Author: lahiru
Date: Fri Feb 1 22:00:30 2013
New Revision: 1441647
URL: http://svn.apache.org/viewvc?rev=1441647&view=rev
Log:
Adding test case to test input file stagin.
Added:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
Added:
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java?rev=1441647&view=auto
==============================================================================
---
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
(added)
+++
airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
Fri Feb 1 22:00:30 2013
@@ -0,0 +1,291 @@
+/*
+ *
+ * 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.
+ *
+*/
+package org.apache.airavata.core.gfac.services.impl;
+
+import org.apache.airavata.commons.gfac.type.*;
+import org.apache.airavata.gfac.GFacAPI;
+import org.apache.airavata.gfac.GFacConfiguration;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.ApplicationContext;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.schemas.gfac.*;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+public class ParamChemTest {
+ private JobExecutionContext jobExecutionContext;
+
+ @Before
+ public void setUp() throws Exception {
+
+ GFacConfiguration gFacConfiguration = new GFacConfiguration(null);
+ gFacConfiguration.setMyProxyLifeCycle(3600);
+ gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
+ gFacConfiguration.setMyProxyUser("ccguser");
+ gFacConfiguration.setMyProxyPassphrase("");
+
gFacConfiguration.setTrustedCertLocation("/Users/lahirugunathilake/Downloads/certificates");
+ //have to set InFlwo Handlers and outFlowHandlers
+ jobExecutionContext = new JobExecutionContext(gFacConfiguration);
+ ApplicationContext applicationContext = new ApplicationContext();
+ jobExecutionContext.setApplicationContext(applicationContext);
+ /*
+ * Host
+ */
+ String serviceName = "Prepare_Model_Reference_Data";
+ HostDescription host = new HostDescription(GlobusHostType.type);
+ host.getType().setHostName("trestles");
+ host.getType().setHostAddress("trestles.sdsc.edu");
+ ((GlobusHostType)
host.getType()).addGridFTPEndPoint("gsiftp://trestles-login2.sdsc.edu:2811";);
+ ((GlobusHostType)
host.getType()).addGlobusGateKeeperEndPoint("trestles-login2.sdsc.edu:2119/jobmanager-pbstest2");
+
+ applicationContext.setHostDescription(host);
+ /*
+ * App
+ */
+ ApplicationDescription appDesc =
+ new ApplicationDescription(HpcApplicationDeploymentType.type);
+ ApplicationDeploymentDescriptionType
applicationDeploymentDescriptionType
+ = appDesc.getType();
+
applicationDeploymentDescriptionType.addNewApplicationName().setStringValue(serviceName);
+ String tempDir =
"/oasis/projects/nsf/uic151/gridchem/airavata-workdirs";
+ String date = (new Date()).toString();
+ date = date.replaceAll(" ", "_");
+ date = date.replaceAll(":", "_");
+
+ tempDir = tempDir + File.separator
+ + serviceName + "_" + date + "_" + UUID.randomUUID();
+
applicationDeploymentDescriptionType.setExecutableLocation("/home/gridchem/workflow_script/sys_exec/scripts/step1/step1_model_refdata_prep.sh");
+
applicationDeploymentDescriptionType.setScratchWorkingDirectory(tempDir);
+
applicationDeploymentDescriptionType.setStaticWorkingDirectory(tempDir);
+ applicationDeploymentDescriptionType.setInputDataDirectory(tempDir +
File.separator + "inputData");
+ applicationDeploymentDescriptionType.setOutputDataDirectory(tempDir +
File.separator + "outputData");
+ applicationDeploymentDescriptionType.setStandardOutput(tempDir +
File.separator +
applicationDeploymentDescriptionType.getApplicationName().getStringValue() +
".stdout");
+ applicationDeploymentDescriptionType.setStandardError(tempDir +
File.separator +
applicationDeploymentDescriptionType.getApplicationName().getStringValue() +
".stderr");
+
+ ProjectAccountType projectAccountType =
((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).addNewProjectAccount();
+ projectAccountType.setProjectAccountNumber("uic151");
+
+ QueueType queueType = ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).addNewQueue();
+ queueType.setQueueName("shared");
+
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setJobType(JobTypeType.SERIAL);
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setMaxWallTime(30);
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setMaxMemory(2000);
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setCpuCount(1);
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setNodeCount(1);
+ ((HpcApplicationDeploymentType)
applicationDeploymentDescriptionType).setProcessorsPerNode(1);
+
+ applicationContext.setApplicationDeploymentDescription(appDesc);
+
+ /*
+ * Service
+ */
+ ServiceDescription serv = new ServiceDescription();
+ List<InputParameterType> inputParameters = new
ArrayList<InputParameterType>();
+ List<OutputParameterType> outputParameters = new
ArrayList<OutputParameterType>();
+
+ serv.getType().setName(serviceName);
+ serv.getType().setDescription(serviceName);
+
+ //Creating input parameters
+ InputParameterType parameter =
InputParameterType.Factory.newInstance();
+ parameter.setParameterName("molecule_id");
+ ParameterType parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.STRING);
+ parameterType.setName("String");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("geom_mol2");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.URI);
+ parameterType.setName("URI");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("toppar_main_tgz");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.URI);
+ parameterType.setName("URI");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("toppar_usr_tgz");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.URI);
+ parameterType.setName("URI");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("toppar_mol_str");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.URI);
+ parameterType.setName("URI");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("molecule_dir_in_tgz");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.URI);
+ parameterType.setName("URI");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("GC_UserName");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.STRING);
+ parameterType.setName("String");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("GC_ProjectName");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.STRING);
+ parameterType.setName("String");
+ inputParameters.add(parameter);
+
+ parameter = InputParameterType.Factory.newInstance();
+ parameter.setParameterName("GC_WorkflowName");
+ parameterType = parameter.addNewParameterType();
+ parameterType.setType(DataType.STRING);
+ parameterType.setName("String");
+ inputParameters.add(parameter);
+
+ //Creating output parameters
+ OutputParameterType outputParameter =
OutputParameterType.Factory.newInstance();
+ outputParameter.setParameterName("opt_freq_input_gjf");
+ ParameterType outputParaType = outputParameter.addNewParameterType();
+ outputParaType.setType(DataType.URI);
+ outputParaType.setName("URI");
+ outputParameters.add(outputParameter);
+
+ outputParameter = OutputParameterType.Factory.newInstance();
+ outputParameter.setParameterName("charmm_miminized_crd");
+ outputParaType = outputParameter.addNewParameterType();
+ outputParaType.setType(DataType.URI);
+ outputParaType.setName("URI");
+ outputParameters.add(outputParameter);
+
+ outputParameter = OutputParameterType.Factory.newInstance();
+ outputParameter.setParameterName("step1_log");
+ outputParaType = outputParameter.addNewParameterType();
+ outputParaType.setType(DataType.URI);
+ outputParaType.setName("URI");
+ outputParameters.add(outputParameter);
+
+ outputParameter = OutputParameterType.Factory.newInstance();
+ outputParameter.setParameterName("molecule_dir_out_tgz");
+ outputParaType = outputParameter.addNewParameterType();
+ outputParaType.setType(DataType.URI);
+ outputParaType.setName("URI");
+ outputParameters.add(outputParameter);
+
+ outputParameter = OutputParameterType.Factory.newInstance();
+ outputParameter.setParameterName("gcvars");
+ outputParaType = outputParameter.addNewParameterType();
+ outputParaType.setType(DataType.URI);
+ outputParaType.setName("URI");
+ outputParameters.add(outputParameter);
+
+ //Setting input and output parameters to serviceDescriptor
+ serv.getType().setInputParametersArray(inputParameters.toArray(new
InputParameterType[]{}));
+ serv.getType().setOutputParametersArray(outputParameters.toArray(new
OutputParameterType[]{}));
+
+ applicationContext.setServiceDescription(serv);
+
+ MessageContext inMessage = new MessageContext();
+
+ ActualParameter echo_input = new ActualParameter();
+ ((StringParameterType) echo_input.getType()).setValue("ai");
+ inMessage.addParameter("molecule_id", echo_input);
+
+ ActualParameter geom_mol2 = new ActualParameter(URIParameterType.type);
+ ((URIParameterType)
geom_mol2.getType()).setValue("http://ccg-mw1.ncsa.uiuc.edu/cgenff/leoshen/cgenff_project/ai/ai.mol2";);
+ inMessage.addParameter("geom_mol2", geom_mol2);
+
+ ActualParameter toppar_main_tgz = new
ActualParameter(URIParameterType.type);
+ ((URIParameterType)
toppar_main_tgz.getType()).setValue("/home/gridchem/workflow_script/toppar/cgenff/releases/2b7/main.tgz");
+ inMessage.addParameter("toppar_main_tgz", toppar_main_tgz);
+
+ ActualParameter toppar_usr_tgz = new
ActualParameter(URIParameterType.type);
+ ((URIParameterType)
toppar_usr_tgz.getType()).setValue("gsiftp://trestles.sdsc.edu";);
+ inMessage.addParameter("toppar_usr_tgz", toppar_usr_tgz);
+
+ ActualParameter toppar_mol_str = new
ActualParameter(URIParameterType.type);
+ ((URIParameterType)
toppar_mol_str.getType()).setValue("http://ccg-mw1.ncsa.uiuc.edu/cgenff/leoshen/cgenff_project/ai/toppar/ai.str";);
+ inMessage.addParameter("toppar_mol_str", toppar_mol_str);
+
+ ActualParameter molecule_dir_in_tgz = new
ActualParameter(URIParameterType.type);
+ ((URIParameterType) molecule_dir_in_tgz.getType()).setValue("");
+ inMessage.addParameter("molecule_dir_in_tgz", molecule_dir_in_tgz);
+
+ ActualParameter GC_UserName = new ActualParameter();
+ ((StringParameterType) GC_UserName.getType()).setValue("leoshen");
+ inMessage.addParameter("GC_UserName", GC_UserName);
+
+ ActualParameter GC_ProjectName = new ActualParameter();
+ ((StringParameterType) GC_ProjectName.getType()).setValue("leoshen");
+ inMessage.addParameter("GC_ProjectName", GC_ProjectName);
+
+ ActualParameter GC_WorkflowName = new ActualParameter();
+ ((StringParameterType)
GC_WorkflowName.getType()).setValue("ai__1339258840");
+ inMessage.addParameter("GC_WorkflowName", GC_WorkflowName);
+
+ jobExecutionContext.setInMessageContext(inMessage);
+
+ MessageContext outMessage = new MessageContext();
+
+ ActualParameter opt_freq_input_gjf = new
ActualParameter(URIParameterType.type);
+ outMessage.addParameter("opt_freq_input_gjf", opt_freq_input_gjf);
+
+ ActualParameter charmm_miminized_crd = new
ActualParameter(URIParameterType.type);
+ outMessage.addParameter("charmm_miminized_crd", charmm_miminized_crd);
+
+ ActualParameter step1_log = new ActualParameter(URIParameterType.type);
+ outMessage.addParameter("step1_log", step1_log);
+
+ ActualParameter molecule_dir_out_tgz = new
ActualParameter(URIParameterType.type);
+ outMessage.addParameter("molecule_dir_out_tgz", molecule_dir_out_tgz);
+
+ ActualParameter gcvars = new ActualParameter(URIParameterType.type);
+ outMessage.addParameter("gcvars", gcvars);
+
+ jobExecutionContext.setOutMessageContext(outMessage);
+
+ }
+
+ @Test
+ public void testGramProvider() throws GFacException {
+// GFacAPI gFacAPI = new GFacAPI();
+// gFacAPI.submitJob(jobExecutionContext);
+// MessageContext outMessageContext =
jobExecutionContext.getOutMessageContext();
+// Assert.assertFalse(outMessageContext.getParameters().isEmpty());
+// Assert.assertEquals(MappingFactory.toString((ActualParameter)
outMessageContext.getParameter("echo_output")), "hello");
+ }
+}
