| 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.api.common.Scufl2Tools.PORT_DEFINITION; |
| import static org.apache.taverna.scufl2.translator.t2flow.defaultactivities.RshellActivityParser.ACTIVITY_URI; |
| import static org.junit.Assert.assertEquals; |
| import static org.junit.Assert.assertNotNull; |
| import static org.junit.Assert.assertNull; |
| import static org.junit.Assert.assertTrue; |
| |
| import java.net.URI; |
| import java.net.URL; |
| import java.util.Arrays; |
| import java.util.HashMap; |
| import java.util.HashSet; |
| import java.util.Map; |
| import java.util.Set; |
| |
| import javax.xml.bind.JAXBException; |
| |
| import org.apache.taverna.scufl2.api.activity.Activity; |
| import org.apache.taverna.scufl2.api.common.Scufl2Tools; |
| import org.apache.taverna.scufl2.api.common.URITools; |
| 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.port.OutputActivityPort; |
| import org.apache.taverna.scufl2.api.profiles.Profile; |
| import org.apache.taverna.scufl2.translator.t2flow.T2FlowParser; |
| import org.junit.Before; |
| import org.junit.Test; |
| |
| |
| @SuppressWarnings("unused") |
| public class TestActivityParsingRshell { |
| |
| private static final String WF_RSHELL_2_2 = "/rshell-2-2.t2flow"; |
| private static final String WF_RSHELL_2_3 = "/rshell-2-3.t2flow"; |
| private static final String WF_RSHELL_SIMPLE_2_3 = "/rshell-simple-2-3.t2flow"; |
| |
| private static final String WF_ALL_ACTIVITIES = "/defaultActivitiesTaverna2.2.t2flow"; |
| |
| private static Scufl2Tools scufl2Tools = new Scufl2Tools(); |
| private static URITools uriTools = new URITools(); |
| private T2FlowParser parser; |
| |
| @Before |
| public void makeParser() throws JAXBException { |
| parser = new T2FlowParser(); |
| parser.setValidating(true); |
| parser.setStrict(true); |
| |
| } |
| |
| @Test |
| public void parseRShell22WithReferences() throws Exception { |
| URL wfResource = getClass().getResource(WF_RSHELL_2_2); |
| assertNotNull("Could not find workflow " + WF_RSHELL_2_2, wfResource); |
| WorkflowBundle bundle = parser |
| .parseT2Flow(wfResource.openStream()); |
| Profile profile = bundle.getMainProfile(); |
| Processor proc = bundle.getMainWorkflow().getProcessors() |
| .getByName("Rshell"); |
| assertNotNull(proc); |
| Configuration config = scufl2Tools |
| .configurationForActivityBoundToProcessor(proc, profile); |
| assertNotNull(config); |
| // TODO: Check data types defined (semantic types) |
| |
| } |
| |
| /** FIXME: Update tests for JSON config |
| |
| @Test |
| public void parseRShell23() throws Exception { |
| URL wfResource = getClass().getResource(WF_RSHELL_2_3); |
| assertNotNull("Could not find workflow " + WF_RSHELL_2_3, wfResource); |
| WorkflowBundle bundle = parser |
| .parseT2Flow(wfResource.openStream()); |
| Profile profile = bundle.getMainProfile(); |
| Processor proc = bundle.getMainWorkflow().getProcessors() |
| .getByName("Rshell"); |
| assertNotNull(proc); |
| Configuration config = scufl2Tools |
| .configurationForActivityBoundToProcessor(proc, profile); |
| assertNotNull(config); |
| |
| Activity activity = (Activity) config.getConfigures(); |
| |
| // System.out.println(activity.getInputPorts().getNames()); |
| // System.out.println(activity.getOutputPorts().getNames()); |
| |
| |
| assertEquals(ACTIVITY_URI.resolve("#BOOL_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("logVec"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#R_EXP"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("regxp"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("str"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("str2"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#INTEGER"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("int"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#INTEGER_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("intVector"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#BOOL"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("log"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#BOOL_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("logicVector"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#DOUBLE"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("num"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#DOUBLE_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("numVector"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#PNG_FILE"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("png"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#R_EXP"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("rexpr"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("str"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("strVector"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#TEXT_FILE"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("txt"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| } |
| |
| |
| |
| @Test |
| public void parseRShellAllActiv() throws Exception { |
| URL wfResource = getClass().getResource(WF_ALL_ACTIVITIES); |
| assertNotNull("Could not find workflow " + WF_ALL_ACTIVITIES, wfResource); |
| parser.setStrict(false); // Ignore other broken activities |
| WorkflowBundle bundle = parser |
| .parseT2Flow(wfResource.openStream()); |
| Profile profile = bundle.getMainProfile(); |
| Processor proc = bundle.getMainWorkflow().getProcessors() |
| .getByName("Rshell"); |
| assertNotNull(proc); |
| Configuration config = scufl2Tools |
| .configurationForActivityBoundToProcessor(proc, profile); |
| assertNotNull(config); |
| |
| } |
| |
| @Test |
| public void parseSimpleRShellScript() throws Exception { |
| URL wfResource = getClass().getResource(WF_RSHELL_SIMPLE_2_3); |
| assertNotNull("Could not find workflow " + WF_RSHELL_SIMPLE_2_3, wfResource); |
| WorkflowBundle bundle = parser |
| .parseT2Flow(wfResource.openStream()); |
| Profile profile = bundle.getMainProfile(); |
| Processor proc = bundle.getMainWorkflow().getProcessors() |
| .getByName("Rshell"); |
| assertNotNull(proc); |
| Configuration config = scufl2Tools |
| .configurationForActivityBoundToProcessor(proc, profile); |
| assertNotNull(config); |
| |
| Activity activity = (Activity) config.getConfigures(); |
| assertEquals(ACTIVITY_URI, |
| activity.getType()); |
| assertEquals(ACTIVITY_URI.resolve("#Config"), config |
| .getJson().getTypeURI()); |
| String script = config.getJson().getPropertyAsString( |
| ACTIVITY_URI.resolve("#script")); |
| assertEquals("too\nsimple", script); |
| |
| Set<String> expectedInputs = new HashSet<String>(Arrays.asList( |
| "in1", "in2", "in3")); |
| assertEquals(expectedInputs, activity.getInputPorts().getNames()); |
| InputActivityPort in1 = activity.getInputPorts().getByName("in1"); |
| assertEquals(0, in1.getDepth().intValue()); |
| InputActivityPort in2 = activity.getInputPorts().getByName("in2"); |
| assertEquals(0, in2.getDepth().intValue()); |
| InputActivityPort in3 = activity.getInputPorts().getByName("in3"); |
| assertEquals(0, in3.getDepth().intValue()); |
| |
| Set<PropertyResource> inputDef = config.getJson() |
| .getPropertiesAsResources( |
| PORT_DEFINITION.resolve("#inputPortDefinition")); |
| assertEquals(3, inputDef.size()); |
| |
| Set<URI> expectedPortUris = new HashSet<URI>(); |
| for (InputActivityPort inPort : activity.getInputPorts()) { |
| expectedPortUris.add(uriTools.relativeUriForBean(inPort, |
| config)); |
| PropertyResource portDef = scufl2Tools.portDefinitionFor(inPort, profile); |
| assertNotNull("Could not find port definition for port " + inPort, portDef); |
| } |
| assertEquals(3, expectedPortUris.size()); |
| assertEquals(3, inputDef.size()); |
| |
| Map<URI, URI> dataTypes = new HashMap<URI, URI>(); |
| |
| for (PropertyResource portDef : inputDef) { |
| assertEquals(PORT_DEFINITION.resolve("#InputPortDefinition"), |
| portDef.getTypeURI()); |
| assertNull(portDef.getResourceURI()); |
| URI portURI = portDef.getPropertyAsResourceURI(PORT_DEFINITION |
| .resolve("#definesInputPort")); |
| assertTrue("Unknown port " + portURI, |
| expectedPortUris.contains(portURI)); |
| |
| URI dataType = portDef.getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType")); |
| assertEquals(ACTIVITY_URI.resolve("#samePrefix"), dataType.resolve("#samePrefix")); |
| // For instance http://ns.taverna.org.uk/2010/activity/rshell#BOOL_LIST |
| dataTypes.put(portURI, dataType); |
| |
| |
| } |
| |
| |
| Set<String> expectedOutputs = new HashSet<String>( |
| Arrays.asList("out1", "out2", "out3")); |
| assertEquals(expectedOutputs, activity.getOutputPorts().getNames()); |
| OutputActivityPort out1 = activity.getOutputPorts().getByName("out1"); |
| assertEquals(0, out1.getDepth().intValue()); |
| OutputActivityPort out2 = activity.getOutputPorts().getByName("out2"); |
| assertEquals(1, out2.getDepth().intValue()); |
| OutputActivityPort out3 = activity.getOutputPorts().getByName("out3"); |
| assertEquals(1, out3.getDepth().intValue()); |
| |
| expectedPortUris.clear(); |
| for (OutputActivityPort outPort : activity.getOutputPorts()) { |
| |
| expectedPortUris.add(uriTools.relativeUriForBean(outPort, |
| config)); |
| PropertyResource portDef = scufl2Tools.portDefinitionFor(outPort, profile); |
| assertNotNull("Could not find port definition for port " + outPort, portDef); |
| |
| } |
| |
| Set<PropertyResource> outputDef = config.getJson() |
| .getPropertiesAsResources( |
| PORT_DEFINITION.resolve("#outputPortDefinition")); |
| assertEquals(3, outputDef.size()); |
| for (PropertyResource portDef : outputDef) { |
| assertEquals(PORT_DEFINITION.resolve("#OutputPortDefinition"), |
| portDef.getTypeURI()); |
| assertNull(portDef.getResourceURI()); |
| URI portURI = portDef.getPropertyAsResourceURI(PORT_DEFINITION |
| .resolve("#definesOutputPort")); |
| assertTrue("Unknown port " + portURI, |
| expectedPortUris.contains(portURI)); |
| |
| URI dataType = portDef.getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType")); |
| assertEquals(ACTIVITY_URI.resolve("#samePrefix"), dataType.resolve("#samePrefix")); |
| // For instance http://ns.taverna.org.uk/2010/activity/rshell#BOOL_LIST |
| dataTypes.put(portURI, dataType); |
| |
| } |
| |
| |
| //System.out.println(dataTypes); |
| |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("in1"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| assertEquals(ACTIVITY_URI.resolve("#DOUBLE"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("in2"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getInputPorts().getByName("in3"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("out1"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#BOOL_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("out2"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| assertEquals(ACTIVITY_URI.resolve("#STRING_LIST"), |
| scufl2Tools.portDefinitionFor(activity.getOutputPorts().getByName("out3"), profile). |
| getPropertyAsResourceURI(PORT_DEFINITION.resolve("#dataType"))); |
| |
| |
| PropertyResource connection = config.getJson().getPropertyAsResource(ACTIVITY_URI.resolve("#connection")); |
| assertEquals(ACTIVITY_URI.resolve("#Connection"), connection.getTypeURI()); |
| |
| assertEquals("localhost", connection.getPropertyAsString(ACTIVITY_URI.resolve("#hostname"))); |
| |
| PropertyLiteral portLiteral = connection.getPropertyAsLiteral(ACTIVITY_URI.resolve("#port")); |
| assertEquals(6311, portLiteral.getLiteralValueAsInt()); |
| assertEquals(PropertyLiteral.XSD_UNSIGNEDSHORT, portLiteral.getLiteralType()); |
| |
| assertEquals(false, connection.getPropertyAsLiteral(ACTIVITY_URI.resolve("#keepSessionAlive")).getLiteralValueAsBoolean()); |
| } |
| |
| */ |
| } |
