps = b_configResource.getPropertiesAsResources(DEPENDENCY_URI.resolve("#dependency"));
 		jars = new HashSet<String>();
 		for (PropertyResource dep : deps) {
 			assertEquals(DEPENDENCY_URI.resolve("#LocalJarDependency"), dep.getTypeURI());
 			jars.add(dep.getPropertyAsString(DEPENDENCY_URI.resolve("#jarFile")));
 		}
 		assertEquals(new HashSet<String>(Arrays.asList("libraryB.jar")),
 				jars);
 		assertTrue(b_configResource.hasProperty(DEPENDENCY_URI.resolve("#classLoader")));
 		assertEquals(DEPENDENCY_URI.resolve("#SystemClassLoader"),
 				b_configResource.getPropertyAsResourceURI(DEPENDENCY_URI.resolve("#classLoader")));

  */

 	}


 }
	package org.apache.taverna.scufl2.translator.t2flow;
	/*
	*
	* Licensed to the Apache Software Foundation (ASF) under one
	* or more contributor license agreements. See the NOTICE file
	* distributed with this work for additional information
	* regarding copyright ownership. The ASF licenses this file
	* to you under the Apache License, Version 2.0 (the
	* "License"); you may not use this file except in compliance
	* with the License. You may obtain a copy of the License at
	*
	* http://www.apache.org/licenses/LICENSE-2.0
	*
	* Unless required by applicable law or agreed to in writing,
	* software distributed under the License is distributed on an
	* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
	* KIND, either express or implied. See the License for the
	* specific language governing permissions and limitations
	* under the License.
	*
	*/


	import static org.apache.taverna.scufl2.translator.t2flow.defaultactivities.BeanshellActivityParser.ACTIVITY_URI;
	import static org.junit.Assert.assertEquals;
	import static org.junit.Assert.assertFalse;
	import static org.junit.Assert.assertNotNull;

	import java.net.URL;
	import java.util.Arrays;
	import java.util.HashSet;
	import java.util.Set;

	import org.apache.taverna.scufl2.api.activity.Activity;
	import org.apache.taverna.scufl2.api.common.Scufl2Tools;
	import org.apache.taverna.scufl2.api.configurations.Configuration;
	import org.apache.taverna.scufl2.api.container.WorkflowBundle;
	import org.apache.taverna.scufl2.api.core.Processor;
	import org.apache.taverna.scufl2.api.port.InputActivityPort;
	import org.apache.taverna.scufl2.api.profiles.Profile;
	import org.apache.taverna.scufl2.translator.t2flow.T2FlowParser;
	import org.junit.Test;


	import com.fasterxml.jackson.databind.node.ObjectNode;

	public class TestBeanshellActivityParser {

	private static final String WF_AS = "/as.t2flow";
	private static final String WF_BEANSHELL_DEPS = "/beanshell-deps.t2flow";

	private static Scufl2Tools scufl2Tools = new Scufl2Tools();

	@Test
	public void parseBeanshellScript() throws Exception {
	URL wfResource = getClass().getResource(WF_AS);
	assertNotNull("Could not find workflow " + WF_AS, wfResource);
	T2FlowParser parser = new T2FlowParser();
	parser.setValidating(true);
	parser.setStrict(true);
	WorkflowBundle researchObj = parser
	.parseT2Flow(wfResource.openStream());
	// System.out.println(researchObj.getProfiles().iterator().next()
	// .getConfigurations());
	Profile profile = researchObj.getProfiles().getByName("taverna-2.1.0");
	// Processors: [Workflow19, Echo_List, Concatenate_two_strings,
	// Concatenate_two_strings_2, Concatenate_two_strings_3,
	// Concatenate_two_strings_4, Create_Lots_Of_Strings, String_constant]
	Processor concat = researchObj.getMainWorkflow().getProcessors()
	.getByName("Concatenate_two_strings");

	Configuration concatConfig = scufl2Tools
	.configurationForActivityBoundToProcessor(concat, profile);
	Activity concatAct = (Activity) concatConfig.getConfigures();
	assertEquals(ACTIVITY_URI,
	concatAct.getType());

	ObjectNode configResource = concatConfig.getJsonAsObjectNode();
	assertEquals(ACTIVITY_URI.resolve("#Config"), concatConfig.getType());

	assertEquals("http://ns.taverna.org.uk/2010/activity/localworker/org.embl.ebi.escience.scuflworkers.java.StringConcat",
	configResource.get("derivedFrom").asText());

	String script = configResource.get("script").asText();
	assertEquals("output = string1 + string2;", script);

	assertFalse(configResource.has("classLoader"));
	assertFalse(configResource.has("dependency"));


	Set<String> expectedInputs = new HashSet<String>(Arrays.asList(
	"string1", "string2"));
	assertEquals(expectedInputs, concatAct.getInputPorts().getNames());
	InputActivityPort s1 = concatAct.getInputPorts().getByName("string1");
	assertEquals(0, s1.getDepth().intValue());
	InputActivityPort s2 = concatAct.getInputPorts().getByName("string2");
	assertEquals(0, s2.getDepth().intValue());

	/** TODO: Update tests
	Set<PropertyResource> inputDef = configResource
	.getPropertiesAsResources(
	PORT_DEFINITION.resolve("#inputPortDefinition"));
	assertEquals(2, inputDef.size());

	Set<URI> expectedPortUris = new HashSet<URI>();
	for (InputActivityPort inPort : concatAct.getInputPorts()) {
	expectedPortUris.add(new URITools().relativeUriForBean(inPort,
	concatConfig));
	}
	assertEquals(2, expectedPortUris.size());
	assertEquals(2, inputDef.size());
	for (PropertyResource portDef : inputDef) {
	assertEquals(PORT_DEFINITION.resolve("#InputPortDefinition"),
	portDef.getTypeURI());
	assertNull(portDef.getResourceURI());
	URI dataType = portDef.getPropertyAsResourceURI(PORT_DEFINITION
	.resolve("#dataType"));

	assertEquals("java", dataType.getScheme());
	assertEquals("java.lang.String", dataType
	.getSchemeSpecificPart());

	URI portURI = portDef.getPropertyAsResourceURI(PORT_DEFINITION
	.resolve("#definesInputPort"));
	assertTrue("Unknown port " + portURI,
	expectedPortUris.contains(portURI));

	}

	// TODO: Is java class here OK? It's a beanshell script after all..

	Set<String> expectedOutputs = new HashSet<String>(
	Arrays.asList("output"));
	assertEquals(expectedOutputs, concatAct.getOutputPorts().getNames());
	OutputActivityPort out = concatAct.getOutputPorts().getByName("output");
	assertEquals(0, out.getDepth().intValue());

	Set<PropertyResource> outputDef = configResource
	.getPropertiesAsResources(
	PORT_DEFINITION.resolve("#outputPortDefinition"));
	assertEquals(1, outputDef.size());
	PropertyResource out1Def = outputDef.iterator().next();
	assertEquals(PORT_DEFINITION.resolve("#OutputPortDefinition"),
	out1Def.getTypeURI());

	Set<URI> mimeTypes = out1Def.getPropertiesAsResourceURIs(PORT_DEFINITION
	.resolve("#expectedMimeType"));
	assertEquals(1, mimeTypes.size());

	assertEquals(URI.create("http://purl.org/NET/mediatypes/text/plain"),
	mimeTypes.iterator().next());

	*/

	Processor echoList = researchObj.getMainWorkflow().getProcessors()
	.getByName("Echo_List");
	Configuration echoConfig = scufl2Tools
	.configurationForActivityBoundToProcessor(echoList, profile);
	Activity echoAct = (Activity) echoConfig.getConfigures();

	expectedInputs = new HashSet<String>(Arrays.asList("inputlist"));
	assertEquals(expectedInputs, echoAct.getInputPorts().getNames());
	InputActivityPort inputList = echoAct.getInputPorts().getByName(
	"inputlist");
	assertEquals(1, inputList.getDepth().intValue());
	/* TODO: Update tests
	expectedOutputs = new HashSet<String>(Arrays.asList("outputlist"));
	assertEquals(expectedOutputs, echoAct.getOutputPorts().getNames());
	OutputActivityPort outputList = echoAct.getOutputPorts().getByName(
	"outputlist");
	assertEquals(1, outputList.getDepth().intValue());
	*/
	}


	@Test
	public void beanshellDependencies() throws Exception {
	URL wfResource = getClass().getResource(WF_BEANSHELL_DEPS);
	assertNotNull("Could not find workflow " + WF_BEANSHELL_DEPS, wfResource);
	T2FlowParser parser = new T2FlowParser();
	parser.setValidating(true);
	parser.setStrict(true);
	WorkflowBundle wfBundle = parser
	.parseT2Flow(wfResource.openStream());

	Profile profile = wfBundle.getMainProfile();
	// Processors: [Workflow19, Echo_List, Concatenate_two_strings,
	// Concatenate_two_strings_2, Concatenate_two_strings_3,
	// Concatenate_two_strings_4, Create_Lots_Of_Strings, String_constant]
	Processor a_c_workflow = wfBundle.getMainWorkflow().getProcessors()
	.getByName("A_C_workflow");
	Configuration a_c_config = scufl2Tools
	.configurationForActivityBoundToProcessor(a_c_workflow, profile);
	assertNotNull(a_c_config);
	Configuration c2 = a_c_workflow.getActivityConfiguration(profile);
	assertEquals(a_c_config,c2);
	/* TODO: Update tests
	PropertyResource a_c_configResource = a_c_config.getJson();

	assertFalse(a_c_configResource.hasProperty(ACTIVITY_URI.resolve("#derivedFrom")));
	SortedSet<PropertyResource> deps = a_c_configResource.getPropertiesAsResources(DEPENDENCY_URI.resolve("#dependency"));
	Set<String> jars = new HashSet<String>();
	for (PropertyResource dep : deps) {
	assertEquals(DEPENDENCY_URI.resolve("#LocalJarDependency"), dep.getTypeURI());
	jars.add(dep.getPropertyAsString(DEPENDENCY_URI.resolve("#jarFile")));
	}
	assertEquals(new HashSet<String>(Arrays.asList("libraryA.jar", "libraryC.jar")),
	jars);
	assertFalse(a_c_configResource.hasProperty(DEPENDENCY_URI.resolve("#classLoader")));


	Processor b_system = wfBundle.getMainWorkflow().getProcessors()
	.getByName("B_system");
	Configuration b_config = scufl2Tools
	.configurationForActivityBoundToProcessor(b_system, profile);

	PropertyResource b_configResource = b_config.getJson();

	deps = b_configResource.getPropertiesAsResources(DEPENDENCY_URI.resolve("#dependency"));
	jars = new HashSet<String>();
	for (PropertyResource dep : deps) {
	assertEquals(DEPENDENCY_URI.resolve("#LocalJarDependency"), dep.getTypeURI());
	jars.add(dep.getPropertyAsString(DEPENDENCY_URI.resolve("#jarFile")));
	}
	assertEquals(new HashSet<String>(Arrays.asList("libraryB.jar")),
	jars);
	assertTrue(b_configResource.hasProperty(DEPENDENCY_URI.resolve("#classLoader")));
	assertEquals(DEPENDENCY_URI.resolve("#SystemClassLoader"),
	b_configResource.getPropertyAsResourceURI(DEPENDENCY_URI.resolve("#classLoader")));

	*/

	}


	}