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Posted to commits@airavata.apache.org by la...@apache.org on 2014/04/24 15:54:08 UTC
[2/4] separating gsissh package
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTestWithMyProxyAuth.java
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diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTestWithMyProxyAuth.java
deleted file mode 100644
index 4e739df..0000000
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTestWithMyProxyAuth.java
+++ /dev/null
@@ -1,306 +0,0 @@
-/*
- *
- * 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 java.io.File;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.commons.gfac.type.HostDescription;
-import org.apache.airavata.commons.gfac.type.ServiceDescription;
-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.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.handler.GFacHandlerConfig;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.DataType;
-import org.apache.airavata.schemas.gfac.GlobusHostType;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.InputParameterType;
-import org.apache.airavata.schemas.gfac.JobTypeType;
-import org.apache.airavata.schemas.gfac.OutputParameterType;
-import org.apache.airavata.schemas.gfac.ParameterType;
-import org.apache.airavata.schemas.gfac.ProjectAccountType;
-import org.apache.airavata.schemas.gfac.QueueType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ParamChemTestWithMyProxyAuth extends GFacBaseTestWithMyProxyAuth {
- private JobExecutionContext jobExecutionContext;
-
- @Before
- public void setUp() throws Exception {
-
- GFacConfiguration gFacConfiguration = new GFacConfiguration(null);
- GSISecurityContext context = getSecurityContext();
-
- //have to set InFlwo Handlers and outFlowHandlers
- gFacConfiguration.setInHandlers(Arrays.asList(new GFacHandlerConfig[]{new GFacHandlerConfig(null,"org.apache.airavata.gfac.handler.GramDirectorySetupHandler"), new GFacHandlerConfig(null,"org.apache.airavata.gfac.handler.GridFTPInputHandler")}));
- gFacConfiguration.setOutHandlers(Arrays.asList(new GFacHandlerConfig[] {new GFacHandlerConfig(null,"org.apache.airavata.gfac.handler.GridFTPOutputHandler")}));
- /*
- * 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-dm.sdsc.edu:2811");
- ((GlobusHostType) host.getType()).addGlobusGateKeeperEndPoint("trestles-login2.sdsc.edu:2119/jobmanager-pbstest2");
-
- /*
- * 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);
-
-
- /*
- * 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[]{}));
-
- jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName());
- jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT, context);
- ApplicationContext applicationContext = new ApplicationContext();
- applicationContext.setHostDescription(host);
- applicationContext.setApplicationDeploymentDescription(appDesc);
- jobExecutionContext.setApplicationContext(applicationContext);
- 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 {
-// GFacImpl gFacAPI = new GFacImpl();
-// gFacAPI.submitJob(jobExecutionContext);
-// MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
-// Assert.assertFalse(outMessageContext.getParameters().isEmpty());
-// Assert.assertEquals(MappingFactory.toString((ActualParameter) outMessageContext.getParameter("echo_output")), "hello");
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
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diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
deleted file mode 100644
index 43f655d..0000000
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
+++ /dev/null
@@ -1,152 +0,0 @@
-/*
- *
- * 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 java.io.File;
-import java.util.Date;
-import java.util.UUID;
-
-import org.apache.airavata.commons.gfac.type.ActualParameter;
-import org.apache.airavata.commons.gfac.type.ApplicationDescription;
-import org.apache.airavata.gfac.context.ApplicationContext;
-import org.apache.airavata.gfac.context.MessageContext;
-import org.apache.airavata.gfac.cpi.GFacImpl;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
-import org.apache.airavata.schemas.gfac.ExtendedKeyValueType;
-import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
-import org.apache.airavata.schemas.gfac.JobTypeType;
-import org.apache.airavata.schemas.gfac.StringParameterType;
-import org.apache.airavata.schemas.gfac.URIParameterType;
-import org.junit.Before;
-import org.junit.Test;
-//
-//public class US3TestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
-//
-//
-// @Before
-// public void initJobContext() throws Exception {
-// initTest();
-// }
-//
-// @Test
-// public void submitJob() throws Exception {
-// JobTypeType jobType = JobTypeType.Factory.newInstance();
-// jobType.set(JobTypeType.MPI);
-// ApplicationContext appContext = getApplicationContext();
-// appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
-// jobExecutionContext.setApplicationContext(appContext);
-// GFacImpl gFacAPI = new GFacImpl();
-// gFacAPI.submitJob(jobExecutionContext);
-// }
-//
-//
-// protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
-// ApplicationDescription appDesc = new ApplicationDescription(
-// HpcApplicationDeploymentType.type);
-// HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) appDesc
-// .getType();
-// ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
-// .newInstance();
-// name.setStringValue("US3-Job");
-// appDepType.setApplicationName(name);
-//
-//// ProjectAccountType projectAccountType = appDepType.addNewProjectAccount();
-//// projectAccountType.setProjectAccountNumber("TG-AST110064");
-//
-//// QueueType queueType = appDepType.addNewQueue();
-//// queueType.setQueueName("development");
-//
-// // TODO: also handle parallel jobs
-// if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
-// appDepType.setJobType(JobTypeType.SERIAL);
-// }
-// else if (jobType.enumValue() == JobTypeType.MPI) {
-// appDepType.setJobType(JobTypeType.MPI);
-// }
-// else {
-// appDepType.setJobType(JobTypeType.OPEN_MP);
-// }
-//
-// appDepType.setNodeCount(4);
-// appDepType.setProcessorsPerNode(8);
-//
-// appDepType.setMaxWallTime(15);
-//
-// appDepType.setExecutableLocation("us_mpi_analysis");
-//
-// ExtendedKeyValueType extKV = appDepType.addNewKeyValuePairs();
-// // using jsdl spmd standard
-// extKV.setName("NumberOfProcesses");
-// // this will be transformed into mpiexec -n 4
-// extKV.setStringValue("32");
-//
-// /*
-// * Default tmp location
-// */
-// String date = (new Date()).toString();
-// date = date.replaceAll(" ", "_");
-// date = date.replaceAll(":", "_");
-//
-// String remoteTempDir = scratchDir + File.separator + "US3" + "_" + date + "_"
-// + UUID.randomUUID();
-//
-// System.out.println(remoteTempDir);
-//
-// // no need of these parameters, as unicore manages by itself
-// appDepType.setScratchWorkingDirectory(remoteTempDir);
-// appDepType.setStaticWorkingDirectory(remoteTempDir);
-// appDepType.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
-// appDepType.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
-//
-// appDepType.setStandardOutput(appDepType.getOutputDataDirectory()+"/stdout");
-//
-// appDepType.setStandardError(appDepType.getOutputDataDirectory()+"/stderr");
-//
-// return appDesc;
-// }
-// protected MessageContext getInMessageContext() {
-// MessageContext inMessage = new MessageContext();
-//
-// ActualParameter a1 = new ActualParameter();
-// a1.getType().changeType(StringParameterType.type);
-// ((StringParameterType)a1.getType()).setValue("hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
-// inMessage.addParameter("arg1", a1);
-//
-// ActualParameter i1 = new ActualParameter();
-// i1.getType().changeType(URIParameterType.type);
-// ((URIParameterType)i1.getType()).setValue("file:///"+System.getProperty("user.home")+"/juelich-us3/hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
-// inMessage.addParameter("i1", i1);
-//
-// return inMessage;
-// }
-//
-// protected MessageContext getOutMessageContext() {
-// MessageContext outMessage = new MessageContext();
-//
-// ActualParameter a1 = new ActualParameter();
-// a1.getType().changeType(StringParameterType.type);
-// ((StringParameterType)a1.getType()).setValue("output/analysis-results.tar");
-// outMessage.addParameter("o1", a1);
-//
-// return outMessage;
-// }
-
-//}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
deleted file mode 100644
index 9a24931..0000000
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- *
- * 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.gfac.context.security;
-
-import junit.framework.Assert;
-import org.apache.airavata.common.utils.AiravataUtils;
-import org.apache.airavata.common.utils.DatabaseTestCases;
-import org.apache.airavata.common.utils.DerbyUtil;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.credential.store.store.CredentialReader;
-import org.apache.airavata.credential.store.store.CredentialReaderFactory;
-import org.apache.airavata.gfac.RequestData;
-import org.apache.log4j.Logger;
-import org.ietf.jgss.GSSCredential;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-
-public class GSISecurityContextTestWithMyProxyAuth extends DatabaseTestCases {
-
- private static String userName;
- private static String password;
-
- private static final Logger log = Logger.getLogger(GSISecurityContextTestWithMyProxyAuth.class);
-
- @BeforeClass
- public static void setUpClass() throws Exception {
- AiravataUtils.setExecutionAsServer();
-
-// System.setProperty("myproxy.username", "ogce");
-// System.setProperty("myproxy.password", "");
- userName = System.getProperty("myproxy.username");
- password = System.getProperty("myproxy.password");
- System.setProperty("myproxy.server", "myproxy.teragrid.org");
- System.setProperty("myproxy.life", "3600");
- System.setProperty("credential.store.keystore.url", "../configuration/server/src/main/resources/airavata.jks");
- System.setProperty("credential.store.keystore.alias", "airavata");
- System.setProperty("credential.store.keystore.password", "airavata");
-
- if (userName == null || password == null || userName.trim().equals("") || password.trim().equals("")) {
- log.error("===== Please set myproxy.username and myproxy.password system properties. =======");
- Assert.fail("Please set myproxy.user and myproxy.password system properties.");
- }
-
- log.info("Using my proxy user name - " + userName);
-
- setUpDatabase();
-
- }
-
- public static void setUpDatabase() throws Exception {
- DerbyUtil.startDerbyInServerMode(getHostAddress(), getPort(), getUserName(), getPassword());
-
- waitTillServerStarts();
-
-
- String createTable = "CREATE TABLE CREDENTIALS\n" + "(\n"
- + " GATEWAY_ID VARCHAR(256) NOT NULL,\n"
- + " TOKEN_ID VARCHAR(256) NOT NULL,\n"
- + // Actual token used to identify the credential
- " CREDENTIAL BLOB NOT NULL,\n" + " PORTAL_USER_ID VARCHAR(256) NOT NULL,\n"
- + " TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,\n"
- + " PRIMARY KEY (GATEWAY_ID, TOKEN_ID)\n" + ")";
-
- String dropTable = "drop table CREDENTIALS";
-
- try {
- executeSQL(dropTable);
- } catch (Exception e) {
- }
-
- executeSQL(createTable);
-
- }
-
- @AfterClass
- public static void shutDownDatabase() throws Exception {
- DerbyUtil.stopDerbyServer();
- }
-
- private GSSCredential getGSSCredentials() throws Exception {
-
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
-
- return gsiSecurityContext.getGssCredentials();
- }
-
- private GSISecurityContext getGSISecurityContext() throws Exception {
-
- RequestData requestData = new RequestData();
-
- requestData.setMyProxyUserName(userName);
- requestData.setMyProxyPassword(password);
- requestData.setMyProxyServerUrl(ServerSettings.getMyProxyServer());
- requestData.setMyProxyLifeTime(ServerSettings.getMyProxyLifetime());
- CredentialReader credentialReader = CredentialReaderFactory.createCredentialStoreReader(getDbUtil());
-
- return new GSISecurityContext(credentialReader, requestData);
- }
-
- @Test
- public void testGetGssCredentials() throws Exception {
-
- Assert.assertNotNull(getGSSCredentials());
- }
- /*
- @Test
- public void testRenewCredentials() throws Exception {
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
- gsiSecurityContext.getGssCredentials();
- Assert.assertNotNull(gsiSecurityContext.renewCredentials());
-
- }
-
- @Test
- public void testGetCredentialsFromStore() throws Exception {
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
- Assert.assertNotNull(gsiSecurityContext.getCredentialsFromStore());
-
- } */
-
- @Test
- public void testGetDefaultCredentials() throws Exception {
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
- Assert.assertNotNull(gsiSecurityContext.getDefaultCredentials());
-
- }
-
- @Test
- public void testGetProxyCredentials() throws Exception {
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
- Assert.assertNotNull(gsiSecurityContext.getProxyCredentials());
-
- }
- /*
- @Test
- public void testRenewCredentialsAsATrustedHost() throws Exception {
- GSISecurityContext gsiSecurityContext = getGSISecurityContext();
- gsiSecurityContext.getGssCredentials();
- Assert.assertNotNull(gsiSecurityContext.renewCredentialsAsATrustedHost());
- } */
-
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/pom.xml b/modules/gfac/gfac-gsissh/pom.xml
new file mode 100644
index 0000000..2f67b76
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/pom.xml
@@ -0,0 +1,132 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!--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 (theÏ "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. -->
+
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <parent>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>gfac</artifactId>
+ <version>0.12-SNAPSHOT</version>
+ <relativePath>../pom.xml</relativePath>
+ </parent>
+
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>airavata-gfac-gsissh</artifactId>
+ <name>Airavata GFac GSI-SSH implementation</name>
+ <description>This is the extension of </description>
+ <url>http://airavata.apache.org/</url>
+
+ <dependencies>
+ <!-- Logging -->
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-api</artifactId>
+ </dependency>
+
+ <!-- GFAC schemas -->
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-gfac-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <!-- Credential Store -->
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-credential-store</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-server-configuration</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-client-configuration</artifactId>
+ <scope>test</scope>
+ </dependency>
+
+
+ <!-- Test -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.1.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>jcl-over-slf4j</artifactId>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.slf4j</groupId>
+ <artifactId>slf4j-log4j12</artifactId>
+ <scope>test</scope>
+ </dependency>
+
+ <!-- gsi-ssh api dependencies -->
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>gsissh</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-data-models</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.jcraft</groupId>
+ <artifactId>jsch</artifactId>
+ <version>0.1.50</version>
+ </dependency>
+ <dependency>
+ <groupId>org.ogce</groupId>
+ <artifactId>bcgss</artifactId>
+ <version>146</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.xmlbeans</groupId>
+ <artifactId>xmlbeans</artifactId>
+ <version>${xmlbeans.version}</version>
+ </dependency>
+
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <executions>
+ <execution>
+ <id>copy-dependencies</id>
+ <phase>package</phase>
+ <goals>
+ <goal>copy-dependencies</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>target/lib</outputDirectory>
+ <overWriteReleases>false</overWriteReleases>
+ <overWriteSnapshots>true</overWriteSnapshots>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+</project>
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
new file mode 100644
index 0000000..3eb020f
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
@@ -0,0 +1,288 @@
+/*
+ *
+ * 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.gfac.context.security;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.ServerSettings;
+import org.apache.airavata.credential.store.credential.Credential;
+import org.apache.airavata.credential.store.credential.impl.certificate.CertificateCredential;
+import org.apache.airavata.credential.store.store.CredentialReader;
+import org.apache.airavata.gfac.AbstractSecurityContext;
+import org.apache.airavata.gfac.Constants;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.RequestData;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.globus.gsi.X509Credential;
+import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
+import org.globus.gsi.provider.GlobusProvider;
+import org.globus.myproxy.GetParams;
+import org.globus.myproxy.MyProxy;
+import org.globus.myproxy.MyProxyException;
+import org.gridforum.jgss.ExtendedGSSCredential;
+import org.ietf.jgss.GSSCredential;
+import org.ietf.jgss.GSSException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.security.Security;
+import java.security.cert.X509Certificate;
+
+/**
+ * Handles GRID related security.
+ */
+public class GSISecurityContext extends AbstractSecurityContext {
+
+ protected static final Logger log = LoggerFactory.getLogger(GSISecurityContext.class);
+ /*
+ * context name
+ */
+ public static final String GSI_SECURITY_CONTEXT = "gsi";
+
+ public static int CREDENTIAL_RENEWING_THRESH_HOLD = 10 * 90;
+
+ private GSSCredential gssCredentials = null;
+
+ private Cluster pbsCluster = null;
+
+ // Set trusted cert path and add provider
+ static {
+ Security.addProvider(new GlobusProvider());
+ try {
+ setUpTrustedCertificatePath();
+ } catch (ApplicationSettingsException e) {
+ log.error(e.getLocalizedMessage(), e);
+ }
+ }
+
+ public static void setUpTrustedCertificatePath(String trustedCertificatePath) {
+
+ File file = new File(trustedCertificatePath);
+
+ if (!file.exists() || !file.canRead()) {
+ File f = new File(".");
+ log.info("Current directory " + f.getAbsolutePath());
+ throw new RuntimeException("Cannot read trusted certificate path " + trustedCertificatePath);
+ } else {
+ System.setProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY, file.getAbsolutePath());
+ }
+ }
+
+ private static void setUpTrustedCertificatePath() throws ApplicationSettingsException {
+
+ String trustedCertificatePath = ServerSettings.getSetting(Constants.TRUSTED_CERT_LOCATION);
+
+ setUpTrustedCertificatePath(trustedCertificatePath);
+ }
+
+ /**
+ * Gets the trusted certificate path. Trusted certificate path is stored in "X509_CERT_DIR"
+ * system property.
+ * @return The trusted certificate path as a string.
+ */
+ public static String getTrustedCertificatePath() {
+ return System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY);
+ }
+
+
+ public GSISecurityContext(CredentialReader credentialReader, RequestData requestData) {
+ super(credentialReader, requestData);
+ }
+
+
+ public GSISecurityContext(Cluster pbsCluster) {
+ this.setPbsCluster(pbsCluster);
+ }
+
+ /**
+ * Gets GSSCredentials. The process is as follows;
+ * If credentials were queried for the first time create credentials.
+ * 1. Try creating credentials using certificates stored in the credential store
+ * 2. If 1 fails use user name and password to create credentials
+ * If credentials are already created check the remaining life time of the credential. If
+ * remaining life time is less than CREDENTIAL_RENEWING_THRESH_HOLD, then renew credentials.
+ * @return GSSCredentials to be used.
+ * @throws org.apache.airavata.gfac.GFacException If an error occurred while creating credentials.
+ * @throws org.apache.airavata.common.exception.ApplicationSettingsException
+ */
+ public GSSCredential getGssCredentials() throws GFacException, ApplicationSettingsException {
+
+ if (gssCredentials == null) {
+
+ try {
+ gssCredentials = getCredentialsFromStore();
+ } catch (Exception e) {
+ log.error("An exception occurred while retrieving credentials from the credential store. " +
+ "Will continue with my proxy user name and password.", e);
+ }
+
+ // If store does not have credentials try to get from user name and password
+ if (gssCredentials == null) {
+ gssCredentials = getDefaultCredentials();
+ }
+
+ // if still null, throw an exception
+ if (gssCredentials == null) {
+ throw new GFacException("Unable to retrieve my proxy credentials to continue operation.");
+ }
+ } else {
+ try {
+ if (gssCredentials.getRemainingLifetime() < CREDENTIAL_RENEWING_THRESH_HOLD) {
+ return renewCredentials();
+ }
+ } catch (GSSException e) {
+ throw new GFacException("Unable to retrieve remaining life time from credentials.", e);
+ }
+ }
+
+ return gssCredentials;
+ }
+
+ /**
+ * Renews credentials. First try to renew credentials as a trusted renewer. If that failed
+ * use user name and password to renew credentials.
+ * @return Renewed credentials.
+ * @throws org.apache.airavata.gfac.GFacException If an error occurred while renewing credentials.
+ * @throws org.apache.airavata.common.exception.ApplicationSettingsException
+ */
+ public GSSCredential renewCredentials() throws GFacException, ApplicationSettingsException {
+
+ // First try to renew credentials as a trusted renewer
+ try {
+ gssCredentials = renewCredentialsAsATrustedHost();
+ } catch (Exception e) {
+ log.warn("Renewing credentials as a trusted renewer failed", e);
+ gssCredentials = getProxyCredentials();
+ }
+
+ return gssCredentials;
+ }
+
+ /**
+ * Reads the credentials from credential store.
+ * @return If token is found in the credential store, will return a valid credential. Else returns null.
+ * @throws Exception If an error occurred while retrieving credentials.
+ */
+ public GSSCredential getCredentialsFromStore() throws Exception {
+
+ if (getCredentialReader() == null) {
+ return null;
+ }
+
+ Credential credential = getCredentialReader().getCredential(getRequestData().getGatewayId(),
+ getRequestData().getTokenId());
+
+ if (credential != null) {
+ if (credential instanceof CertificateCredential) {
+
+ log.info("Successfully found credentials for token id - " + getRequestData().getTokenId() +
+ " gateway id - " + getRequestData().getGatewayId());
+
+ CertificateCredential certificateCredential = (CertificateCredential) credential;
+
+ X509Certificate[] certificates = certificateCredential.getCertificates();
+ X509Credential newCredential = new X509Credential(certificateCredential.getPrivateKey(), certificates);
+
+ GlobusGSSCredentialImpl cred = new GlobusGSSCredentialImpl(newCredential, GSSCredential.INITIATE_AND_ACCEPT);
+ System.out.print(cred.export(ExtendedGSSCredential.IMPEXP_OPAQUE));
+ return cred;
+ //return new GlobusGSSCredentialImpl(newCredential,
+ // GSSCredential.INITIATE_AND_ACCEPT);
+ } else {
+ log.info("Credential type is not CertificateCredential. Cannot create mapping globus credentials. " +
+ "Credential type - " + credential.getClass().getName());
+ }
+ } else {
+ log.info("Could not find credentials for token - " + getRequestData().getTokenId() + " and "
+ + "gateway id - " + getRequestData().getGatewayId());
+ }
+
+ return null;
+ }
+
+ /**
+ * Gets the default proxy certificate.
+ * @return Default my proxy credentials.
+ * @throws org.apache.airavata.gfac.GFacException If an error occurred while retrieving credentials.
+ * @throws org.apache.airavata.common.exception.ApplicationSettingsException
+ */
+ public GSSCredential getDefaultCredentials() throws GFacException, ApplicationSettingsException{
+ MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
+ try {
+ return myproxy.get(getRequestData().getMyProxyUserName(), getRequestData().getMyProxyPassword(),
+ getRequestData().getMyProxyLifeTime());
+ } catch (MyProxyException e) {
+ throw new GFacException("An error occurred while retrieving default security credentials.", e);
+ }
+ }
+
+ /**
+ * Gets a new proxy certificate given current credentials.
+ * @return The short lived GSSCredentials
+ * @throws org.apache.airavata.gfac.GFacException If an error is occurred while retrieving credentials.
+ * @throws org.apache.airavata.common.exception.ApplicationSettingsException
+ */
+ public GSSCredential getProxyCredentials() throws GFacException, ApplicationSettingsException {
+
+ MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
+ try {
+ return myproxy.get(gssCredentials, getRequestData().getMyProxyUserName(), getRequestData().getMyProxyPassword(),
+ getRequestData().getMyProxyLifeTime());
+ } catch (MyProxyException e) {
+ throw new GFacException("An error occurred while renewing security credentials using user/password.", e);
+ }
+ }
+
+ /**
+ * Renew GSSCredentials.
+ * Before executing we need to add current host as a trusted renewer. Note to renew credentials
+ * we dont need user name and password.
+ * To do that execute following command
+ * > myproxy-logon -t <LIFETIME></LIFETIME> -s <MY PROXY SERVER> -l <USER NAME>
+ * E.g :- > myproxy-logon -t 264 -s myproxy.teragrid.org -l us3
+ * Enter MyProxy pass phrase:
+ * A credential has been received for user us3 in /tmp/x509up_u501.
+ * > myproxy-init -A --cert /tmp/x509up_u501 --key /tmp/x509up_u501 -l ogce -s myproxy.teragrid.org
+ * @return Renewed credentials.
+ * @throws org.apache.airavata.gfac.GFacException If an error occurred while renewing credentials.
+ * @throws org.apache.airavata.common.exception.ApplicationSettingsException
+ */
+ public GSSCredential renewCredentialsAsATrustedHost() throws GFacException, ApplicationSettingsException {
+ MyProxy myproxy = new MyProxy(getRequestData().getMyProxyServerUrl(), getRequestData().getMyProxyPort());
+ GetParams getParams = new GetParams();
+ getParams.setAuthzCreds(gssCredentials);
+ getParams.setUserName(getRequestData().getMyProxyUserName());
+ getParams.setLifetime(getRequestData().getMyProxyLifeTime());
+ try {
+ return myproxy.get(gssCredentials, getParams);
+ } catch (MyProxyException e) {
+ throw new GFacException("An error occurred while renewing security credentials.", e);
+ }
+ }
+
+ public Cluster getPbsCluster() {
+ return pbsCluster;
+ }
+
+ public void setPbsCluster(Cluster pbsCluster) {
+ this.pbsCluster = pbsCluster;
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHDirectorySetupHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHDirectorySetupHandler.java
new file mode 100644
index 0000000..66b8094
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHDirectorySetupHandler.java
@@ -0,0 +1,98 @@
+/*
+ *
+ * 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.gfac.handler;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.util.GFACGSISSHUtils;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.model.workspace.experiment.*;
+import org.apache.airavata.registry.cpi.ChildDataType;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+public class GSISSHDirectorySetupHandler extends AbstractHandler{
+ private static final Logger log = LoggerFactory.getLogger(GSISSHDirectorySetupHandler.class);
+
+ public void invoke(JobExecutionContext jobExecutionContext) throws GFacException {
+ if(jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null){
+ try {
+ GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
+ } catch (ApplicationSettingsException e) {
+ log.error(e.getMessage());
+ throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
+ }
+ }
+ log.info("Setup SSH job directorties");
+ super.invoke(jobExecutionContext);
+ makeDirectory(jobExecutionContext);
+
+ }
+ private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacException {
+ Cluster cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ if (cluster == null) {
+ throw new GFacHandlerException("Security context is not set properly");
+ } else {
+ log.info("Successfully retrieved the Security Context");
+ }
+ ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
+ try {
+ String workingDirectory = app.getScratchWorkingDirectory();
+ cluster.makeDirectory(workingDirectory);
+ cluster.makeDirectory(app.getScratchWorkingDirectory());
+ cluster.makeDirectory(app.getInputDataDirectory());
+ cluster.makeDirectory(app.getOutputDataDirectory());
+ DataTransferDetails detail = new DataTransferDetails();
+ TransferStatus status = new TransferStatus();
+ status.setTransferState(TransferState.DIRECTORY_SETUP);
+ detail.setTransferStatus(status);
+ detail.setTransferDescription("Working directory = " + workingDirectory);
+
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+
+ } catch (SSHApiException e) {
+ throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
+ } catch (Exception e) {
+ DataTransferDetails detail = new DataTransferDetails();
+ TransferStatus status = new TransferStatus();
+ status.setTransferState(TransferState.FAILED);
+ detail.setTransferStatus(status);
+ try {
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE, jobExecutionContext.getTaskData().getTaskID());
+ } catch (Exception e1) {
+ throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
+ }
+ throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
+ }
+ }
+
+ public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHInputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHInputHandler.java
new file mode 100644
index 0000000..80f30f0
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHInputHandler.java
@@ -0,0 +1,137 @@
+/*
+ *
+ * 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.gfac.handler;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.StringUtil;
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.MappingFactory;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.util.GFACGSISSHUtils;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.model.workspace.experiment.*;
+import org.apache.airavata.registry.cpi.ChildDataType;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.URIArrayType;
+import org.apache.airavata.schemas.gfac.URIParameterType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.*;
+
+public class GSISSHInputHandler extends AbstractHandler {
+
+ private static final Logger log = LoggerFactory.getLogger(GSISSHInputHandler.class);
+
+
+ public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
+ if(jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null){
+ try {
+ GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
+ } catch (ApplicationSettingsException e) {
+ log.error(e.getMessage());
+ throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
+ }
+ }
+ log.info("Invoking SCPInputHandler");
+ super.invoke(jobExecutionContext);
+
+ DataTransferDetails detail = new DataTransferDetails();
+ TransferStatus status = new TransferStatus();
+
+ MessageContext inputNew = new MessageContext();
+ try {
+ MessageContext input = jobExecutionContext.getInMessageContext();
+ Set<String> parameters = input.getParameters().keySet();
+ for (String paramName : parameters) {
+ ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
+ String paramValue = MappingFactory.toString(actualParameter);
+ //TODO: Review this with type
+ if ("URI".equals(actualParameter.getType().getType().toString())) {
+ ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(jobExecutionContext, paramValue));
+ } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
+ List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
+ List<String> newFiles = new ArrayList<String>();
+ for (String paramValueEach : split) {
+ String stageInputFiles = stageInputFiles(jobExecutionContext, paramValueEach);
+ status.setTransferState(TransferState.UPLOAD);
+ detail.setTransferStatus(status);
+ detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
+ newFiles.add(stageInputFiles);
+ }
+ ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
+ }
+ inputNew.getParameters().put(paramName, actualParameter);
+ }
+ } catch (Exception e) {
+ log.error(e.getMessage());
+ status.setTransferState(TransferState.FAILED);
+ detail.setTransferStatus(status);
+ try {
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE, jobExecutionContext.getTaskData().getTaskID());
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
+ } catch (Exception e1) {
+ throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
+ }
+ throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
+ }
+ jobExecutionContext.setInMessageContext(inputNew);
+ }
+
+ private static String stageInputFiles(JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
+ Cluster cluster = null;
+ if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ } else {
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ }
+ if (cluster == null) {
+ throw new GFacException("Security context is not set properly");
+ } else {
+ log.info("Successfully retrieved the Security Context");
+ }
+ ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
+ int i = paramValue.lastIndexOf(File.separator);
+ String substring = paramValue.substring(i + 1);
+ try {
+ String targetFile = app.getInputDataDirectory() + File.separator + substring;
+ if(paramValue.startsWith("file")){
+ paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
+ }
+ cluster.scpTo(targetFile, paramValue);
+ return targetFile;
+ } catch (SSHApiException e) {
+ throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
+ }
+ }
+
+ public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHOutputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHOutputHandler.java
new file mode 100644
index 0000000..fd80d56
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/handler/GSISSHOutputHandler.java
@@ -0,0 +1,216 @@
+/*
+ *
+ * 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.gfac.handler;
+
+import net.schmizz.sshj.connection.ConnectionException;
+import net.schmizz.sshj.transport.TransportException;
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.Constants;
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gfac.util.GFACGSISSHUtils;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.apache.airavata.gfac.utils.OutputUtils;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.model.workspace.experiment.*;
+import org.apache.airavata.registry.cpi.ChildDataType;
+import org.apache.airavata.registry.cpi.DataType;
+import org.apache.airavata.registry.cpi.RegistryException;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GsisshHostType;
+import org.apache.airavata.schemas.gfac.URIParameterType;
+import org.apache.xmlbeans.XmlException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class GSISSHOutputHandler extends AbstractHandler{
+ private static final Logger log = LoggerFactory.getLogger(GSISSHOutputHandler.class);
+
+ public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException, GFacException {
+ if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GsisshHostType) { // this is because we don't have the right jobexecution context
+ // so attempting to get it from the registry
+ if (Constants.PUSH.equals(((GsisshHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getMonitorMode())) {
+ log.warn("During the out handler chain jobExecution context came null, so trying to handler");
+ ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
+ TaskDetails taskData = null;
+ try {
+ taskData = (TaskDetails) jobExecutionContext.getRegistry().get(DataType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
+ } catch (RegistryException e) {
+ log.error("Error retrieving job details from Registry");
+ throw new GFacHandlerException("Error retrieving job details from Registry", e);
+ }
+ JobDetails jobDetails = taskData.getJobDetailsList().get(0);
+ String jobDescription = jobDetails.getJobDescription();
+ if (jobDescription != null) {
+ JobDescriptor jobDescriptor = null;
+ try {
+ jobDescriptor = JobDescriptor.fromXML(jobDescription);
+ } catch (XmlException e1) {
+ e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+ applicationDeploymentDescription.getType().setScratchWorkingDirectory(
+ jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
+ applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
+ applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
+ applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
+ applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
+ }
+ }
+ }
+
+ if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
+ try {
+ GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
+ } catch (ApplicationSettingsException e) {
+ log.error(e.getMessage());
+ throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
+ }
+ }
+ super.invoke(jobExecutionContext);
+ DataTransferDetails detail = new DataTransferDetails();
+ TransferStatus status = new TransferStatus();
+
+ ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
+ .getApplicationDeploymentDescription().getType();
+ try {
+ Cluster cluster = null;
+ if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ } else {
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ }
+ if (cluster == null) {
+ throw new GFacProviderException("Security context is not set properly");
+ } else {
+ log.info("Successfully retrieved the Security Context");
+ }
+
+ // Get the Stdouts and StdErrs
+ String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());
+
+ TaskDetails taskData = jobExecutionContext.getTaskData();
+ String outputDataDir = null;
+ File localStdOutFile;
+ File localStdErrFile;
+
+ if (taskData.getAdvancedOutputDataHandling() != null) {
+ outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
+ }
+ if (outputDataDir == null) {
+ outputDataDir = File.separator + "tmp";
+ }
+ outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
+ (new File(outputDataDir)).mkdirs();
+
+
+ localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
+ localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
+// cluster.makeDirectory(outputDataDir);
+ cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
+ Thread.sleep(1000);
+ cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
+ Thread.sleep(1000);
+
+ String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
+ String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
+ status.setTransferState(TransferState.COMPLETE);
+ detail.setTransferStatus(status);
+ detail.setTransferDescription("STDOUT:" + stdOutStr);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+
+ status.setTransferState(TransferState.COMPLETE);
+ detail.setTransferStatus(status);
+ detail.setTransferDescription("STDERR:" + stdErrStr);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+
+
+ Map<String, ActualParameter> stringMap = new HashMap<String, ActualParameter>();
+ Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
+ Set<String> keys = output.keySet();
+ for (String paramName : keys) {
+ ActualParameter actualParameter = (ActualParameter) output.get(paramName);
+ if ("URI".equals(actualParameter.getType().getType().toString())) {
+
+ List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
+ if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
+ stringMap = OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr);
+ } else {
+ String valueList = outputList.get(0);
+ cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
+ jobExecutionContext.addOutputFile(outputDataDir + File.separator + valueList);
+ ((URIParameterType) actualParameter.getType()).setValue(valueList);
+ stringMap = new HashMap<String, ActualParameter>();
+ stringMap.put(paramName, actualParameter);
+ }
+ } else {
+ stringMap = OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr);
+ }
+ }
+ if (stringMap == null || stringMap.isEmpty()) {
+ throw new GFacHandlerException(
+ "Empty Output returned from the Application, Double check the application"
+ + "and ApplicationDescriptor output Parameter Names");
+ }
+ status.setTransferState(TransferState.DOWNLOAD);
+ detail.setTransferStatus(status);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+
+ app.setStandardError(localStdErrFile.getAbsolutePath());
+ app.setStandardOutput(localStdOutFile.getAbsolutePath());
+ app.setOutputDataDirectory(outputDataDir);
+ } catch (XmlException e) {
+ throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
+ } catch (ConnectionException e) {
+ throw new GFacHandlerException(e.getMessage(), e);
+ } catch (TransportException e) {
+ throw new GFacHandlerException(e.getMessage(), e);
+ } catch (IOException e) {
+ throw new GFacHandlerException(e.getMessage(), e);
+ } catch (Exception e) {
+ try {
+ status.setTransferState(TransferState.FAILED);
+ detail.setTransferStatus(status);
+ registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
+ GFacUtils.saveErrorDetails(e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE, jobExecutionContext.getTaskData().getTaskID());
+ } catch (Exception e1) {
+ throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
+ }
+ throw new GFacHandlerException("Error in retrieving results", e);
+ }
+
+ }
+
+ public void initProperties(Map<String, String> properties) throws GFacHandlerException, GFacException {
+
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
new file mode 100644
index 0000000..06e2f4a
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
@@ -0,0 +1,114 @@
+/*
+ *
+ * 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.gfac.provider.impl;
+
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gfac.notification.events.StartExecutionEvent;
+import org.apache.airavata.gfac.provider.GFacProviderException;
+import org.apache.airavata.gfac.utils.GFacUtils;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
+import org.apache.airavata.model.workspace.experiment.ErrorCategory;
+import org.apache.airavata.model.workspace.experiment.JobDetails;
+import org.apache.airavata.model.workspace.experiment.JobState;
+import org.apache.airavata.schemas.gfac.HostDescriptionType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Map;
+
+public class GSISSHProvider extends AbstractProvider{
+ private static final Logger log = LoggerFactory.getLogger(GSISSHProvider.class);
+
+ public void initProperties(Map<String, String> properties) throws GFacProviderException, GFacException {
+
+ }
+
+ public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+ super.initialize(jobExecutionContext);
+ }
+
+ public void execute(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+ log.info("Invoking GSISSH Provider Invoke ...");
+ jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
+ HostDescriptionType host = jobExecutionContext.getApplicationContext().
+ getHostDescription().getType();
+ HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
+ getApplicationDeploymentDescription().getType();
+ JobDetails jobDetails = new JobDetails();
+ String taskID = jobExecutionContext.getTaskData().getTaskID();
+ try {
+ Cluster cluster = null;
+ if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ }
+ if (cluster == null) {
+ throw new GFacProviderException("Security context is not set properly");
+ } else {
+ log.info("Successfully retrieved the Security Context");
+ }
+ // This installed path is a mandetory field, because this could change based on the computing resource
+ JobDescriptor jobDescriptor = GFacUtils.createJobDescriptor(jobExecutionContext, app, cluster);
+
+ log.info(jobDescriptor.toXML());
+
+ jobDetails.setJobDescription(jobDescriptor.toXML());
+
+ String jobID = cluster.submitBatchJob(jobDescriptor);
+ jobExecutionContext.setJobDetails(jobDetails);
+ if(jobID == null){
+ jobDetails.setJobID("none");
+ GFacUtils.saveJobStatus(jobDetails, JobState.FAILED, taskID);
+ }else{
+ jobDetails.setJobID(jobID);
+ GFacUtils.saveJobStatus(jobDetails, JobState.SUBMITTED, taskID);
+ }
+
+ } catch (SSHApiException e) {
+ String error = "Error submitting the job to host " + host.getHostAddress() + " message: " + e.getMessage();
+ log.error(error);
+ jobDetails.setJobID("none");
+ GFacUtils.saveJobStatus(jobDetails,JobState.FAILED,taskID);
+ GFacUtils.saveErrorDetails(error, CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ throw new GFacProviderException(error, e);
+ } catch (Exception e) {
+ String error = "Error submitting the job to host " + host.getHostAddress() + " message: " + e.getMessage();
+ log.error(error);
+ jobDetails.setJobID("none");
+ GFacUtils.saveJobStatus(jobDetails,JobState.FAILED,taskID);
+ GFacUtils.saveErrorDetails(error, CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
+ throw new GFacProviderException(error, e);
+ }
+ }
+
+ public void dispose(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
+ //To change body of implemented methods use File | Settings | File Templates.
+ }
+
+ public void cancelJob(String jobId, JobExecutionContext jobExecutionContext) throws GFacException {
+ //To change body of implemented methods use File | Settings | File Templates.
+ }
+}
http://git-wip-us.apache.org/repos/asf/airavata/blob/3361df33/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
new file mode 100644
index 0000000..29952de
--- /dev/null
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/util/GFACGSISSHUtils.java
@@ -0,0 +1,98 @@
+/*
+ *
+ * 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.gfac.util;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.gfac.Constants;
+import org.apache.airavata.gfac.GFacException;
+import org.apache.airavata.gfac.RequestData;
+import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
+import org.apache.airavata.gsi.ssh.api.Cluster;
+import org.apache.airavata.gsi.ssh.api.SSHApiException;
+import org.apache.airavata.gsi.ssh.api.ServerInfo;
+import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
+import org.apache.airavata.gsi.ssh.impl.PBSCluster;
+import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.util.CommonUtils;
+import org.apache.airavata.schemas.gfac.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+
+public class GFACGSISSHUtils {
+ private final static Logger logger = LoggerFactory.getLogger(GFACGSISSHUtils.class);
+
+ public static final String PBS_JOB_MANAGER = "pbs";
+ public static final String SLURM_JOB_MANAGER = "slurm";
+ public static final String SUN_GRID_ENGINE_JOB_MANAGER = "sge";
+
+ public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
+ RequestData requestData = new RequestData("default");
+ GSISecurityContext context = null;
+ try {
+ //todo fix this
+ context = new GSISecurityContext(null, requestData);
+ } catch (Exception e) {
+ throw new GFacException("An error occurred while creating GSI security context", e);
+ }
+ HostDescription registeredHost = jobExecutionContext.getApplicationContext().getHostDescription();
+ if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType
+ || registeredHost.getType() instanceof SSHHostType) {
+ logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
+ } else if (registeredHost.getType() instanceof GsisshHostType) {
+ GSIAuthenticationInfo authenticationInfo
+ = new MyProxyAuthenticationInfo(requestData.getMyProxyUserName(), requestData.getMyProxyPassword(), requestData.getMyProxyServerUrl(),
+ requestData.getMyProxyPort(), requestData.getMyProxyLifeTime(), System.getProperty(Constants.TRUSTED_CERTIFICATE_SYSTEM_PROPERTY));
+ GsisshHostType gsisshHostType = (GsisshHostType) registeredHost.getType();
+ ServerInfo serverInfo = new ServerInfo(requestData.getMyProxyUserName(), registeredHost.getType().getHostAddress(),
+ gsisshHostType.getPort());
+
+ Cluster pbsCluster = null;
+ try {
+ JobManagerConfiguration jConfig = null;
+ String installedParentPath = ((HpcApplicationDeploymentType)
+ jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
+ String jobManager = ((GsisshHostType) registeredHost.getType()).getJobManager();
+ if (jobManager == null) {
+ logger.error("No Job Manager is configured, so we are picking pbs as the default job manager");
+ jConfig = CommonUtils.getPBSJobManager(installedParentPath);
+ } else {
+ if (PBS_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
+ jConfig = CommonUtils.getPBSJobManager(installedParentPath);
+ } else if (SLURM_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
+ jConfig = CommonUtils.getSLURMJobManager(installedParentPath);
+ } else if (SUN_GRID_ENGINE_JOB_MANAGER.equalsIgnoreCase(jobManager)) {
+ jConfig = CommonUtils.getSGEJobManager(installedParentPath);
+ }
+ }
+ pbsCluster = new PBSCluster(serverInfo, authenticationInfo, jConfig);
+ } catch (SSHApiException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+
+ context.setPbsCluster(pbsCluster);
+ }
+
+ }
+}