Repository: airavata Updated Branches: refs/heads/master 8b978c62e -> 8cfe4f9ea
Removed airavata-client-api dependency from other modules Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d70b9d39 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d70b9d39 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d70b9d39 Branch: refs/heads/master Commit: d70b9d39d8aa9f1e7aa823b025dfe0c963fb0d55 Parents: 2b73d47 Author: shamrath <shameerai...@gmail.com> Authored: Wed Oct 8 11:40:32 2014 -0400 Committer: shamrath <shameerai...@gmail.com> Committed: Wed Oct 8 11:40:32 2014 -0400 ---------------------------------------------------------------------- .../client/tools/DocumentCreatorNew.java | 4 + .../client/tools/DocumentCreatorUtils.java | 4 + modules/gfac/airavata-gfac-service/pom.xml | 10 +- .../gfac/client/GfacClientFactoryTest.java | 13 +- modules/integration-tests/pom.xml | 22 +- .../apache/airavata/integration/BaseCaseIT.java | 17 +- .../airavata/integration/DataRetrievalIT.java | 6 +- .../airavata/integration/SimpleEchoIT.java | 2 +- .../integration/tools/DocumentCreatorNew.java | 832 +++++++++++++++++++ .../integration/tools/DocumentCreatorUtils.java | 160 ++++ .../client/OrchestratorClientFactoryTest.java | 12 +- modules/orchestrator/orchestrator-core/pom.xml | 10 +- .../orchestrator/core/BaseOrchestratorTest.java | 6 +- .../engine/interpretor/ExperimentTemplate.java | 37 - .../interpretor/WorkflowExecutionTemplate.java | 51 -- .../workflow/engine/util/XBayaUtil.java | 36 +- 16 files changed, 1063 insertions(+), 159 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java ---------------------------------------------------------------------- diff --git a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java index 1cf6a3c..d4604f1 100644 --- a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java +++ b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorNew.java @@ -40,6 +40,10 @@ import org.apache.thrift.TException; import java.io.File; import java.util.*; +/** + * This class has been moved to integration-tests module, use that instead of this + */ +@Deprecated public class DocumentCreatorNew { private AppCatalog appcatalog = null; http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorUtils.java ---------------------------------------------------------------------- diff --git a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorUtils.java b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorUtils.java index d510979..19e7e23 100644 --- a/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorUtils.java +++ b/modules/airavata-client/src/main/java/org/apache/airavata/client/tools/DocumentCreatorUtils.java @@ -40,6 +40,10 @@ import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager; import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType; import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; +/** + * This class has been moved to integration-tests module, use that instead of this + */ +@Deprecated public class DocumentCreatorUtils { public static ComputeResourcePreference createComputeResourcePreference(String computeResourceId, String scratchLocation, http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/gfac/airavata-gfac-service/pom.xml ---------------------------------------------------------------------- diff --git a/modules/gfac/airavata-gfac-service/pom.xml b/modules/gfac/airavata-gfac-service/pom.xml index ca12b41..683d523 100644 --- a/modules/gfac/airavata-gfac-service/pom.xml +++ b/modules/gfac/airavata-gfac-service/pom.xml @@ -35,11 +35,11 @@ <artifactId>slf4j-log4j12</artifactId> <version>${org.slf4j.version}</version> </dependency> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-client-api</artifactId> - <version>${project.version}</version> - </dependency> + <!--<dependency>--> + <!--<groupId>org.apache.airavata</groupId>--> + <!--<artifactId>airavata-client-api</artifactId>--> + <!--<version>${project.version}</version>--> + <!--</dependency>--> <dependency> <groupId>org.apache.airavata</groupId> <artifactId>airavata-common-utils</artifactId> http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/gfac/airavata-gfac-service/src/test/java/org/apache/airavata/gfac/client/GfacClientFactoryTest.java ---------------------------------------------------------------------- diff --git a/modules/gfac/airavata-gfac-service/src/test/java/org/apache/airavata/gfac/client/GfacClientFactoryTest.java b/modules/gfac/airavata-gfac-service/src/test/java/org/apache/airavata/gfac/client/GfacClientFactoryTest.java index b7a8104..21c137f 100644 --- a/modules/gfac/airavata-gfac-service/src/test/java/org/apache/airavata/gfac/client/GfacClientFactoryTest.java +++ b/modules/gfac/airavata-gfac-service/src/test/java/org/apache/airavata/gfac/client/GfacClientFactoryTest.java @@ -21,10 +21,10 @@ package org.apache.airavata.gfac.client; -import org.apache.airavata.client.AiravataAPIFactory; -import org.apache.airavata.client.api.AiravataAPI; -import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; -import org.apache.airavata.client.tools.DocumentCreator; +//import org.apache.airavata.client.AiravataAPIFactory; +//import org.apache.airavata.client.api.AiravataAPI; +//import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; +//import org.apache.airavata.client.tools.DocumentCreator; import org.apache.airavata.common.exception.ApplicationSettingsException; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.common.utils.AiravataZKUtils; @@ -46,14 +46,14 @@ import java.net.URL; public class GfacClientFactoryTest { private final static Logger logger = LoggerFactory.getLogger(GfacClientFactoryTest.class); - private DocumentCreator documentCreator; +// private DocumentCreator documentCreator; private GfacService.Client gfacClient; private Registry registry; private int NUM_CONCURRENT_REQUESTS = 1; Initialize initialize; GfacServer service; private static ServerCnxnFactory cnxnFactory; - +/* @Test public void setUp() { AiravataUtils.setExecutionAsServer(); @@ -93,6 +93,7 @@ public class GfacClientFactoryTest { } return airavataAPI; } +*/ private void storeDescriptors() { http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/pom.xml ---------------------------------------------------------------------- diff --git a/modules/integration-tests/pom.xml b/modules/integration-tests/pom.xml index 0b644ba..010f848 100644 --- a/modules/integration-tests/pom.xml +++ b/modules/integration-tests/pom.xml @@ -196,17 +196,17 @@ </exclusion> </exclusions> </dependency> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-client-api</artifactId> - <version>${project.version}</version> - <exclusions> - <exclusion> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-simple</artifactId> - </exclusion> - </exclusions> - </dependency> + <!--<dependency>--> + <!--<groupId>org.apache.airavata</groupId>--> + <!--<artifactId>airavata-client-api</artifactId>--> + <!--<version>${project.version}</version>--> + <!--<exclusions>--> + <!--<exclusion>--> + <!--<groupId>org.slf4j</groupId>--> + <!--<artifactId>slf4j-simple</artifactId>--> + <!--</exclusion>--> + <!--</exclusions>--> + <!--</dependency>--> <dependency> <groupId>org.apache.airavata</groupId> <artifactId>airavata-data-models</artifactId> http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java ---------------------------------------------------------------------- diff --git a/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java b/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java index 2d651c6..0b44013 100644 --- a/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java +++ b/modules/integration-tests/src/test/java/org/apache/airavata/integration/BaseCaseIT.java @@ -28,8 +28,9 @@ import java.util.Set; import junit.framework.Assert; -import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; -import org.apache.airavata.client.tools.DocumentCreatorNew; +//import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; +//import org.apache.airavata.client.tools.DocumentCreatorNew; +import org.apache.airavata.integration.tools.DocumentCreatorNew; import org.apache.airavata.model.util.ExperimentModelUtil; import org.apache.airavata.model.util.ProjectModelUtil; import org.apache.airavata.model.workspace.Project; @@ -40,12 +41,12 @@ import org.apache.airavata.model.workspace.experiment.Experiment; import org.apache.airavata.model.workspace.experiment.JobState; import org.apache.airavata.model.workspace.experiment.JobStatus; import org.apache.airavata.model.workspace.experiment.UserConfigurationData; -import org.apache.airavata.workflow.model.wf.Workflow; -import org.apache.airavata.ws.monitor.EventData; -import org.apache.airavata.ws.monitor.EventDataListenerAdapter; -import org.apache.airavata.ws.monitor.EventDataRepository; -import org.apache.airavata.ws.monitor.Monitor; -import org.apache.airavata.ws.monitor.MonitorUtil; +//import org.apache.airavata.workflow.model.wf.Workflow; +//import org.apache.airavata.ws.monitor.EventData; +//import org.apache.airavata.ws.monitor.EventDataListenerAdapter; +//import org.apache.airavata.ws.monitor.EventDataRepository; +//import org.apache.airavata.ws.monitor.Monitor; +//import org.apache.airavata.ws.monitor.MonitorUtil; import org.testng.annotations.BeforeTest; import org.testng.annotations.Test; http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/src/test/java/org/apache/airavata/integration/DataRetrievalIT.java ---------------------------------------------------------------------- diff --git a/modules/integration-tests/src/test/java/org/apache/airavata/integration/DataRetrievalIT.java b/modules/integration-tests/src/test/java/org/apache/airavata/integration/DataRetrievalIT.java index ec7707a..af9a729 100644 --- a/modules/integration-tests/src/test/java/org/apache/airavata/integration/DataRetrievalIT.java +++ b/modules/integration-tests/src/test/java/org/apache/airavata/integration/DataRetrievalIT.java @@ -23,9 +23,8 @@ package org.apache.airavata.integration; import org.airavata.appcatalog.cpi.AppCatalogException; import org.apache.airavata.api.Airavata.Client; -import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; -import org.apache.airavata.client.tools.DocumentCreatorNew; import org.apache.airavata.common.exception.ApplicationSettingsException; +import org.apache.airavata.integration.tools.DocumentCreatorNew; import org.apache.airavata.model.error.*; import org.apache.airavata.model.util.ExperimentModelUtil; import org.apache.airavata.model.util.ProjectModelUtil; @@ -174,8 +173,7 @@ public class DataRetrievalIT extends AbstractIntegrationTest { return getClient().getAllUserProjects(user); } - public String runExperiment(String user, String project) throws AiravataAPIInvocationException, - ApplicationSettingsException, AiravataClientConnectException, + public String runExperiment(String user, String project) throws ApplicationSettingsException, AiravataClientConnectException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException, ExperimentNotFoundException { List<DataObjectType> exInputs = new ArrayList<DataObjectType>(); http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/src/test/java/org/apache/airavata/integration/SimpleEchoIT.java ---------------------------------------------------------------------- diff --git a/modules/integration-tests/src/test/java/org/apache/airavata/integration/SimpleEchoIT.java b/modules/integration-tests/src/test/java/org/apache/airavata/integration/SimpleEchoIT.java index 68b6a0c..499dcda 100644 --- a/modules/integration-tests/src/test/java/org/apache/airavata/integration/SimpleEchoIT.java +++ b/modules/integration-tests/src/test/java/org/apache/airavata/integration/SimpleEchoIT.java @@ -24,7 +24,7 @@ package org.apache.airavata.integration; import java.util.ArrayList; import java.util.List; -import org.apache.airavata.client.tools.DocumentCreatorNew; +import org.apache.airavata.integration.tools.DocumentCreatorNew; import org.apache.airavata.model.util.ExperimentModelUtil; import org.apache.airavata.model.util.ProjectModelUtil; import org.apache.airavata.model.workspace.Project; http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorNew.java ---------------------------------------------------------------------- diff --git a/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorNew.java b/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorNew.java new file mode 100644 index 0000000..a94d32c --- /dev/null +++ b/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorNew.java @@ -0,0 +1,832 @@ +/* + * + * 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.integration.tools; + +import org.airavata.appcatalog.cpi.AppCatalog; +import org.airavata.appcatalog.cpi.AppCatalogException; +import org.apache.airavata.api.Airavata; +import org.apache.airavata.common.utils.ClientSettings; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; +import org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription; +import org.apache.airavata.model.appcatalog.appinterface.DataType; +import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription; +import org.apache.airavata.model.appcatalog.computeresource.JobManagerCommand; +import org.apache.airavata.model.appcatalog.computeresource.LOCALDataMovement; +import org.apache.airavata.model.appcatalog.computeresource.LOCALSubmission; +import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager; +import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType; +import org.apache.airavata.model.appcatalog.computeresource.SCPDataMovement; +import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission; +import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol; +import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; +import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile; +import org.apache.airavata.model.error.AiravataClientException; +import org.apache.airavata.model.error.AiravataSystemException; +import org.apache.airavata.model.error.InvalidRequestException; +import org.apache.thrift.TException; + +import java.io.File; +import java.util.Arrays; +import java.util.Date; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Map; +import java.util.UUID; + +public class DocumentCreatorNew { + + private AppCatalog appcatalog = null; + private String trestleshpcHostAddress = "trestles.sdsc.edu"; + private String lonestarHostAddress = "lonestar.tacc.utexas.edu"; + private String stampedeHostAddress = "stampede.tacc.xsede.org"; + private String gridftpAddress = "gsiftp://trestles-dm1.sdsc.edu:2811";; + private String gramAddress = "trestles-login1.sdsc.edu:2119/jobmanager-pbstest2"; + private String bigRed2HostAddress = "bigred2.uits.iu.edu"; + + //App Module Id's + private static String echoModuleId; + private static String amberModuleId; + private static String autoDockModuleId; + private static String espressoModuleId; + private static String gromacsModuleId; + private static String lammpsModuleId; + private static String nwChemModuleId; + private static String trinityModuleId; + private static String wrfModuleId; + private Airavata.Client client; + private GatewayResourceProfile gatewayResourceProfile; + + public DocumentCreatorNew(Airavata.Client client) throws AppCatalogException { + this.client = client; + } + + public String createLocalHostDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + //Define compute resource host + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription( + "localhost", new HashSet<String>(Arrays.asList(new String[]{"127.0.0.1"})), new HashSet<String>(Arrays.asList(new String[]{"127.0.0.1"}))); +// host.setIsEmpty(true); + host.setComputeResourceId(client.registerComputeResource(host)); + + LOCALSubmission localSubmission = new LOCALSubmission(); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.FORK, null, null, null); + localSubmission.setResourceJobManager(resourceJobManager); + client.addLocalSubmissionDetails(host.getComputeResourceId(), 1, localSubmission); + + LOCALDataMovement localDataMovement = new LOCALDataMovement(); + client.addLocalDataMovementDetails(host.getComputeResourceId(), 1, localDataMovement); + + //Define application module + ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.0.0", "Local host echo applications"); + module.setAppModuleId(client.registerApplicationModule(module)); + + //Define application interfaces + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); +// application.setIsEmpty(false); + application.setApplicationName("SimpleEcho0"); + application.addToApplicationModules(module.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", "Echo Input Data", null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + //Define application deployment + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "Local echo app depoyment"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + //Define gateway profile + ComputeResourcePreference computeResourcePreference = DocumentCreatorUtils.createComputeResourcePreference( + host.getComputeResourceId(), "/tmp", null, + false, null, + null, null); + gatewayResourceProfile = new GatewayResourceProfile(); +// gatewayResourceProfile.setGatewayID("default"); + gatewayResourceProfile.setGatewayName(ClientSettings.getSetting("gateway_id", "php_reference_gateway")); + gatewayResourceProfile.addToComputeResourcePreferences(computeResourcePreference); + String gatewayId = client.registerGatewayResourceProfile(gatewayResourceProfile); + gatewayResourceProfile.setGatewayID(gatewayId); + client.addGatewayComputeResourcePreference(gatewayResourceProfile.getGatewayID(), host.getComputeResourceId(), computeResourcePreference); + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + private GatewayResourceProfile getGatewayResourceProfile() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException { +// if (gatewayResourceProfile==null){ +// try { +// gatewayResourceProfile = client.getGatewayResourceProfile(ga); +// } catch (Exception e) { +// +// } + if (gatewayResourceProfile == null) { + gatewayResourceProfile = new GatewayResourceProfile(); +// gatewayResourceProfile.setGatewayID("default"); + gatewayResourceProfile.setGatewayName("default"); + gatewayResourceProfile.setGatewayID(client.registerGatewayResourceProfile(gatewayResourceProfile)); + } +// } + return gatewayResourceProfile; + + } + + public String createSSHHostDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("gw111.iu.xsede.org", null, null); + host.addToIpAddresses("gw111.iu.xsede.org"); + host.addToHostAliases("gw111.iu.xsede.org"); + host.setResourceDescription("gw111 ssh access"); + host.setComputeResourceId(client.registerComputeResource(host)); + + + SSHJobSubmission jobSubmission = new SSHJobSubmission(); + jobSubmission.setSshPort(22); + jobSubmission.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.FORK, null, null, null); + jobSubmission.setResourceJobManager(resourceJobManager); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, jobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.1", null); + module.setAppModuleId(client.registerApplicationModule(module)); + ; + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "SSHEchoApplication"); + client.registerApplicationDeployment(deployment); + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); +// application.setIsEmpty(false); + application.setApplicationName("SSHEcho1"); + application.addToApplicationModules(module.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", null, null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + client.registerApplicationInterface(application); + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/tmp", null, false, null, null, null)); + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + // +// public void createGramDocs() { +//// /* +//// creating host descriptor for gram +//// */ +//// HostDescription host = new HostDescription(GlobusHostType.type); +//// host.getType().setHostAddress(trestleshpcHostAddress); +//// host.getType().setHostName(trestleshpcHostAddress); +//// ((GlobusHostType) host.getType()).setGlobusGateKeeperEndPointArray(new String[]{gramAddress}); +//// ((GlobusHostType) host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress}); +//// try { +//// airavataAPI.getApplicationManager().saveHostDescription(host); +//// } catch (AiravataAPIInvocationException e) { +//// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. +//// } +//// +//// +//// /* +//// * Service Description creation and saving +//// */ +//// String serviceName = "SimpleEcho1"; +//// ServiceDescription serv = new ServiceDescription(); +//// serv.getType().setName(serviceName); +//// +//// List<InputParameterType> inputList = new ArrayList<InputParameterType>(); +//// List<OutputParameterType> outputList = new ArrayList<OutputParameterType>(); +//// +//// InputParameterType input = InputParameterType.Factory.newInstance(); +//// input.setParameterName("echo_input"); +//// ParameterType parameterType = input.addNewParameterType(); +//// parameterType.setType(DataType.STRING); +//// parameterType.setName("String"); +//// +//// OutputParameterType output = OutputParameterType.Factory.newInstance(); +//// output.setParameterName("echo_output"); +//// ParameterType parameterType1 = output.addNewParameterType(); +//// parameterType1.setType(DataType.STRING); +//// parameterType1.setName("String"); +//// +//// inputList.add(input); +//// outputList.add(output); +//// +//// InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList.size()]); +//// OutputParameterType[] outputParamList = outputList.toArray(new OutputParameterType[outputList.size()]); +//// +//// serv.getType().setInputParametersArray(inputParamList); +//// serv.getType().setOutputParametersArray(outputParamList); +//// try { +//// airavataAPI.getApplicationManager().saveServiceDescription(serv); +//// } catch (AiravataAPIInvocationException e) { +//// e.printStackTrace(); +//// } +//// +//// /* +//// Application descriptor creation and saving +//// */ +//// ApplicationDescription appDesc = new ApplicationDescription(HpcApplicationDeploymentType.type); +//// HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc.getType(); +//// ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance(); +//// name.setStringValue("EchoLocal"); +//// app.setApplicationName(name); +//// ProjectAccountType projectAccountType = app.addNewProjectAccount(); +//// projectAccountType.setProjectAccountNumber("sds128"); +//// +//// QueueType queueType = app.addNewQueue(); +//// queueType.setQueueName("normal"); +//// +//// app.setCpuCount(1); +//// app.setJobType(JobTypeType.SERIAL); +//// app.setNodeCount(1); +//// app.setProcessorsPerNode(1); +//// +//// /* +//// * Use bat file if it is compiled on Windows +//// */ +//// app.setExecutableLocation("/bin/echo"); +//// +//// /* +//// * Default tmp location +//// */ +//// String tempDir = "/home/ogce/scratch"; +//// app.setScratchWorkingDirectory(tempDir); +//// app.setMaxMemory(10); +//// +//// +//// try { +//// airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, trestleshpcHostAddress, appDesc); +//// } catch (AiravataAPIInvocationException e) { +//// e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. +//// } +// } +// + public String createPBSDocsForOGCE_Echo() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null); + host.addToIpAddresses(trestleshpcHostAddress); + host.addToHostAliases(trestleshpcHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(22); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule module1 = DocumentCreatorUtils.createApplicationModule("echo", "1.2", null); + module1.setAppModuleId(client.registerApplicationModule(module1)); + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); +// application.setIsEmpty(false); + application.setApplicationName("SimpleEcho2"); + application.addToApplicationModules(module1.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", "echo_input", null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module1.getAppModuleId(), "/home/ogce/echo.sh", ApplicationParallelismType.SERIAL, "Echo application"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null)); + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + public String createPBSDocsForOGCE_WRF() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null); + host.addToIpAddresses(trestleshpcHostAddress); + host.addToHostAliases(trestleshpcHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(22); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null)); + + ApplicationModule module2 = DocumentCreatorUtils.createApplicationModule("wrf", "1.0.0", null); + module2.setAppModuleId(client.registerApplicationModule(module2)); + ApplicationInterfaceDescription application2 = new ApplicationInterfaceDescription(); +// application2.setIsEmpty(false); + application2.setApplicationName("WRF"); + application2.addToApplicationModules(module2.getAppModuleId()); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Namelist", "WRF_Namelist", null, null, DataType.URI)); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Boundary_File", "WRF_Boundary_File", null, null, DataType.URI)); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Input_File", "WRF_Input_File", null, null, DataType.URI)); + + application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Output", null, DataType.URI)); + application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Execution_Log", null, DataType.URI)); + application2.setApplicationInterfaceId(client.registerApplicationInterface(application2)); + + ApplicationDeploymentDescription deployment2 = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module2.getAppModuleId(), "/home/ogce/production/app_wrappers/wrf_wrapper.sh", ApplicationParallelismType.MPI, "WRF"); + deployment2.setAppDeploymentId(client.registerApplicationDeployment(deployment2)); + return host.getComputeResourceId() + "," + application2.getApplicationInterfaceId(); + } + + public String createSlumWRFDocs() throws AppCatalogException, TException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null); + host.addToHostAliases(stampedeHostAddress); + host.addToIpAddresses(stampedeHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push"); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(2222); + + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null)); + + ApplicationModule module2 = DocumentCreatorUtils.createApplicationModule("wrf", "1.0.0", null); + module2.setAppModuleId(client.registerApplicationModule(module2)); + ApplicationInterfaceDescription application2 = new ApplicationInterfaceDescription(); + // application2.setIsEmpty(false); + application2.setApplicationName("WRF"); + application2.addToApplicationModules(module2.getAppModuleId()); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Namelist", "WRF_Namelist", null, null, DataType.URI)); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Boundary_File", "WRF_Boundary_File", null, null, DataType.URI)); + application2.addToApplicationInputs(DocumentCreatorUtils.createAppInput("WRF_Input_File", "WRF_Input_File", null, null, DataType.URI)); + + application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Output", null, DataType.URI)); + application2.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("WRF_Execution_Log", null, DataType.URI)); + application2.setApplicationInterfaceId(client.registerApplicationInterface(application2)); + + ApplicationDeploymentDescription deployment2 = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module2.getAppModuleId(), "/home1/01437/ogce/production/app_wrappers/wrf_wrapper.sh", ApplicationParallelismType.MPI, "WRF"); + deployment2.setAppDeploymentId(client.registerApplicationDeployment(deployment2)); + return host.getComputeResourceId() + "," + application2.getApplicationInterfaceId(); + + } + + public String createSlurmDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null); + host.addToHostAliases(stampedeHostAddress); + host.addToIpAddresses(stampedeHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push"); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(2222); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.3", null); + module.setAppModuleId(client.registerApplicationModule(module)); + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); +// application.setIsEmpty(false); + application.setApplicationName("SimpleEcho3"); + application.addToApplicationModules(module.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", null, null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "EchoLocal"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null)); + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + public String createSGEDocs() throws AppCatalogException, InvalidRequestException, AiravataClientException, AiravataSystemException, TException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(lonestarHostAddress, null, null); + host.addToHostAliases(lonestarHostAddress); + host.addToIpAddresses(lonestarHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.UGE, "/opt/sge6.2/bin/lx24-amd64/", null, null); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(22); + + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.4", null); + module.setAppModuleId(client.registerApplicationModule(module)); + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); +// application.setIsEmpty(false); + application.setApplicationName("SimpleEcho4"); + application.addToApplicationModules(module.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", null, null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/bin/echo", ApplicationParallelismType.SERIAL, "EchoLocal"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null)); + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + +// public void createEchoHostDocs() { +// String serviceName = "Echo"; +// ServiceDescription serviceDescription = new ServiceDescription(); +// List<InputParameterType> inputParameters = new ArrayList<InputParameterType>(); +// List<OutputParameterType> outputParameters = new ArrayList<OutputParameterType>(); +// serviceDescription.getType().setName(serviceName); +// serviceDescription.getType().setDescription("Echo service"); +// // Creating input parameters +// InputParameterType parameter = InputParameterType.Factory.newInstance(); +// parameter.setParameterName("echo_input"); +// parameter.setParameterDescription("echo input"); +// ParameterType parameterType = parameter.addNewParameterType(); +// parameterType.setType(DataType.STRING); +// parameterType.setName("String"); +// inputParameters.add(parameter); +// +// // Creating output parameters +// OutputParameterType outputParameter = OutputParameterType.Factory.newInstance(); +// outputParameter.setParameterName("echo_output"); +// outputParameter.setParameterDescription("Echo output"); +// ParameterType outputParaType = outputParameter.addNewParameterType(); +// outputParaType.setType(DataType.STRING); +// outputParaType.setName("String"); +// outputParameters.add(outputParameter); +// +// // Setting input and output parameters to serviceDescriptor +// serviceDescription.getType().setInputParametersArray(inputParameters.toArray(new InputParameterType[] {})); +// serviceDescription.getType().setOutputParametersArray(outputParameters.toArray(new OutputParameterType[] {})); +// +// try { +// airavataAPI.getApplicationManager().saveServiceDescription(serviceDescription); +// } catch (AiravataAPIInvocationException e) { +// e.printStackTrace(); // To change body of catch statement use File | +// // Settings | File Templates. +// } +// // Localhost +// ApplicationDescription applicationDeploymentDescription = new ApplicationDescription(); +// ApplicationDeploymentDescriptionType applicationDeploymentDescriptionType = applicationDeploymentDescription.getType(); +// applicationDeploymentDescriptionType.addNewApplicationName().setStringValue(serviceName); +// applicationDeploymentDescriptionType.setExecutableLocation("/bin/echo"); +// applicationDeploymentDescriptionType.setScratchWorkingDirectory("/tmp"); +// +// try { +// airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, "localhost", applicationDeploymentDescription); +// } catch (AiravataAPIInvocationException e) { +// e.printStackTrace(); // To change body of catch statement use File | +// // Settings | File Templates. +// } +// // Stampede +// /* +// * Application descriptor creation and saving +// */ +// ApplicationDescription appDesc1 = new ApplicationDescription(HpcApplicationDeploymentType.type); +// HpcApplicationDeploymentType app1 = (HpcApplicationDeploymentType) appDesc1.getType(); +// ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance(); +// name.setStringValue(serviceName); +// app1.setApplicationName(name); +// ProjectAccountType projectAccountType = app1.addNewProjectAccount(); +// projectAccountType.setProjectAccountNumber("TG-STA110014S"); +// +// QueueType queueType = app1.addNewQueue(); +// queueType.setQueueName("normal"); +// +// app1.setCpuCount(1); +// app1.setJobType(JobTypeType.SERIAL); +// app1.setNodeCount(1); +// app1.setProcessorsPerNode(1); +// app1.setMaxWallTime(10); +// /* +// * Use bat file if it is compiled on Windows +// */ +// app1.setExecutableLocation("/bin/echo"); +// +// /* +// * Default tmp location +// */ +// String tempDir = "/home1/01437/ogce"; +// +// app1.setScratchWorkingDirectory(tempDir); +// app1.setInstalledParentPath("/usr/bin/"); +// +// try { +// airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, stampedeHostAddress, appDesc1); +// } catch (AiravataAPIInvocationException e) { +// e.printStackTrace(); // To change body of catch statement use File | +// // Settings | File Templates. +// } +// // Trestles +// /* +// * Application descriptor creation and saving +// */ +// ApplicationDescription appDesc2 = new ApplicationDescription(HpcApplicationDeploymentType.type); +// HpcApplicationDeploymentType app2 = (HpcApplicationDeploymentType) appDesc2.getType(); +// ApplicationDeploymentDescriptionType.ApplicationName name2 = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance(); +// name2.setStringValue(serviceName); +// app2.setApplicationName(name); +// ProjectAccountType projectAccountType2 = app2.addNewProjectAccount(); +// projectAccountType2.setProjectAccountNumber("sds128"); +// +// QueueType queueType2 = app2.addNewQueue(); +// queueType2.setQueueName("normal"); +// +// app2.setCpuCount(1); +// app2.setJobType(JobTypeType.SERIAL); +// app2.setNodeCount(1); +// app2.setProcessorsPerNode(1); +// app2.setMaxWallTime(10); +// /* +// * Use bat file if it is compiled on Windows +// */ +// app2.setExecutableLocation("/bin/echo"); +// +// /* +// * Default tmp location +// */ +// String tempDir2 = "/home/ogce/scratch"; +// +// app2.setScratchWorkingDirectory(tempDir2); +// app2.setInstalledParentPath("/opt/torque/bin/"); +// +// try { +// airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, trestleshpcHostAddress, appDesc2); +// } catch (AiravataAPIInvocationException e) { +// e.printStackTrace(); // To change body of catch statement use File | +// // Settings | File Templates. +// } +// // Lonestar +// /* +// * Application descriptor creation and saving +// */ +// ApplicationDescription appDesc3 = new ApplicationDescription(HpcApplicationDeploymentType.type); +// HpcApplicationDeploymentType app3 = (HpcApplicationDeploymentType) appDesc3.getType(); +// ApplicationDeploymentDescriptionType.ApplicationName name3 = ApplicationDeploymentDescriptionType.ApplicationName.Factory.newInstance(); +// name3.setStringValue(serviceName); +// app3.setApplicationName(name); +// ProjectAccountType projectAccountType3 = app3.addNewProjectAccount(); +// projectAccountType3.setProjectAccountNumber("TG-STA110014S"); +// +// QueueType queueType3 = app3.addNewQueue(); +// queueType3.setQueueName("normal"); +// +// app3.setCpuCount(1); +// app3.setJobType(JobTypeType.SERIAL); +// app3.setNodeCount(1); +// app3.setProcessorsPerNode(1); +// app3.setMaxWallTime(10); +// /* +// * Use bat file if it is compiled on Windows +// */ +// app3.setExecutableLocation("/bin/echo"); +// +// /* +// * Default tmp location +// */ +// String tempDir3 = "/home1/01437/ogce"; +// +// app3.setScratchWorkingDirectory(tempDir3); +// app3.setInstalledParentPath("/opt/sge6.2/bin/lx24-amd64/"); +// +// try { +// airavataAPI.getApplicationManager().saveApplicationDescription(serviceName, lonestarHostAddress, appDesc3); +// } catch (AiravataAPIInvocationException e) { +// e.printStackTrace(); // To change body of catch statement use File | +// // Settings | File Templates. +// } +// +// } + + public String createBigRedDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("bigred2", null, null); + host.addToHostAliases(bigRed2HostAddress); + host.addToIpAddresses(bigRed2HostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + + Map<JobManagerCommand, String> commands = new HashMap<JobManagerCommand, String>(); + commands.put(JobManagerCommand.SUBMISSION, "aprun -n"); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.UGE, "/opt/torque/torque-4.2.3.1/bin/", commands, null); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + sshJobSubmission.setSshPort(22); + + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule module = DocumentCreatorUtils.createApplicationModule("echo", "1.5", null); + module.setAppModuleId(client.registerApplicationModule(module)); + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); + application.setApplicationName("SimpleEchoBR"); + application.addToApplicationModules(module.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("echo_input", "echo_input", null, null, DataType.STRING)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("echo_output", null, DataType.STRING)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), module.getAppModuleId(), "/N/u/lginnali/BigRed2/myjob/test.sh", ApplicationParallelismType.SERIAL, "EchoLocal"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + String date = (new Date()).toString(); + date = date.replaceAll(" ", "_"); + date = date.replaceAll(":", "_"); + String tempDir = "/N/u/lginnali/BigRed2/myjob"; + tempDir = tempDir + File.separator + "SimpleEcho" + "_" + date + "_" + UUID.randomUUID(); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), tempDir, "TG-STA110014S", false, null, null, null)); + + + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + public String createBigRedAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription("bigred2", null, null); + host.addToHostAliases(bigRed2HostAddress); + host.addToIpAddresses(bigRed2HostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + + Map<JobManagerCommand, String> commands = new HashMap<JobManagerCommand, String>(); + commands.put(JobManagerCommand.SUBMISSION, "aprun -n 4"); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.UGE, "/opt/torque/torque-4.2.3.1/bin/", commands, null); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + sshJobSubmission.setSshPort(22); + + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.SSH_KEYS); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + + ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null); + amodule.setAppModuleId(client.registerApplicationModule(amodule)); + + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); + application.setApplicationName("AmberBR2"); + application.addToApplicationModules(amodule.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/N/u/cgateway/BigRed2/sandbox/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberBR2"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + + String date = (new Date()).toString(); + date = date.replaceAll(" ", "_"); + date = date.replaceAll(":", "_"); + String tempDir = "/N/u/cgateway/BigRed2/sandbox/jobs"; + tempDir = tempDir + File.separator + + "Amber"; + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), tempDir, null, false, null, null, null)); + + + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + } + + public String createStampedeAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(stampedeHostAddress, null, null); + host.addToHostAliases(stampedeHostAddress); + host.addToIpAddresses(stampedeHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.SLURM, "/usr/bin/", null, "push"); + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(2222); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null); + amodule.setAppModuleId(client.registerApplicationModule(amodule)); + + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); + application.setApplicationName("AmberBR2"); + application.addToApplicationModules(amodule.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/home1/01437/ogce/production/app_wrappers/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberStampede"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/home1/01437/ogce", "TG-STA110014S", false, null, null, null)); + + + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + + } + + public String createTrestlesAmberDocs() throws InvalidRequestException, AiravataClientException, AiravataSystemException, TException, AppCatalogException { + ComputeResourceDescription host = DocumentCreatorUtils.createComputeResourceDescription(trestleshpcHostAddress, null, null); + host.addToIpAddresses(trestleshpcHostAddress); + host.addToHostAliases(trestleshpcHostAddress); + host.setComputeResourceId(client.registerComputeResource(host)); + + SSHJobSubmission sshJobSubmission = new SSHJobSubmission(); + ResourceJobManager resourceJobManager = DocumentCreatorUtils.createResourceJobManager(ResourceJobManagerType.PBS, "/opt/torque/bin/", null, null); + sshJobSubmission.setResourceJobManager(resourceJobManager); + sshJobSubmission.setSecurityProtocol(SecurityProtocol.GSI); + sshJobSubmission.setSshPort(22); + client.addSSHJobSubmissionDetails(host.getComputeResourceId(), 1, sshJobSubmission); + + SCPDataMovement scpDataMovement = new SCPDataMovement(); + scpDataMovement.setSecurityProtocol(SecurityProtocol.GSI); + scpDataMovement.setSshPort(22); + client.addSCPDataMovementDetails(host.getComputeResourceId(), 1, scpDataMovement); + + ApplicationModule amodule = DocumentCreatorUtils.createApplicationModule("Amber", "12.0", null); + amodule.setAppModuleId(client.registerApplicationModule(amodule)); + + + ApplicationInterfaceDescription application = new ApplicationInterfaceDescription(); + application.setApplicationName("AmberTrestles"); + application.addToApplicationModules(amodule.getAppModuleId()); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_HEAT_RST", "AMBER_HEAT_RST", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PROD_IN", "AMBER_PROD_IN", null, null, DataType.URI)); + application.addToApplicationInputs(DocumentCreatorUtils.createAppInput("AMBER_PRMTOP", "AMBER_PRMTOP", null, null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.info", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.mdcrd", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.out", null, DataType.URI)); + application.addToApplicationOutputs(DocumentCreatorUtils.createAppOutput("AMBER_Prod.rst", null, DataType.URI)); + application.setApplicationInterfaceId(client.registerApplicationInterface(application)); + + ApplicationDeploymentDescription deployment = DocumentCreatorUtils.createApplicationDeployment(host.getComputeResourceId(), amodule.getAppModuleId(), "/home/ogce/production/app_wrappers/amber_wrapper.sh", ApplicationParallelismType.SERIAL, "AmberStampede"); + deployment.setAppDeploymentId(client.registerApplicationDeployment(deployment)); + + client.addGatewayComputeResourcePreference(getGatewayResourceProfile().getGatewayID(), host.getComputeResourceId(), DocumentCreatorUtils.createComputeResourcePreference(host.getComputeResourceId(), "/oasis/scratch/trestles/ogce/temp_project/", "sds128", false, null, null, null)); + + + return host.getComputeResourceId() + "," + application.getApplicationInterfaceId(); + + } + + +} + http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorUtils.java ---------------------------------------------------------------------- diff --git a/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorUtils.java b/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorUtils.java new file mode 100644 index 0000000..7805d1f --- /dev/null +++ b/modules/integration-tests/src/test/java/org/apache/airavata/integration/tools/DocumentCreatorUtils.java @@ -0,0 +1,160 @@ +/* + * + * 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.integration.tools; + +import org.airavata.appcatalog.cpi.AppCatalogException; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule; +import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; +import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType; +import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType; +import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription; +import org.apache.airavata.model.appcatalog.computeresource.DataMovementInterface; +import org.apache.airavata.model.appcatalog.computeresource.DataMovementProtocol; +import org.apache.airavata.model.appcatalog.computeresource.JobManagerCommand; +import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface; +import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol; +import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManager; +import org.apache.airavata.model.appcatalog.computeresource.ResourceJobManagerType; +import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; + +import java.util.Map; +import java.util.Set; + +public class DocumentCreatorUtils { + + public static ComputeResourcePreference createComputeResourcePreference(String computeResourceId, String scratchLocation, + String allocationProjectNumber, boolean overridebyAiravata, + String preferredBatchQueue, String preferredJobSubmissionProtocol, + String preferredDataMovementProtocol) throws AppCatalogException { + ComputeResourcePreference computeResourcePreference = new ComputeResourcePreference(); + computeResourcePreference.setComputeResourceId(computeResourceId); + computeResourcePreference.setOverridebyAiravata(overridebyAiravata); + computeResourcePreference.setAllocationProjectNumber(allocationProjectNumber); + computeResourcePreference.setPreferredBatchQueue(preferredBatchQueue); + computeResourcePreference.setPreferredDataMovementProtocol(preferredDataMovementProtocol); + computeResourcePreference.setPreferredJobSubmissionProtocol(preferredJobSubmissionProtocol); + computeResourcePreference.setScratchLocation(scratchLocation); + return computeResourcePreference; + } + + public static ApplicationDeploymentDescription createApplicationDeployment( + String computeResourceId, String appModuleId, + String executablePath, ApplicationParallelismType parallelism, String appDeploymentDescription) { + ApplicationDeploymentDescription deployment = new ApplicationDeploymentDescription(); +// deployment.setIsEmpty(false); + deployment.setAppDeploymentDescription(appDeploymentDescription); + deployment.setAppModuleId(appModuleId); + deployment.setComputeHostId(computeResourceId); + deployment.setExecutablePath(executablePath); + deployment.setParallelism(parallelism); + return deployment; + } + + public static ApplicationModule createApplicationModule(String appModuleName, + String appModuleVersion, String appModuleDescription) { + ApplicationModule module = new ApplicationModule(); + module.setAppModuleDescription(appModuleDescription); + module.setAppModuleName(appModuleName); + module.setAppModuleVersion(appModuleVersion); + return module; + } + + public static DataMovementInterface createDataMovementInterface( + String dataMovementInterfaceId, + DataMovementProtocol dataMovementProtocolType, int priorityOrder) { + DataMovementInterface dataMovementInterface = new DataMovementInterface(); + dataMovementInterface.setDataMovementInterfaceId(dataMovementInterfaceId); + dataMovementInterface.setDataMovementProtocol(dataMovementProtocolType); + dataMovementInterface.setPriorityOrder(priorityOrder); + return dataMovementInterface; + } + + public static JobSubmissionInterface createJobSubmissionInterface( + String jobSubmissionInterfaceId, + JobSubmissionProtocol jobSubmissionProtocolType, int priorityOrder) { + JobSubmissionInterface jobSubmissionInterface = new JobSubmissionInterface(); + jobSubmissionInterface.setJobSubmissionInterfaceId(jobSubmissionInterfaceId); + jobSubmissionInterface.setJobSubmissionProtocol(jobSubmissionProtocolType); + jobSubmissionInterface.setPriorityOrder(priorityOrder); + return jobSubmissionInterface; + } + + public static ComputeResourceDescription createComputeResourceDescription( + String hostName, Set<String> hostAliases, Set<String> ipAddresses) { + ComputeResourceDescription host = new ComputeResourceDescription(); + host.setHostName(hostName); + host.setIpAddresses(ipAddresses); + host.setHostAliases(hostAliases); + return host; + } + + public static ResourceJobManager createResourceJobManager( + ResourceJobManagerType resourceJobManagerType, + String jobManagerBinPath, + Map<JobManagerCommand, String> jobManagerCommands, + String pushMonitoringEndpoint) { + ResourceJobManager resourceJobManager=new ResourceJobManager();; + resourceJobManager.setResourceJobManagerType(resourceJobManagerType); + resourceJobManager.setJobManagerBinPath(jobManagerBinPath); + resourceJobManager.setJobManagerCommands(jobManagerCommands); + resourceJobManager.setPushMonitoringEndpoint(pushMonitoringEndpoint); + return resourceJobManager; + } + + public static InputDataObjectType createAppInput (String inputName, String argumentName, String description, String value, org.apache.airavata.model.appcatalog.appinterface.DataType type ){ + InputDataObjectType input = new InputDataObjectType(); +// input.setIsEmpty(false); + if (inputName!=null) { + input.setName(inputName); + } + if (value!=null) { + input.setValue(value); + } + if (type!=null) { + input.setType(type); + } + if (argumentName!=null) { + input.setApplicationArgument(argumentName); + } + if (description!=null) { + input.setUserFriendlyDescription(description); + } + return input; + } + + public static OutputDataObjectType createAppOutput (String inputName, String value, org.apache.airavata.model.appcatalog.appinterface.DataType type ){ + OutputDataObjectType outputDataObjectType = new OutputDataObjectType(); +// outputDataObjectType.setIsEmpty(false); + if (inputName!=null) { + outputDataObjectType.setName(inputName); + } + if (value!=null) { + outputDataObjectType.setValue(value); + } + if (type!=null) { + outputDataObjectType.setType(type); + } + return outputDataObjectType; + } + +} http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java b/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java index 72d912b..28687c9 100644 --- a/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java +++ b/modules/orchestrator/airavata-orchestrator-service/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java @@ -23,10 +23,10 @@ package org.apache.airavata.orchestrator.client; import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; -import org.apache.airavata.client.AiravataAPIFactory; -import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; -import org.apache.airavata.client.tools.DocumentCreator; -import org.apache.airavata.client.tools.DocumentCreatorNew; +//import org.apache.airavata.client.AiravataAPIFactory; +//import org.apache.airavata.client.api.exception.AiravataAPIInvocationException; +//import org.apache.airavata.client.tools.DocumentCreator; +//import org.apache.airavata.client.tools.DocumentCreatorNew; import org.apache.airavata.common.exception.ApplicationSettingsException; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.common.utils.AiravataZKUtils; @@ -42,7 +42,7 @@ import org.apache.zookeeper.server.ServerCnxnFactory; import org.junit.Test; public class OrchestratorClientFactoryTest { - private DocumentCreatorNew documentCreator; +/* private DocumentCreatorNew documentCreator; private OrchestratorService.Client orchestratorClient; private Registry registry; private int NUM_CONCURRENT_REQUESTS = 1; @@ -88,5 +88,5 @@ public class OrchestratorClientFactoryTest { private void storeDescriptors() { - } + }*/ } http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/orchestrator/orchestrator-core/pom.xml ---------------------------------------------------------------------- diff --git a/modules/orchestrator/orchestrator-core/pom.xml b/modules/orchestrator/orchestrator-core/pom.xml index 61a7efc..7f6d991 100644 --- a/modules/orchestrator/orchestrator-core/pom.xml +++ b/modules/orchestrator/orchestrator-core/pom.xml @@ -54,11 +54,11 @@ the License. --> <artifactId>airavata-gfac-core</artifactId> <version>${project.version}</version> </dependency> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-client-api</artifactId> - <version>${project.version}</version> - </dependency> + <!--<dependency>--> + <!--<groupId>org.apache.airavata</groupId>--> + <!--<artifactId>airavata-client-api</artifactId>--> + <!--<version>${project.version}</version>--> + <!--</dependency>--> <dependency> <groupId>org.apache.airavata</groupId> <artifactId>airavata-gfac-service</artifactId> http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java ---------------------------------------------------------------------- diff --git a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java index cbfb573..a27281e 100644 --- a/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java +++ b/modules/orchestrator/orchestrator-core/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java @@ -23,7 +23,7 @@ package org.apache.airavata.orchestrator.core; import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; -import org.apache.airavata.client.tools.DocumentCreatorNew; +//import org.apache.airavata.client.tools.DocumentCreatorNew; import org.apache.airavata.common.utils.ServerSettings; import org.apache.airavata.model.error.AiravataClientConnectException; import org.apache.airavata.orchestrator.core.util.Initialize; @@ -34,7 +34,7 @@ import org.apache.airavata.persistance.registry.jpa.resources.WorkerResource; public class BaseOrchestratorTest { - private GatewayResource gatewayResource; +/* private GatewayResource gatewayResource; private WorkerResource workerResource; private UserResource userResource; private Initialize initialize; @@ -90,5 +90,5 @@ public class BaseOrchestratorTest { private void settingServerProperties(){ - } + }*/ } http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/ExperimentTemplate.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/ExperimentTemplate.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/ExperimentTemplate.java deleted file mode 100644 index 3a7cb3d..0000000 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/ExperimentTemplate.java +++ /dev/null @@ -1,37 +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.workflow.engine.interpretor; - -import java.util.List; - -public class ExperimentTemplate { - private List<WorkflowExecutionTemplate> workflowExecutionTemplates; - - public List<WorkflowExecutionTemplate> getWorkflowExecutionTemplates() { - return workflowExecutionTemplates; - } - - public void setWorkflowExecutionTemplates( - List<WorkflowExecutionTemplate> workflowExecutionTemplates) { - this.workflowExecutionTemplates = workflowExecutionTemplates; - } -} http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowExecutionTemplate.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowExecutionTemplate.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowExecutionTemplate.java deleted file mode 100644 index 49af89b..0000000 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/interpretor/WorkflowExecutionTemplate.java +++ /dev/null @@ -1,51 +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.workflow.engine.interpretor; - -import java.util.List; - -import org.apache.airavata.client.api.ExperimentAdvanceOptions; -import org.apache.airavata.workflow.model.wf.WorkflowInput; - -public class WorkflowExecutionTemplate { - private String workflowTemplateName; - private List<WorkflowInput> input; - private ExperimentAdvanceOptions advanceOptions; - public String getWorkflowTemplateName() { - return workflowTemplateName; - } - public void setWorkflowTemplateName(String workflowTemplateName) { - this.workflowTemplateName = workflowTemplateName; - } - public List<WorkflowInput> getInput() { - return input; - } - public void setInput(List<WorkflowInput> input) { - this.input = input; - } - public ExperimentAdvanceOptions getAdvanceOptions() { - return advanceOptions; - } - public void setAdvanceOptions(ExperimentAdvanceOptions advanceOptions) { - this.advanceOptions = advanceOptions; - } -} http://git-wip-us.apache.org/repos/asf/airavata/blob/d70b9d39/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java ---------------------------------------------------------------------- diff --git a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java index 9735c52..ddee1ec 100644 --- a/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java +++ b/modules/workflow-model/workflow-engine/src/main/java/org/apache/airavata/workflow/engine/util/XBayaUtil.java @@ -21,22 +21,6 @@ package org.apache.airavata.workflow.engine.util; -import java.io.ByteArrayInputStream; -import java.io.IOException; -import java.net.HttpURLConnection; -import java.net.SocketTimeoutException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collection; -import java.util.Iterator; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; - -import javax.xml.parsers.ParserConfigurationException; - -import org.apache.airavata.client.stub.interpretor.NameValue; import org.apache.airavata.common.utils.StringUtil; import org.apache.airavata.workflow.engine.interpretor.WorkFlowInterpreterException; import org.apache.airavata.workflow.engine.invoker.Invoker; @@ -50,15 +34,23 @@ import org.apache.airavata.workflow.model.graph.system.EndForEachNode; import org.apache.airavata.workflow.model.graph.system.EndifNode; import org.apache.airavata.workflow.model.graph.system.ForEachNode; import org.apache.airavata.workflow.model.graph.system.InputNode; -import org.apache.axis2.util.XMLUtils; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import org.w3c.dom.Document; -import org.xml.sax.SAXException; import org.xmlpull.infoset.XmlElement; - import xsul5.XmlConstants; +import java.net.HttpURLConnection; +import java.net.SocketTimeoutException; +import java.net.URL; +import java.util.Arrays; +import java.util.Collection; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; + +//import org.apache.airavata.client.stub.interpretor.NameValue; + public class XBayaUtil { private static final Logger logger = LoggerFactory.getLogger(XBayaUtil.class); @@ -193,7 +185,7 @@ public class XBayaUtil { } - public static List<NameValue> getIOParameterData(String xml) throws ParserConfigurationException, SAXException, IOException{ +/* public static List<NameValue> getIOParameterData(String xml) throws ParserConfigurationException, SAXException, IOException{ List<NameValue> parameters=new ArrayList<NameValue>(); Document parameterDocument = XMLUtils.newDocument(new ByteArrayInputStream(xml.getBytes())); org.w3c.dom.NodeList childNodes = parameterDocument.getDocumentElement().getChildNodes(); @@ -205,7 +197,7 @@ public class XBayaUtil { parameters.add(pair); } return parameters; - } + }*/ // public static AiravataRegistry2 getRegistry(URL url) throws IOException, RepositoryException, URISyntaxException { // Properties properties = new Properties();
