org.apache.airavata.client.samples.CreateLaunchExperiment Maven / Gradle / Ivy
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package org.apache.airavata.client.samples;
import org.apache.airavata.api.Airavata;
import org.apache.airavata.api.client.AiravataClientFactory;
import org.apache.airavata.client.tools.RegisterSampleApplications;
import org.apache.airavata.client.tools.RegisterSampleApplicationsUtils;
import org.apache.airavata.model.appcatalog.appinterface.DataType;
import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType;
import org.apache.airavata.model.appcatalog.appinterface.OutputDataObjectType;
import org.apache.airavata.model.appcatalog.computeresource.*;
import org.apache.airavata.model.error.*;
import org.apache.airavata.model.util.ExperimentModelUtil;
import org.apache.airavata.model.util.ProjectModelUtil;
import org.apache.airavata.model.workspace.Gateway;
import org.apache.airavata.model.workspace.Project;
import org.apache.airavata.model.workspace.experiment.*;
import org.apache.thrift.TException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
public class CreateLaunchExperiment {
//FIXME: Read from a config file
public static final String THRIFT_SERVER_HOST = "localhost";
public static final int THRIFT_SERVER_PORT = 8930;
// public static final String THRIFT_SERVER_HOST = "gw111.iu.xsede.org";
// public static final int THRIFT_SERVER_PORT = 9930;
private final static Logger logger = LoggerFactory.getLogger(CreateLaunchExperiment.class);
private static final String DEFAULT_USER = "default.registry.user";
private static final String DEFAULT_GATEWAY = "default";
private static Airavata.Client airavataClient;
private static String echoAppId = "Echo_066691af-2507-4bf1-905a-d6bb7a2d2bd1";
private static String mpiAppId = "HelloMPI_bfd56d58-6085-4b7f-89fc-646576830518";
private static String wrfAppId = "WRF_7ad5da38-c08b-417c-a9ea-da9298839762";
private static String amberAppId = "Amber_cb54b269-cf79-4276-8dbb-2ec16b759cc6";
private static String gromacsAppId = "GROMACS_05622038-9edd-4cb1-824e-0b7cb993364b";
private static String espressoAppId = "ESPRESSO_10cc2820-5d0b-4c63-9546-8a8b595593c1";
private static String lammpsAppId = "LAMMPS_2472685b-8acf-497e-aafe-cc66fe5f4cb6";
private static String nwchemAppId = "NWChem_2c8fee64-acf9-4a89-b6d3-91eb53c7640c";
private static String trinityAppId = "Trinity_e894acf5-9bca-46e8-a1bd-7e2d5155191a";
private static String autodockAppId = "AutoDock_43d9fdd0-c404-49f4-b913-3abf9080a8c9";
private static String localHost = "localhost";
private static String trestlesHostName = "trestles.sdsc.xsede.org";
private static String unicoreHostName = "fsd-cloud15.zam.kfa-juelich.de";
private static String stampedeHostName = "stampede.tacc.xsede.org";
private static String br2HostName = "bigred2.uits.iu.edu";
private static String umassrcHostName = "ghpcc06.umassrc.org";
private static String gatewayId;
// unicore service endpoint url
private static final String unicoreEndPointURL = "https://fsd-cloud15.zam.kfa-juelich.de:7000/INTEROP1/services/BESFactory?res=default_bes_factory";
public static void main(String[] args) throws Exception {
airavataClient = AiravataClientFactory.createAiravataClient(THRIFT_SERVER_HOST, THRIFT_SERVER_PORT);
System.out.println("API version is " + airavataClient.getAPIVersion());
// testCredentialStore();
// registerApplications(); // run this only the first time
// createAndLaunchExp();
}
private static String fsdResourceId;
public static void testCredentialStore() throws Exception {
// String token = airavataClient.generateAndRegisterSSHKeys(DEFAULT_GATEWAY, "admin");
// System.out.println(token);
String sshPubKey = airavataClient.getSSHPubKey("90438471-507d-4a9f-9287-081fc816e0f2", DEFAULT_GATEWAY);
System.out.println(sshPubKey);
Map sshPubKeys = airavataClient.getAllUserSSHPubKeys("admin");
for (String token : sshPubKeys.keySet()){
System.out.println(token + " : " + sshPubKeys.get(token));
}
}
public static void getAvailableAppInterfaceComputeResources(String appInterfaceId) {
try {
Map availableAppInterfaceComputeResources = airavataClient.getAvailableAppInterfaceComputeResources(appInterfaceId);
for (String key : availableAppInterfaceComputeResources.keySet()) {
System.out.println("id : " + key);
System.out.println("name : " + availableAppInterfaceComputeResources.get(key));
}
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
}
public static void createGateway() {
try {
Gateway gateway = new Gateway();
gateway.setGatewayId("testGatewayId2");
gateway.setGatewayName("testGateway2");
gatewayId = airavataClient.addGateway(gateway);
System.out.println(gatewayId);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
}
public static void getGateway(String gatewayId) {
try {
Gateway gateway = airavataClient.getGateway(gatewayId);
gateway.setDomain("testDomain");
airavataClient.updateGateway(gatewayId, gateway);
List allGateways = airavataClient.getAllGateways();
System.out.println(allGateways.size());
if (airavataClient.isGatewayExist(gatewayId)) {
Gateway gateway1 = airavataClient.getGateway(gatewayId);
System.out.println(gateway1.getGatewayName());
}
boolean b = airavataClient.deleteGateway("testGatewayId2");
System.out.println(b);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
}
public static void createAndLaunchExp() throws TException {
List experimentIds = new ArrayList();
try {
for (int i = 0; i < 1; i++) {
// final String expId = createExperimentForSSHHost(airavata);
// final String expId = createEchoExperimentForFSD(airavataClient);
// final String expId = createMPIExperimentForFSD(airavataClient);
final String expId = createEchoExperimentForStampede(airavataClient);
// final String expId = createEchoExperimentForTrestles(airavataClient);
// final String expId = createExperimentEchoForLocalHost(airavataClient);
// final String expId = createExperimentWRFTrestles(airavataClient);
// final String expId = createExperimentForBR2(airavataClient);
// final String expId = createExperimentForBR2Amber(airavataClient);
// final String expId = createExperimentWRFStampede(airavataClient);
// final String expId = createExperimentForStampedeAmber(airavataClient);
// String expId = createExperimentForTrestlesAmber(airavataClient);
// final String expId = createExperimentGROMACSStampede(airavataClient);
// final String expId = createExperimentESPRESSOStampede(airavataClient);
// final String expId = createExperimentLAMMPSStampede(airavataClient);
// final String expId = createExperimentNWCHEMStampede(airavataClient);
// final String expId = createExperimentTRINITYStampede(airavataClient);
// final String expId = createExperimentAUTODOCKStampede(airavataClient); // this is not working , we need to register AutoDock app on stampede
// final String expId = createExperimentForLSF(airavataClient);
// final String expId = createExperimentLAMMPSForLSF(airavataClient);
// final String expId = "Ultrascan_ln_eb029947-391a-4ccf-8ace-9bafebe07cc0";
experimentIds.add(expId);
System.out.println("Experiment ID : " + expId);
// updateExperiment(airavata, expId);
launchExperiment(airavataClient, expId);
}
boolean allNotFinished = true;
while(allNotFinished) {
allNotFinished = false;
for (String exId : experimentIds) {
Experiment experiment = airavataClient.getExperiment(exId);
if(!experiment.getExperimentStatus().getExperimentState().equals(ExperimentState.COMPLETED)&&
!experiment.getExperimentStatus().getExperimentState().equals(ExperimentState.FAILED)
&&!experiment.getExperimentStatus().getExperimentState().equals(ExperimentState.CANCELED)){
allNotFinished = true;
}
System.out.println(experiment.getExperimentID() + " " + experiment.getExperimentStatus().getExperimentState().name());
}
System.out.println("----------------------------------------------------");
Thread.sleep(10000);
}
} catch (Exception e) {
logger.error("Error while connecting with server", e.getMessage());
e.printStackTrace();
}
}
public static void registerApplications() {
RegisterSampleApplications registerSampleApplications = new RegisterSampleApplications(airavataClient);
// register localhost compute host
registerSampleApplications.registerLocalHost();
//Register all compute hosts
registerSampleApplications.registerXSEDEHosts();
registerSampleApplications.registerNonXSEDEHosts();
//Register Gateway Resource Preferences
registerSampleApplications.registerGatewayResourceProfile();
//Register all application modules
registerSampleApplications.registerAppModules();
//Register all application deployments
registerSampleApplications.registerAppDeployments();
//Register all application interfaces
registerSampleApplications.registerAppInterfaces();
}
public static String registerUnicoreEndpoint(String hostName, String hostDesc, JobSubmissionProtocol protocol, SecurityProtocol securityProtocol) throws TException {
ComputeResourceDescription computeResourceDescription = RegisterSampleApplicationsUtils
.createComputeResourceDescription(hostName, hostDesc, null, null);
fsdResourceId = airavataClient.registerComputeResource(computeResourceDescription);
if (fsdResourceId.isEmpty())
throw new AiravataClientException();
System.out.println("FSD Compute ResourceID: " + fsdResourceId);
JobSubmissionInterface jobSubmission = RegisterSampleApplicationsUtils.createJobSubmissionInterface(fsdResourceId, protocol, 2);
UnicoreJobSubmission ucrJobSubmission = new UnicoreJobSubmission();
ucrJobSubmission.setSecurityProtocol(securityProtocol);
ucrJobSubmission.setUnicoreEndPointURL(unicoreEndPointURL);
return jobSubmission.getJobSubmissionInterfaceId();
}
public static String createEchoExperimentForTrestles(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
inputDataObjectType.setValue("Hello World");
}
}
List exOut = client.getApplicationOutputs(echoAppId);
Project project = ProjectModelUtil.createProject("default", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "echoExperiment", "SimpleEcho3", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(trestlesHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createEchoExperimentForFSD(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
inputDataObjectType.setValue("Hello World");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo2")) {
inputDataObjectType.setValue("http://www.textfiles.com/100/ad.txt");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo3")) {
inputDataObjectType.setValue("file:///tmp/test.txt");
}
}
List exOut = client.getApplicationOutputs(echoAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "echoExperiment", "SimpleEcho2", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(unicoreHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1048576, "sds128");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
userConfigurationData.setGenerateCert(false);
userConfigurationData.setUserDN("");
// set output directory
AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling();
dataHandling.setOutputDataDir("/tmp/airavata/output/" + UUID.randomUUID().toString() + "/");
userConfigurationData.setAdvanceOutputDataHandling(dataHandling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createMPIExperimentForFSD(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(mpiAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Sample_Input")) {
inputDataObjectType.setValue("");
}
}
List exOut = client.getApplicationOutputs(mpiAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "mpiExperiment", "HelloMPI", mpiAppId, null);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(mpiAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(unicoreHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 2, 1, 2, "normal", 30, 0, 1048576, "sds128");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
userConfigurationData.setGenerateCert(false);
userConfigurationData.setUserDN("");
// set output directory
AdvancedOutputDataHandling dataHandling = new AdvancedOutputDataHandling();
dataHandling.setOutputDataDir("/tmp/airavata/output/" + UUID.randomUUID().toString() + "/");
userConfigurationData.setAdvanceOutputDataHandling(dataHandling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentWRFStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(wrfAppId);
setWRFInputs(exInputs);
List exOut = client.getApplicationOutputs(wrfAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "WRFExperiment", "Testing", wrfAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(wrfAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 2, 32, 1, "development", 90, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setWRFInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Config_Namelist_File")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/namelist.input");
} else if (inputDataObjectType.getName().equalsIgnoreCase("WRF_Initial_Conditions")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfinput_d01");
} else if (inputDataObjectType.getName().equalsIgnoreCase("WRF_Boundary_File")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/WRF_FILES/wrfbdy_d01");
}
}
}
public static String createExperimentGROMACSStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(gromacsAppId);
setGROMACSInputs(exInputs);
List exOut = client.getApplicationOutputs(gromacsAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "GromacsExperiment", "Testing", gromacsAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(gromacsAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setGROMACSInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("GROMOS_Coordinate_File")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.gro");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Portable_Input_Binary_File")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/GROMMACS_FILES/pdb1y6l-EM-vacuum.tpr");
}
}
}
public static String createExperimentESPRESSOStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(espressoAppId);
setESPRESSOInputs(exInputs);
List exOut = client.getApplicationOutputs(espressoAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "EspressoExperiment", "Testing", espressoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(espressoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setESPRESSOInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("AI_Pseudopotential_File")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.sample.in");
} else if (inputDataObjectType.getName().equalsIgnoreCase("AI_Primitive_Cell")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/ESPRESSO_FILES/Al.pz-vbc.UPF");
}
}
}
public static String createExperimentTRINITYStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(trinityAppId);
setTRINITYInputs(exInputs);
List exOut = client.getApplicationOutputs(trinityAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "TrinityExperiment", "Testing", trinityAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(trinityAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setTRINITYInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("RNA_Seq_Left_Input")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.left.fq");
} else if (inputDataObjectType.getName().equalsIgnoreCase("RNA_Seq_Right_Input")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/TRINITY_FILES/reads.right.fq");
}
}
}
public static String createExperimentLAMMPSStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(lammpsAppId);
setLAMMPSInputs(exInputs);
List exOut = client.getApplicationOutputs(lammpsAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "LAMMPSExperiment", "Testing", lammpsAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(lammpsAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setLAMMPSInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Friction_Simulation_Input")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/LAMMPS_FILES/in.friction");
}
}
}
public static String createExperimentNWCHEMStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(nwchemAppId);
setNWCHEMInputs(exInputs);
List exOut = client.getApplicationOutputs(nwchemAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "NWchemExperiment", "Testing", nwchemAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(nwchemAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setNWCHEMInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Water_Molecule_Input")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/NWCHEM_FILES/water.nw");
}
}
}
public static String createExperimentAUTODOCKStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(nwchemAppId);
setAUTODOCKInputs(exInputs);
List exOut = client.getApplicationOutputs(nwchemAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "AutoDockExperiment", "Testing", autodockAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(autodockAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 16, 1, "development", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
private static void setAUTODOCKInputs(List exInputs) {
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("AD4_parameters.dat")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/AD4_parameters.dat");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.A.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.A.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.C.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.C.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.d.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.d.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.e.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.e.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.HD.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.HD.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.maps.fld")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.maps.fld");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.NA.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.NA.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.N.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.N.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("hsg1.OA.map")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/hsg1.OA.map");
} else if (inputDataObjectType.getName().equalsIgnoreCase("ind.dpf")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.dpf");
} else if (inputDataObjectType.getName().equalsIgnoreCase("ind.pdbqt")) {
inputDataObjectType.setValue("/Users/shameera/Downloads/PHP-Gateway-Scripts/appScripts/AUTODOCK_FILES/ind.pdbqt");
}
}
}
public static String createExperimentWRFTrestles(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(wrfAppId);
setWRFInputs(exInputs);
List exOut = client.getApplicationOutputs(wrfAppId);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "admin", "WRFExperiment", "Testing", wrfAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(wrfAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(trestlesHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, "sds128");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String cloneExperiment(Airavata.Client client, String expId) throws TException {
try {
return client.cloneExperiment(expId, "cloneExperiment1");
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
}
public static void updateExperiment(Airavata.Client client, String expId) throws TException {
try {
Experiment experiment = client.getExperiment(expId);
experiment.setDescription("updatedDescription");
client.updateExperiment(expId, experiment);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
}
public static String createExperimentEchoForLocalHost(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
inputDataObjectType.setValue("Hello World");
}
}
List exOut = client.getApplicationOutputs(echoAppId);
Project project = ProjectModelUtil.createProject("project1", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "echoExperiment", "Echo Test", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(localHost)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, "");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
// public static String createExperimentForSSHHost(Airavata.Client client) throws TException {
// try {
// List exInputs = new ArrayList();
// OutputDataObjectType input = new OutputDataObjectType();
// input.setName("echo_input");
// input.setType(DataType.STRING);
// input.setValue("Echoed_Output=Hello World");
// exInputs.add(input);
//
// List exOut = new ArrayList();
// OutputDataObjectType output = new OutputDataObjectType();
// output.setName("Echoed_Output");
// output.setType(DataType.STRING);
// output.setValue("");
// exOut.add(output);
//
// Project project = ProjectModelUtil.createProject("default", "admin", "test project");
// String projectId = client.createProject(project);
//
// Experiment simpleExperiment =
// ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "sshEchoExperiment", "SSHEcho1", sshHostAppId.split(",")[1], exInputs);
// simpleExperiment.setExperimentOutputs(exOut);
//
// ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(sshHostAppId.split(",")[0], 1, 1, 1, "normal", 1, 0, 1, "sds128");
// scheduling.setResourceHostId("gw111.iu.xsede.org");
// UserConfigurationData userConfigurationData = new UserConfigurationData();
// userConfigurationData.setAiravataAutoSchedule(false);
// userConfigurationData.setOverrideManualScheduledParams(false);
// userConfigurationData.setComputationalResourceScheduling(scheduling);
// simpleExperiment.setUserConfigurationData(userConfigurationData);
// return client.createExperiment(simpleExperiment);
// } catch (AiravataSystemException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new AiravataSystemException(e);
// } catch (InvalidRequestException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new InvalidRequestException(e);
// } catch (AiravataClientException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new AiravataClientException(e);
// } catch (TException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new TException(e);
// }
// }
public static String createEchoExperimentForStampede(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
inputDataObjectType.setValue("Hello World");
}
}
List exOut = client.getApplicationOutputs(echoAppId);
Project project = ProjectModelUtil.createProject("default", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "echoExperiment", "SimpleEcho3", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
// public static String createEchoExperimentForLonestar(Airavata.Client client) throws TException {
// try {
// List exInputs = new ArrayList();
// OutputDataObjectType input = new OutputDataObjectType();
// input.setName("echo_input");
// input.setType(DataType.STRING);
// input.setValue("Echoed_Output=Hello World");
// exInputs.add(input);
//
// List exOut = new ArrayList();
// OutputDataObjectType output = new OutputDataObjectType();
// output.setName("Echoed_Output");
// output.setType(DataType.STRING);
// output.setValue("");
// exOut.add(output);
//
// Project project = ProjectModelUtil.createProject("default", "admin", "test project");
// String projectId = client.createProject(project);
//
// Experiment simpleExperiment =
// ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "echoExperiment", "SimpleEcho4", echoAppId, exInputs);
// simpleExperiment.setExperimentOutputs(exOut);
//
// Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
// if (computeResources != null && computeResources.size() != 0){
// for (String id : computeResources.keySet()){
// String resourceName = computeResources.get(id);
// if (resourceName.equals(stampedeHostName)){
// ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 1, 0, 1, "TG-STA110014S");
// UserConfigurationData userConfigurationData = new UserConfigurationData();
// userConfigurationData.setAiravataAutoSchedule(false);
// userConfigurationData.setOverrideManualScheduledParams(false);
// userConfigurationData.setComputationalResourceScheduling(scheduling);
// simpleExperiment.setUserConfigurationData(userConfigurationData);
// return client.createExperiment(simpleExperiment);
// }
// }
// }
// ComputationalResourceScheduling scheduling =
// ExperimentModelUtil.createComputationResourceScheduling(sgeAppId.split(",")[0], 1, 1, 1, "normal", 1, 0, 1, "TG-STA110014S");
// UserConfigurationData userConfigurationData = new UserConfigurationData();
// userConfigurationData.setAiravataAutoSchedule(false);
// userConfigurationData.setOverrideManualScheduledParams(false);
// userConfigurationData.setComputationalResourceScheduling(scheduling);
// simpleExperiment.setUserConfigurationData(userConfigurationData);
// return client.createExperiment(simpleExperiment);
// } catch (AiravataSystemException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new AiravataSystemException(e);
// } catch (InvalidRequestException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new InvalidRequestException(e);
// } catch (AiravataClientException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new AiravataClientException(e);
// } catch (LaunchValidationException e) {
// logger.error("Validation failed" + e.getErrorMessage());
// org.apache.airavata.model.error.ValidationResults validationResult = e.getValidationResult();
// for (org.apache.airavata.model.error.ValidatorResult vResult : validationResult.getValidationResultList()) {
// if (!vResult.isSetResult()) {
// System.out.println("Error:" + vResult.getErrorDetails());
// }
// }
// throw e;
// } catch (TException e) {
// logger.error("Error occured while creating the experiment...", e.getMessage());
// throw new TException(e);
// }
// }
public static String createExperimentForBR2(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Input_to_Echo")) {
inputDataObjectType.setValue("Hello World");
}
}
List exOut = client.getApplicationOutputs(echoAppId);
Project project = ProjectModelUtil.createProject("default", "lahiru", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "lahiru", "sshEchoExperiment", "SimpleEchoBR", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(br2HostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 1, 1, 1, "normal", 30, 0, 1, null);
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentForLSF(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(echoAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
inputDataObjectType.setValue("Hello World");
}
List exOut = client.getApplicationOutputs(echoAppId);
Project project = ProjectModelUtil.createProject("default", "lg11w", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "lg11w", "sshEchoExperiment", "StressMem", echoAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
simpleExperiment.setExperimentInputs(exInputs);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(echoAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(umassrcHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 10, 1, 1, "long", 60, 0, 1000, "airavata");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
simpleExperiment.setEmailAddresses(Arrays.asList(new String[]{"[email protected]"}));
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentLAMMPSForLSF(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(lammpsAppId);
for (InputDataObjectType inputDataObjectType : exInputs) {
inputDataObjectType.setName("Friction_Simulation_Input");
inputDataObjectType.setValue("/Users/lginnali/Downloads/data/in.friction");
inputDataObjectType.setType(DataType.URI);
}
List exOut = client.getApplicationOutputs(echoAppId);
/*OutputDataObjectType outputDataObjectType = exOut.get(0);
outputDataObjectType.setName("LAMMPS_Simulation_Log");
outputDataObjectType.setType(DataType.URI);
outputDataObjectType.setValue("");
OutputDataObjectType output1 = exOut.get(1);
output1.setName("LAMMPS.oJobID");
output1.setType(DataType.URI);
output1.setValue("");
exOut.add(outputDataObjectType);
exOut.add(output1);*/
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment("default", "lg11w", "LAMMPSExperiment", "Testing", lammpsAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(lammpsAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(umassrcHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 10, 16, 1, "long", 60, 0, 1000, "airavata");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentForBR2Amber(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(amberAppId);
// for (InputDataObjectType inputDataObjectType : exInputs) {
// if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/02_Heat.rst");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/03_Prod.in");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/prmtop");
// }
//
// }
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
inputDataObjectType.setValue("file://[email protected]:/var/www/experimentData/admin101a290e6330f15a91349159553ae8b6bb1/02_Heat.rst");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
inputDataObjectType.setValue("file://[email protected]:/var/www/experimentData/admin101a290e6330f15a91349159553ae8b6bb1/03_Prod.in");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
inputDataObjectType.setValue("file://[email protected]:/var/www/experimentData/admin101a290e6330f15a91349159553ae8b6bb1/prmtop");
}
}
List exOut = client.getApplicationOutputs(amberAppId);
Project project = ProjectModelUtil.createProject("default", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "sshEchoExperiment", "SimpleEchoBR", amberAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(amberAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(br2HostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "cpu", 20, 0, 1, null);
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentForStampedeAmber(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(amberAppId);
// for (InputDataObjectType inputDataObjectType : exInputs) {
// if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/02_Heat.rst");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/03_Prod.in");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/prmtop");
// }
//
// }
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
inputDataObjectType.setValue("/Users/lginnali/Downloads/02_Heat.rst");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
inputDataObjectType.setValue("/Users/lginnali/Downloads/03_Prod.in");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
inputDataObjectType.setValue("/Users/lginnali/Downloads/prmtop");
}
}
List exOut = client.getApplicationOutputs(amberAppId);
Project project = ProjectModelUtil.createProject("default", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "sshEchoExperiment", "SimpleEchoBR", amberAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(amberAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(stampedeHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "development", 20, 0, 1, "TG-STA110014S");
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static String createExperimentForTrestlesAmber(Airavata.Client client) throws TException {
try {
List exInputs = client.getApplicationInputs(amberAppId);
// for (InputDataObjectType inputDataObjectType : exInputs) {
// if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/02_Heat.rst");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/03_Prod.in");
// } else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
// inputDataObjectType.setValue("/Users/raminder/Documents/Sample/Amber/prmtop");
// }
//
// }
for (InputDataObjectType inputDataObjectType : exInputs) {
if (inputDataObjectType.getName().equalsIgnoreCase("Heat_Restart_File")) {
inputDataObjectType.setValue("/Users/chathuri/dev/airavata/source/php/inputs/AMBER_FILES/02_Heat.rst");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Production_Control_File")) {
inputDataObjectType.setValue("/Users/chathuri/dev/airavata/source/php/inputs/AMBER_FILES/03_Prod.in");
} else if (inputDataObjectType.getName().equalsIgnoreCase("Parameter_Topology_File")) {
inputDataObjectType.setValue("/Users/chathuri/dev/airavata/source/php/inputs/AMBER_FILES/prmtop");
}
}
List exOut = client.getApplicationOutputs(amberAppId);
Project project = ProjectModelUtil.createProject("default", "admin", "test project");
String projectId = client.createProject(DEFAULT_GATEWAY, project);
Experiment simpleExperiment =
ExperimentModelUtil.createSimpleExperiment(projectId, "admin", "sshEchoExperiment", "SimpleEchoBR", amberAppId, exInputs);
simpleExperiment.setExperimentOutputs(exOut);
simpleExperiment.setEnableEmailNotification(true);
// simpleExperiment.addToEmailAddresses("[email protected]");
Map computeResources = airavataClient.getAvailableAppInterfaceComputeResources(amberAppId);
if (computeResources != null && computeResources.size() != 0) {
for (String id : computeResources.keySet()) {
String resourceName = computeResources.get(id);
if (resourceName.equals(trestlesHostName)) {
ComputationalResourceScheduling scheduling = ExperimentModelUtil.createComputationResourceScheduling(id, 4, 1, 1, "normal", 20, 0, 1, null);
UserConfigurationData userConfigurationData = new UserConfigurationData();
userConfigurationData.setAiravataAutoSchedule(false);
userConfigurationData.setOverrideManualScheduledParams(false);
userConfigurationData.setComputationalResourceScheduling(scheduling);
simpleExperiment.setUserConfigurationData(userConfigurationData);
return client.createExperiment(DEFAULT_GATEWAY, simpleExperiment);
}
}
}
} catch (AiravataSystemException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while creating the experiment...", e.getMessage());
throw new TException(e);
}
return null;
}
public static void launchExperiment(Airavata.Client client, String expId)
throws TException {
try {
String tokenId = "-0bbb-403b-a88a-42b6dbe198e9";
client.launchExperiment(expId, tokenId);
} catch (ExperimentNotFoundException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
throw new ExperimentNotFoundException(e);
} catch (AiravataSystemException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
throw new AiravataSystemException(e);
} catch (InvalidRequestException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
throw new InvalidRequestException(e);
} catch (AiravataClientException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
throw new AiravataClientException(e);
} catch (TException e) {
logger.error("Error occured while launching the experiment...", e.getMessage());
throw new TException(e);
}
}
public static List getExperimentsForUser(Airavata.Client client, String user) {
try {
return client.getAllUserExperiments(DEFAULT_GATEWAY, user);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List getAllUserProject(Airavata.Client client, String user) {
try {
return client.getAllUserProjects(DEFAULT_GATEWAY, user);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List searchProjectsByProjectName(Airavata.Client client, String user, String projectName) {
try {
return client.searchProjectsByProjectName(DEFAULT_GATEWAY, user, projectName);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List searchProjectsByProjectDesc(Airavata.Client client, String user, String desc) {
try {
return client.searchProjectsByProjectDesc(DEFAULT_GATEWAY, user, desc);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List searchExperimentsByName(Airavata.Client client, String user, String expName) {
try {
return client.searchExperimentsByName(DEFAULT_GATEWAY, user, expName);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List searchExperimentsByDesc(Airavata.Client client, String user, String desc) {
try {
return client.searchExperimentsByDesc(DEFAULT_GATEWAY, user, desc);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static List searchExperimentsByApplication(Airavata.Client client, String user, String app) {
try {
return client.searchExperimentsByApplication(DEFAULT_GATEWAY, user, app);
} catch (AiravataSystemException e) {
e.printStackTrace();
} catch (InvalidRequestException e) {
e.printStackTrace();
} catch (AiravataClientException e) {
e.printStackTrace();
} catch (TException e) {
e.printStackTrace();
}
return null;
}
public static void getExperiment(Airavata.Client client, String expId) throws Exception {
try {
Experiment experiment = client.getExperiment(expId);
List errors = experiment.getErrors();
if (errors != null && !errors.isEmpty()) {
for (ErrorDetails error : errors) {
System.out.println("ERROR MESSAGE : " + error.getActualErrorMessage());
}
}
} catch (ExperimentNotFoundException e) {
logger.error("Experiment does not exist", e);
throw new ExperimentNotFoundException("Experiment does not exist");
} catch (AiravataSystemException e) {
logger.error("Error while retrieving experiment", e);
throw new AiravataSystemException(AiravataErrorType.INTERNAL_ERROR);
} catch (InvalidRequestException e) {
logger.error("Error while retrieving experiment", e);
throw new InvalidRequestException("Error while retrieving experiment");
} catch (AiravataClientException e) {
logger.error("Error while retrieving experiment", e);
throw new AiravataClientException(AiravataErrorType.INTERNAL_ERROR);
}
}
}
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