Author: chathuri
Date: Wed Nov 13 18:22:07 2013
New Revision: 1541649
URL: http://svn.apache.org/r1541649
Log:
integrating thrift client with airavata client
Added:
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/ExecutionManagerThriftImpl.java
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/InterpreterServiceHandler.java
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/MappingUtils.java
Modified:
airavata/trunk/modules/airavata-client/pom.xml
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java
airavata/trunk/modules/xbaya-gui/src/main/resources/airavata-client.properties
Modified: airavata/trunk/modules/airavata-client/pom.xml
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/pom.xml?rev=1541649&r1=1541648&r2=1541649&view=diff
==============================================================================
--- airavata/trunk/modules/airavata-client/pom.xml (original)
+++ airavata/trunk/modules/airavata-client/pom.xml Wed Nov 13 18:22:07 2013
@@ -54,6 +54,11 @@
<version>${project.version}</version>
</dependency>
<dependency>
+ <groupId>org.apache.airavata</groupId>
+ <artifactId>airavata-interpreter-service-client</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
<groupId>javax.jcr</groupId>
<artifactId>jcr</artifactId>
<version>${jcr.version}</version>
Modified:
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java?rev=1541649&r1=1541648&r2=1541649&view=diff
==============================================================================
---
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
(original)
+++
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/AiravataClient.java
Wed Nov 13 18:22:07 2013
@@ -40,13 +40,7 @@ import org.apache.airavata.client.api.Us
import org.apache.airavata.client.api.WorkflowManager;
import org.apache.airavata.client.api.builder.DescriptorBuilder;
import org.apache.airavata.client.api.exception.AiravataAPIInvocationException;
-import org.apache.airavata.client.impl.AiravataManagerImpl;
-import org.apache.airavata.client.impl.ApplicationManagerImpl;
-import org.apache.airavata.client.impl.ExecutionManagerImpl;
-import org.apache.airavata.client.impl.PasswordCallBackImpl;
-import org.apache.airavata.client.impl.ProvenanceManagerImpl;
-import org.apache.airavata.client.impl.UserManagerImpl;
-import org.apache.airavata.client.impl.WorkflowManagerImpl;
+import org.apache.airavata.client.impl.*;
import org.apache.airavata.common.exception.AiravataConfigurationException;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.ApplicationSettings;
@@ -92,7 +86,8 @@ public class AiravataClient extends Obse
private WorkflowManagerImpl workflowManagerImpl;
private ProvenanceManagerImpl provenanceManagerImpl;
private UserManagerImpl userManagerImpl;
- private ExecutionManagerImpl executionManagerImpl;
+// private ExecutionManagerThriftImpl executionManagerImpl;
+ private ExecutionManagerImpl executionManagerImpl;
private String gateway;
private boolean configCreated = false;
@@ -353,6 +348,7 @@ public class AiravataClient extends Obse
public ExecutionManager getExecutionManager() {
if (executionManagerImpl == null) {
+// executionManagerImpl = new
ExecutionManagerThriftImpl(this);
executionManagerImpl = new ExecutionManagerImpl(this);
}
return executionManagerImpl;
Added:
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/ExecutionManagerThriftImpl.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/ExecutionManagerThriftImpl.java?rev=1541649&view=auto
==============================================================================
---
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/ExecutionManagerThriftImpl.java
(added)
+++
airavata/trunk/modules/airavata-client/src/main/java/org/apache/airavata/client/impl/ExecutionManagerThriftImpl.java
Wed Nov 13 18:22:07 2013
@@ -0,0 +1,466 @@
+/*
+ *
+ * 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.client.impl;
+
+import org.apache.airavata.client.AiravataClient;
+import org.apache.airavata.client.api.*;
+import org.apache.airavata.client.api.ExperimentAdvanceOptions;
+import org.apache.airavata.client.api.HPCSettings;
+import org.apache.airavata.client.api.HostSchedulingSettings;
+import org.apache.airavata.client.api.NodeSettings;
+import org.apache.airavata.client.api.OutputDataSettings;
+import org.apache.airavata.client.api.SecuritySettings;
+import org.apache.airavata.client.api.WorkflowOutputDataSettings;
+import org.apache.airavata.client.api.WorkflowSchedulingSettings;
+import org.apache.airavata.client.api.exception.AiravataAPIInvocationException;
+import org.apache.airavata.client.tools.NameValuePairType;
+import org.apache.airavata.registry.api.ExecutionErrors;
+import org.apache.airavata.registry.api.workflow.*;
+import org.apache.airavata.workflow.model.wf.Workflow;
+import org.apache.airavata.workflow.model.wf.WorkflowInput;
+import org.apache.airavata.ws.monitor.*;
+import org.apache.airavata.interpreter.service.client.ExecutionClient;
+import org.apache.thrift.TException;
+
+import java.net.URISyntaxException;
+import java.util.*;
+
+public class ExecutionManagerThriftImpl implements ExecutionManager {
+ private AiravataClient client;
+
+ public ExecutionManagerThriftImpl(AiravataClient client) {
+ setClient(client);
+ }
+
+ public AiravataClient getClient() {
+ return client;
+ }
+
+ public void setClient(AiravataClient client) {
+ this.client = client;
+ }
+
+ public String runExperiment(String workflowTemplateId, List<WorkflowInput>
inputs) throws AiravataAPIInvocationException {
+ ExperimentAdvanceOptions options =
createExperimentAdvanceOptions(workflowTemplateId + "_" +
Calendar.getInstance().getTime().toString(), getClient().getCurrentUser(),
null);
+ return runExperimentGeneral(workflowTemplateId, inputs, options, null);
+
+ }
+
+ public String runExperiment(String workflow, List<WorkflowInput> inputs,
ExperimentAdvanceOptions options) throws AiravataAPIInvocationException {
+ return runExperimentGeneral(workflow, inputs, options, null);
+ }
+
+ public String runExperiment(String workflow, List<WorkflowInput> inputs,
ExperimentAdvanceOptions options, EventDataListener listener) throws
AiravataAPIInvocationException {
+ return runExperimentGeneral(workflow, inputs, options, listener);
+ }
+
+ public String runExperiment(Workflow workflow, List<WorkflowInput> inputs,
ExperimentAdvanceOptions options) throws AiravataAPIInvocationException {
+ return runExperimentGeneral(workflow.getName(), inputs, options, null);
+ }
+
+ private String runExperimentGeneral(String wfname, List<WorkflowInput>
inputs, ExperimentAdvanceOptions options, EventDataListener listener) throws
AiravataAPIInvocationException {
+ Workflow workflowObj = null;
+ try {
+ workflowObj = extractWorkflow(wfname);
+ String experimentID = options.getCustomExperimentId();
+ String workflowTemplateName = workflowObj.getName();
+ if (experimentID == null || experimentID.isEmpty()) {
+ experimentID = workflowTemplateName + "_" + UUID.randomUUID();
+ }
+ options.setCustomExperimentId(experimentID);
+
getClient().getProvenanceManager().setWorkflowInstanceTemplateName(experimentID,
workflowTemplateName);
+
+ String submissionUser =
getClient().getUserManager().getAiravataUser();
+ String executionUser=options.getExperimentExecutionUser();
+ if (executionUser==null){
+ executionUser=submissionUser;
+ }
+ options.setExperimentExecutionUser(executionUser);
+ runPreWorkflowExecutionTasks(experimentID, executionUser,
options.getExperimentMetadata(), options.getExperimentName());
+
+ String workflowContent = extractWorkflowContent(wfname);
+ Map<String, String> workflowInputs = new HashMap<String, String>();
+ for (WorkflowInput workflowInput : inputs){
+ String name = workflowInput.getName();
+ String value = (String)workflowInput.getValue();
+ workflowInputs.put(name, value);
+ }
+ if (listener!=null){
+ getExperimentMonitor(experimentID, listener).startMonitoring();
+ }
+ org.apache.airavata.experiment.execution.ExperimentAdvanceOptions
experimentAdvanceOptions = generateAdvancedOptions(options);
+ return getExecutionClient().runExperiment(workflowContent,
workflowInputs, experimentAdvanceOptions);
+ } catch (AiravataAPIInvocationException e) {
+ throw new AiravataAPIInvocationException("Error occured while
running the workflow", e);
+ } catch (TException e) {
+ throw new AiravataAPIInvocationException("Error occured while
running the workflow", e);
+ }
+ }
+
+ private void runPreWorkflowExecutionTasks(String experimentId, String user,
+ String metadata, String
experimentName) throws AiravataAPIInvocationException {
+ if (user != null) {
+ getClient().getProvenanceManager().setExperimentUser(experimentId,
user);
+ }
+ if (metadata != null) {
+
getClient().getProvenanceManager().setExperimentMetadata(experimentId,
metadata);
+ }
+ if (experimentName == null) {
+ experimentName = experimentId;
+ }
+ getClient().getProvenanceManager().setExperimentName(experimentId,
experimentName);
+ }
+
+ public Monitor getExperimentMonitor(String experimentId) throws
AiravataAPIInvocationException {
+ return getExperimentMonitor(experimentId,null);
+ }
+
+ public Monitor getExperimentMonitor(String experimentId, EventDataListener
listener) throws AiravataAPIInvocationException {
+ MonitorConfiguration monitorConfiguration;
+ try {
+ monitorConfiguration = new MonitorConfiguration(
+
getClient().getClientConfiguration().getMessagebrokerURL().toURI(),
experimentId,
+ true,
getClient().getClientConfiguration().getMessageboxURL().toURI());
+ final Monitor monitor = new Monitor(monitorConfiguration);
+ monitor.printRawMessage(false);
+ if (listener!=null) {
+
monitor.getEventDataRepository().registerEventListener(listener);
+ listener.setExperimentMonitor(monitor);
+ }
+ if (!monitor.getExperimentId().equals(">")){
+ monitor.getEventDataRepository().registerEventListener(new
EventDataListenerAdapter() {
+ public void notify(EventDataRepository eventDataRepo,
EventData eventData) {
+ if (eventData.getType()==
MonitorUtil.EventType.WORKFLOW_TERMINATED || eventData.getType()==
MonitorUtil.EventType.SENDING_FAULT){
+ monitor.stopMonitoring();
+ }
+ }
+ });
+ }
+ return monitor;
+ } catch (URISyntaxException e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public ExperimentAdvanceOptions createExperimentAdvanceOptions() throws
AiravataAPIInvocationException {
+ return new ExperimentAdvanceOptions();
+ }
+
+ public ExperimentAdvanceOptions createExperimentAdvanceOptions(String
experimentName, String experimentUser, String experimentMetadata) throws
AiravataAPIInvocationException {
+ ExperimentAdvanceOptions options = createExperimentAdvanceOptions();
+ options.setExperimentName(experimentName);
+ options.setExperimentCustomMetadata(experimentMetadata);
+ options.setExperimentExecutionUser(experimentUser);
+ return options;
+ }
+
+ public void waitForExperimentTermination(String experimentId) throws
AiravataAPIInvocationException {
+ Monitor experimentMonitor = getExperimentMonitor(experimentId, new
EventDataListenerAdapter() {
+ public void notify(EventDataRepository eventDataRepo,
+ EventData eventData) {
+ if (eventData.getType()==
MonitorUtil.EventType.WORKFLOW_TERMINATED){
+ getMonitor().stopMonitoring();
+ }
+ }
+ });
+ experimentMonitor.startMonitoring();
+ try {
+ WorkflowExecutionStatus workflowInstanceStatus =
getClient().getProvenanceManager().getWorkflowInstanceStatus(experimentId,
experimentId);
+ if (workflowInstanceStatus.getExecutionStatus()==
WorkflowExecutionStatus.State.FINISHED ||
workflowInstanceStatus.getExecutionStatus()==
WorkflowExecutionStatus.State.FAILED){
+ experimentMonitor.stopMonitoring();
+ return;
+ }
+ } catch (AiravataAPIInvocationException e) {
+ //Workflow may not have started yet. Best to use the monitor to
follow the progress
+ }
+ experimentMonitor.waitForCompletion();
+
+ }
+
+ public List<ExperimentExecutionError> getExperimentExecutionErrors(String
experimentId) throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getExperimentExecutionErrors(experimentId);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public List<WorkflowExecutionError> getWorkflowExecutionErrors(String
experimentId, String workflowInstanceId) throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getWorkflowExecutionErrors(experimentId,
+ workflowInstanceId);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public List<NodeExecutionError> getNodeExecutionErrors(String
experimentId, String workflowInstanceId, String nodeId) throws
AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getNodeExecutionErrors(experimentId,
+ workflowInstanceId, nodeId);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public List<ApplicationJobExecutionError> getApplicationJobErrors(String
experimentId, String workflowInstanceId, String nodeId, String gfacJobId)
throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getApplicationJobErrors(experimentId,
+ workflowInstanceId, nodeId, gfacJobId);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public List<ApplicationJobExecutionError> getApplicationJobErrors(String
gfacJobId) throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getApplicationJobErrors(gfacJobId);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public List<ExecutionError> getExecutionErrors(String experimentId, String
workflowInstanceId, String nodeId, String gfacJobId, ExecutionErrors.Source...
filterBy) throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().getExecutionErrors(experimentId,
+ workflowInstanceId, nodeId, gfacJobId, filterBy);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public int addExperimentError(ExperimentExecutionError error) throws
AiravataAPIInvocationException {
+ try {
+ return getClient().getRegistryClient().addExperimentError(error);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public int addWorkflowExecutionError(WorkflowExecutionError error) throws
AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().addWorkflowExecutionError(error);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public int addNodeExecutionError(NodeExecutionError error) throws
AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().addNodeExecutionError(error);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public int addApplicationJobExecutionError(ApplicationJobExecutionError
error) throws AiravataAPIInvocationException {
+ try {
+ return
getClient().getRegistryClient().addApplicationJobExecutionError(error);
+ } catch (Exception e) {
+ throw new AiravataAPIInvocationException(e);
+ }
+ }
+
+ public org.apache.airavata.experiment.execution.InterpreterService.Client
getExecutionClient (){
+ ExecutionClient executionClient = new ExecutionClient();
+ return executionClient.getInterpreterServiceClient();
+
+ }
+
+
+ private String extractWorkflowContent(String workflowName) throws
AiravataAPIInvocationException {
+
if(workflowName.contains("http://airavata.apache.org/xbaya/xwf";)){//(getClient().getWorkflowManager().isWorkflowExists(workflowName))
{
+ return workflowName;
+ }else {
+ return
getClient().getWorkflowManager().getWorkflowAsString(workflowName);
+ }
+ }
+
+ private Workflow extractWorkflow(String workflowName) throws
AiravataAPIInvocationException {
+ Workflow workflowObj = null;
+ //FIXME - There should be a better way to figure-out if the passed
string is a name or an xml
+
if(!workflowName.contains("http://airavata.apache.org/xbaya/xwf";)){//(getClient().getWorkflowManager().isWorkflowExists(workflowName))
{
+ workflowObj =
getClient().getWorkflowManager().getWorkflow(workflowName);
+ }else {
+ try{
+ workflowObj =
getClient().getWorkflowManager().getWorkflowFromString(workflowName);
+ }catch (AiravataAPIInvocationException e){
+ getClient().getWorkflowManager().getWorkflow(workflowName);
+ }
+ }
+ return workflowObj;
+ }
+
+ private org.apache.airavata.experiment.execution.ExperimentAdvanceOptions
generateAdvancedOptions(org.apache.airavata.client.api.ExperimentAdvanceOptions
exAdOpt){
+ try {
+ org.apache.airavata.experiment.execution.ExperimentAdvanceOptions
advanceOptions = new
org.apache.airavata.experiment.execution.ExperimentAdvanceOptions();
+ advanceOptions.setExperimentName(exAdOpt.getExperimentName());
+
advanceOptions.setCustomExperimentId(exAdOpt.getCustomExperimentId());
+
advanceOptions.setExecutionUser(exAdOpt.getExperimentExecutionUser());
+ advanceOptions.setMetadata(exAdOpt.getExperimentMetadata());
+ SecuritySettings customSecuritySettings =
exAdOpt.getCustomSecuritySettings();
+ if (customSecuritySettings != null){
+
advanceOptions.setSecuritySettings(generateSecuritySettingsObj(customSecuritySettings));
+ }
+
+ WorkflowOutputDataSettings outputDataSettings =
exAdOpt.getCustomWorkflowOutputDataSettings();
+ List<org.apache.airavata.experiment.execution.OutputDataSettings>
dataSettingsList = new
ArrayList<org.apache.airavata.experiment.execution.OutputDataSettings>();
+ if (outputDataSettings != null){
+ OutputDataSettings[] outputDataSettingsList =
outputDataSettings.getOutputDataSettingsList();
+ for (OutputDataSettings opds : outputDataSettingsList){
+
org.apache.airavata.experiment.execution.OutputDataSettings dataSettings =
generateOutputDataObject(opds);
+ dataSettingsList.add(dataSettings);
+ }
+
org.apache.airavata.experiment.execution.WorkflowOutputDataSettings
wfOpDSettings = new
org.apache.airavata.experiment.execution.WorkflowOutputDataSettings();
+ wfOpDSettings.setOutputDataSettingsList(dataSettingsList);
+ advanceOptions.setWorkflowOutputDataSettings(wfOpDSettings);
+ }
+ WorkflowSchedulingSettings schedulingSettings =
exAdOpt.getCustomWorkflowSchedulingSettings();
+ if (schedulingSettings != null){
+
org.apache.airavata.experiment.execution.WorkflowSchedulingSettings settings =
generateShedulingSettingsObject(schedulingSettings);
+ advanceOptions.setWorkflowSchedulingSettings(settings);
+ }
+ return advanceOptions;
+ } catch (AiravataAPIInvocationException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private org.apache.airavata.experiment.execution.SecuritySettings
generateSecuritySettingsObj(org.apache.airavata.client.api.SecuritySettings
secSettings) {
+ try {
+ org.apache.airavata.experiment.execution.SecuritySettings settings
= new org.apache.airavata.experiment.execution.SecuritySettings();
+ org.apache.airavata.experiment.execution.AmazonWebServicesSettings
amWSSettings = new
org.apache.airavata.experiment.execution.AmazonWebServicesSettings();
+ org.apache.airavata.client.api.AmazonWebServicesSettings
amazonWSSettings = secSettings.getAmazonWSSettings();
+ if (amazonWSSettings != null){
+
amWSSettings.setAccessKey(amazonWSSettings.getSecretAccessKey());
+ amWSSettings.setAmiID(amazonWSSettings.getAMIId());
+ amWSSettings.setInstanceID(amazonWSSettings.getInstanceId());
+
amWSSettings.setSecretAccessKey(amazonWSSettings.getSecretAccessKey());
+ amWSSettings.setUsername(amazonWSSettings.getUsername());
+ settings.setAmazonWSSettings(amWSSettings);
+ }
+
+
org.apache.airavata.experiment.execution.CredentialStoreSecuritySettings
credSettings = new
org.apache.airavata.experiment.execution.CredentialStoreSecuritySettings();
+ org.apache.airavata.client.api.CredentialStoreSecuritySettings
credStoreSecSettings = secSettings.getCredentialStoreSecuritySettings();
+ if (credStoreSecSettings != null){
+ credSettings.setGatewayID(credStoreSecSettings.getGatewayId());
+
credSettings.setPortalUser(credStoreSecSettings.getPortalUser());
+ credSettings.setTokenId(credStoreSecSettings.getTokenId());
+ settings.setCredentialStoreSettings(credSettings);
+ }
+
+//
org.apache.airavata.experiment.execution.MyProxyRepositorySettings
myProxySettings = new
org.apache.airavata.experiment.execution.MyProxyRepositorySettings();
+// org.apache.airavata.client.api.GridMyProxyRepositorySettings
proxyRepositorySettings = secSettings.getGridMyProxyRepositorySettings();
+// if (proxyRepositorySettings != null){
+//
myProxySettings.setLifetime(proxyRepositorySettings.getLifeTime());
+//
myProxySettings.setMyproxyServer(proxyRepositorySettings.getMyProxyServer());
+//
myProxySettings.setPassword(proxyRepositorySettings.getPassword());
+//
myProxySettings.setUserName(proxyRepositorySettings.getUsername());
+// settings.setMyproxySettings(myProxySettings);
+// }
+//
+//
org.apache.airavata.experiment.execution.SSHAuthenticationSettings authSettings
= new org.apache.airavata.experiment.execution.SSHAuthenticationSettings();
+// org.apache.airavata.client.api.SSHAuthenticationSettings
sshAuthenticationSettings = secSettings.getSSHAuthenticationSettings();
+// if (sshAuthenticationSettings != null){
+//
authSettings.setAccessKeyID(sshAuthenticationSettings.getAccessKeyId());
+//
authSettings.setSecretAccessKey(sshAuthenticationSettings.getSecretAccessKey());
+// settings.setSshAuthSettings(authSettings);
+// }
+ return settings;
+
+ } catch (AiravataAPIInvocationException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private org.apache.airavata.experiment.execution.OutputDataSettings
generateOutputDataObject(OutputDataSettings opDataSettings){
+ org.apache.airavata.experiment.execution.OutputDataSettings
dataSettings = new
org.apache.airavata.experiment.execution.OutputDataSettings();
+ dataSettings.setDataRegURL(opDataSettings.getDataRegistryUrl());
+ dataSettings.setIsdataPersisted(opDataSettings.isDataPersistent());
+ dataSettings.setNodeID(opDataSettings.getNodeId());
+ dataSettings.setOutputdataDir(opDataSettings.getOutputDataDirectory());
+ return dataSettings;
+ }
+
+ private
org.apache.airavata.experiment.execution.WorkflowSchedulingSettings
generateShedulingSettingsObject (WorkflowSchedulingSettings wfschSettings){
+ org.apache.airavata.experiment.execution.WorkflowSchedulingSettings
schedulingSettings = new
org.apache.airavata.experiment.execution.WorkflowSchedulingSettings();
+ NodeSettings[] list = wfschSettings.getNodeSettingsList();
+ List<org.apache.airavata.experiment.execution.NodeSettings> nodes =
new ArrayList<org.apache.airavata.experiment.execution.NodeSettings>();
+ if (list != null){
+ for (NodeSettings ns : list){
+ org.apache.airavata.experiment.execution.NodeSettings
nodeSettings = generateNodeSettingsObject(ns);
+ nodes.add(nodeSettings);
+ }
+ }
+ schedulingSettings.setNodeSettingsList(nodes);
+ return schedulingSettings;
+ }
+
+ private org.apache.airavata.experiment.execution.NodeSettings
generateNodeSettingsObject (NodeSettings settings){
+ org.apache.airavata.experiment.execution.NodeSettings nsettings = new
org.apache.airavata.experiment.execution.NodeSettings();
+ nsettings.setNodeId(settings.getNodeId());
+ nsettings.setServiceId(settings.getServiceId());
+
nsettings.setHostSchedulingSettings(generateHostSchSettings(settings.getHostSettings()));
+
nsettings.setHpcSettings(generateHPCSettingsObject(settings.getHPCSettings()));
+
+ List<NameValuePairType> nameValuePair = settings.getNameValuePair();
+ List<org.apache.airavata.experiment.execution.NameValuePairType>
typeList = new
ArrayList<org.apache.airavata.experiment.execution.NameValuePairType>();
+ if (nameValuePair != null){
+ for (NameValuePairType nvPair : nameValuePair){
+ org.apache.airavata.experiment.execution.NameValuePairType
type = generateNVPairObject(nvPair);
+ typeList.add(type);
+ }
+ }
+ nsettings.setNameValuePairList(typeList);
+ return nsettings;
+ }
+
+ private org.apache.airavata.experiment.execution.HostSchedulingSettings
generateHostSchSettings (HostSchedulingSettings settings){
+ org.apache.airavata.experiment.execution.HostSchedulingSettings
hscheduleSettings = new
org.apache.airavata.experiment.execution.HostSchedulingSettings();
+ hscheduleSettings.setGatekeeperEPR(settings.getGatekeeperEPR());
+ hscheduleSettings.setHostID(settings.getHostId());
+ hscheduleSettings.setIsWSGramPreferred(settings.isWSGRAMPreffered());
+ return hscheduleSettings;
+ }
+
+ private org.apache.airavata.experiment.execution.HPCSettings
generateHPCSettingsObject (HPCSettings settings){
+ org.apache.airavata.experiment.execution.HPCSettings hsettings = new
org.apache.airavata.experiment.execution.HPCSettings();
+ hsettings.setCpuCount(settings.getCPUCount());
+ hsettings.setJobManager(settings.getJobManager());
+ hsettings.setMaxWalltime(settings.getMaxWallTime());
+ hsettings.setNodeCount(settings.getNodeCount());
+ hsettings.setQueueName(settings.getQueueName());
+ return hsettings;
+ }
+
+ private org.apache.airavata.experiment.execution.NameValuePairType
generateNVPairObject (org.apache.airavata.client.tools.NameValuePairType
settings){
+ org.apache.airavata.experiment.execution.NameValuePairType nvType =
new org.apache.airavata.experiment.execution.NameValuePairType();
+ nvType.setName(settings.getName());
+ nvType.setDescription(settings.getDescription());
+ nvType.setValue(settings.getValue());
+ return nvType;
+ }
+}
+
+
Modified:
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java?rev=1541649&r1=1541648&r2=1541649&view=diff
==============================================================================
---
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java
(original)
+++
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/WorkflowInterpretorSkeleton.java
Wed Nov 13 18:22:07 2013
@@ -48,6 +48,7 @@ import org.apache.airavata.common.utils.
import org.apache.airavata.common.utils.ServiceUtils;
import
org.apache.airavata.common.workflow.execution.context.WorkflowContextHeaderBuilder;
import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.experiment.execution.InterpreterService;
import org.apache.airavata.schemas.gfac.GlobusHostType;
import org.apache.airavata.schemas.gfac.GsisshHostType;
import org.apache.airavata.schemas.gfac.SSHHostType;
@@ -63,6 +64,7 @@ import org.apache.airavata.ws.monitor.Mo
import org.apache.airavata.xbaya.XBayaConfiguration;
import org.apache.airavata.xbaya.XBayaConstants;
import org.apache.airavata.xbaya.concurrent.PredicatedTaskRunner;
+import org.apache.airavata.xbaya.interpretor.thrift.InterpreterServiceHandler;
import org.apache.axiom.om.OMElement;
import org.apache.axiom.om.impl.builder.StAXOMBuilder;
import org.apache.axiom.om.impl.llom.util.AXIOMUtil;
@@ -71,6 +73,11 @@ import org.apache.axis2.context.Configur
import org.apache.axis2.context.MessageContext;
import org.apache.axis2.description.AxisService;
import org.apache.axis2.engine.ServiceLifeCycle;
+import org.apache.thrift.server.TServer;
+import org.apache.thrift.server.TSimpleServer;
+import org.apache.thrift.transport.TServerSocket;
+import org.apache.thrift.transport.TServerTransport;
+import org.apache.thrift.transport.TTransportException;
import org.apache.xmlbeans.XmlException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -91,6 +98,7 @@ public class WorkflowInterpretorSkeleton
public static final String MYPROXY_SERVER = "myproxy.server";
public static final String MYPROXY_LIFETIME = "myproxy.life";
public static final String TRUSTED_CERT_LOCATION = "trusted.cert.location";
+ public static final String THRIFT_SERVER_PORT = "thrift.server.port";
public static boolean provenance = false;
public static final String PROVENANCE = "provenance";
@@ -204,12 +212,23 @@ public class WorkflowInterpretorSkeleton
*/
thread = new
WIServiceThread(getAiravataAPI(), configctx);
thread.start();
+
+ InterpreterService.Processor<InterpreterServiceHandler>
processor = new InterpreterService.Processor<InterpreterServiceHandler>(new
InterpreterServiceHandler());
+ String thriftPort =
ServerSettings.getSetting(THRIFT_SERVER_PORT);
+ TServerTransport serverTransport = new
TServerSocket(Integer.parseInt(thriftPort));
+ TServer server = new TSimpleServer(
+ new
TServer.Args(serverTransport).processor(processor));
+
+ log.info("Starting the simple thrift server...");
+ server.serve();
} catch (IOException e) {
e.printStackTrace(); //To change body of catch
statement use File | Settings | File Templates.
} catch (URISyntaxException e) {
e.printStackTrace();
} catch (ApplicationSettingsException e) {
e.printStackTrace(); //To change body of catch statement
use File | Settings | File Templates.
+ } catch (TTransportException e) {
+ e.printStackTrace(); //To change body of catch statement
use File | Settings | File Templates.
}
WorkflowInterpretorSkeleton.configurationContext = configctx;
}
Added:
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/InterpreterServiceHandler.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/InterpreterServiceHandler.java?rev=1541649&view=auto
==============================================================================
---
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/InterpreterServiceHandler.java
(added)
+++
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/InterpreterServiceHandler.java
Wed Nov 13 18:22:07 2013
@@ -0,0 +1,84 @@
+/*
+ *
+ * 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.xbaya.interpretor.thrift;
+
+
+import org.apache.airavata.client.AiravataAPIUtils;
+import org.apache.airavata.experiment.execution.ExperimentAdvanceOptions;
+import org.apache.airavata.experiment.execution.InterpreterService;
+
+import org.apache.airavata.xbaya.interpretor.WorkflowInterpretorSkeleton;
+import org.apache.thrift.TException;
+
+import java.util.Map;
+
+public class InterpreterServiceHandler implements InterpreterService.Iface{
+ private WorkflowInterpretorSkeleton interpreterService;
+
+ public String runExperiment(String workflowTemplateName, Map<String,
String> workflowInputs, ExperimentAdvanceOptions experimentAdOptions) throws
TException {
+ String user = "admin";
+ String gatewayId = "default";
+ try {
+ return getInterpreterService().setupAndLaunch(workflowTemplateName,
+ experimentAdOptions.getCustomExperimentId(),
+ gatewayId,
+ user,
+ workflowInputs,
+ true,
+
AiravataAPIUtils.createWorkflowContextHeaderBuilder(MappingUtils.getExperimentOptionsObject(experimentAdOptions),
experimentAdOptions.getExecutionUser(), user));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ public void cancelExperiment(String experimentID) throws TException {
+ try {
+ getInterpreterService().haltWorkflow(experimentID);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void suspendExperiment(String experimentID) throws TException {
+ try {
+ getInterpreterService().suspendWorkflow(experimentID);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void resumeExperiment(String experimentID) throws TException {
+ try {
+ getInterpreterService().resumeWorkflow(experimentID);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public WorkflowInterpretorSkeleton getInterpreterService() {
+ if (interpreterService==null){
+ interpreterService=new WorkflowInterpretorSkeleton();
+ }
+ return interpreterService;
+ }
+}
Added:
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/MappingUtils.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/MappingUtils.java?rev=1541649&view=auto
==============================================================================
---
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/MappingUtils.java
(added)
+++
airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/interpretor/thrift/MappingUtils.java
Wed Nov 13 18:22:07 2013
@@ -0,0 +1,157 @@
+/*
+ *
+ * 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.xbaya.interpretor.thrift;
+
+import org.apache.airavata.client.api.*;
+import org.apache.airavata.client.api.exception.AiravataAPIInvocationException;
+import org.apache.airavata.client.impl.*;
+import org.apache.airavata.client.tools.NameValuePairType;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class MappingUtils {
+ public static ExperimentAdvanceOptions
getExperimentOptionsObject(org.apache.airavata.experiment.execution.ExperimentAdvanceOptions
advanceOptions){
+ try {
+ ExperimentAdvanceOptions experimentAdvanceOptions = new
ExperimentAdvanceOptions();
+
experimentAdvanceOptions.setCustomExperimentId(advanceOptions.getCustomExperimentId());
+
experimentAdvanceOptions.setExperimentExecutionUser(advanceOptions.getExecutionUser());
+
experimentAdvanceOptions.setExperimentCustomMetadata(advanceOptions.getMetadata());
+
experimentAdvanceOptions.setExperimentName(advanceOptions.getExperimentName());
+
+ if (advanceOptions.getWorkflowSchedulingSettings() != null){
+ List<org.apache.airavata.experiment.execution.NodeSettings>
nodeSettingsList =
advanceOptions.getWorkflowSchedulingSettings().getNodeSettingsList();
+ for (org.apache.airavata.experiment.execution.NodeSettings
nodeSettings : nodeSettingsList){
+ NodeSettings n = getNodeSettingObject(nodeSettings);
+ org.apache.airavata.experiment.execution.HPCSettings
hpcSettings = nodeSettings.getHpcSettings();
+ HPCSettings hpcSettingsObject =
getHPCSettingsObject(hpcSettings);
+ n.setHPCSettings(hpcSettingsObject);
+
org.apache.airavata.experiment.execution.HostSchedulingSettings
hostSchedulingSettings = nodeSettings.getHostSchedulingSettings();
+ HostSchedulingSettings hostSchedulingSettingsObj =
getHostSchedulingSettingsObj(hostSchedulingSettings);
+ n.setHostSettings(hostSchedulingSettingsObj);
+
experimentAdvanceOptions.getCustomWorkflowSchedulingSettings().addNewNodeSettings(n);
+ }
+ }
+
+
org.apache.airavata.experiment.execution.WorkflowOutputDataSettings
workflowOutputDataSettings = advanceOptions.getWorkflowOutputDataSettings();
+ if (workflowOutputDataSettings != null){
+ WorkflowOutputDataSettings dataSettings =
getWorkflowOutputDataSettingsObject(workflowOutputDataSettings);
+
experimentAdvanceOptions.getCustomWorkflowOutputDataSettings().addNewOutputDataSettings(dataSettings.getOutputDataSettingsList());
+ }
+
+ SecuritySettings securitySettings =
experimentAdvanceOptions.getCustomSecuritySettings();
+ org.apache.airavata.experiment.execution.SecuritySettings
securitySettings1 = advanceOptions.getSecuritySettings();
+ if (securitySettings != null && securitySettings1 != null){
+ AmazonWebServicesSettings amazonWSSettings =
securitySettings.getAmazonWSSettings();
+ if (amazonWSSettings != null){
+
amazonWSSettings.setAccessKeyId(securitySettings1.getAmazonWSSettings().getAccessKey());
+
amazonWSSettings.setAMIId(securitySettings1.getAmazonWSSettings().getAmiID());
+
amazonWSSettings.setInstanceId(securitySettings1.getAmazonWSSettings().getInstanceID());
+
amazonWSSettings.setInstanceType(securitySettings1.getAmazonWSSettings().getInstanceType());
+
amazonWSSettings.setSecretAccessKey(securitySettings1.getAmazonWSSettings().getSecretAccessKey());
+
amazonWSSettings.setUsername(securitySettings1.getAmazonWSSettings().getUsername());
+ }
+ CredentialStoreSecuritySettings storeSecuritySettings =
securitySettings.getCredentialStoreSecuritySettings();
+ if (storeSecuritySettings != null){
+
storeSecuritySettings.setGatewayId(securitySettings1.getCredentialStoreSettings().getGatewayID());
+
storeSecuritySettings.setPortalUser(securitySettings1.getCredentialStoreSettings().getPortalUser());
+
storeSecuritySettings.setTokenId(securitySettings1.getCredentialStoreSettings().getTokenId());
+ }
+
+// GridMyProxyRepositorySettings myProxyRepositorySettings =
securitySettings.getGridMyProxyRepositorySettings();
+// if (myProxyRepositorySettings != null){
+//
myProxyRepositorySettings.setUsername(securitySettings1.getMyproxySettings().getUserName());
+//
myProxyRepositorySettings.setPassword(securitySettings1.getMyproxySettings().getPassword());
+//
myProxyRepositorySettings.setLifeTime(securitySettings1.getMyproxySettings().getLifetime());
+//
myProxyRepositorySettings.setMyProxyServer(securitySettings1.getMyproxySettings().getMyproxyServer());
+// }
+//
+// SSHAuthenticationSettings authenticationSettings =
securitySettings.getSSHAuthenticationSettings();
+// if (authenticationSettings != null){
+//
authenticationSettings.setAccessKeyId(securitySettings1.getSshAuthSettings().getAccessKeyID());
+//
authenticationSettings.setSecretAccessKey(securitySettings1.getSshAuthSettings().getSecretAccessKey());
+// }
+ }
+ return experimentAdvanceOptions;
+ } catch (AiravataAPIInvocationException e) {
+ e.printStackTrace();
+ }
+
+ return null;
+ }
+
+ public static NodeSettingsImpl getNodeSettingObject
(org.apache.airavata.experiment.execution.NodeSettings nodeSettings){
+ NodeSettings n = new NodeSettingsImpl(nodeSettings.getNodeId());
+ n.setServiceId(nodeSettings.getServiceId());
+ List<NameValuePairType> nameValuePairTypes = new
ArrayList<NameValuePairType>();
+ List<org.apache.airavata.experiment.execution.NameValuePairType>
nameValuePairList = nodeSettings.getNameValuePairList();
+ for (org.apache.airavata.experiment.execution.NameValuePairType np :
nameValuePairList) {
+ NameValuePairType nameValuePairObject = getNameValuePairObject(np);
+ nameValuePairTypes.add(nameValuePairObject);
+ }
+ n.setNameValuePair(nameValuePairTypes);
+ return (NodeSettingsImpl)n;
+
+ }
+
+ public static NameValuePairType
getNameValuePairObject(org.apache.airavata.experiment.execution.NameValuePairType
nameValuePairType){
+ NameValuePairType nameValuePair = new NameValuePairType();
+ nameValuePair.setName(nameValuePairType.getName());
+ nameValuePair.setValue(nameValuePairType.getValue());
+ nameValuePair.setDescription(nameValuePairType.getDescription());
+ return nameValuePair;
+ }
+
+ public static HPCSettings getHPCSettingsObject
(org.apache.airavata.experiment.execution.HPCSettings hsettings){
+ HPCSettings hpcSettings = new HPCSettingsImpl();
+ hpcSettings.setCPUCount(hsettings.getCpuCount());
+ hpcSettings.setJobManager(hsettings.getJobManager());
+ hpcSettings.setMaxWallTime(hsettings.getMaxWalltime());
+ hpcSettings.setNodeCount(hsettings.getNodeCount());
+ hpcSettings.setQueueName(hsettings.getQueueName());
+ return hpcSettings;
+ }
+
+ public static HostSchedulingSettings getHostSchedulingSettingsObj
(org.apache.airavata.experiment.execution.HostSchedulingSettings
schedulingSettings){
+ HostSchedulingSettings hostSchedulingSettings = new
HostSchedulingSettingsImpl();
+ hostSchedulingSettings.setHostId(schedulingSettings.getHostID());
+
hostSchedulingSettings.setGatekeeperEPR(schedulingSettings.getGatekeeperEPR());
+
hostSchedulingSettings.setWSGramPreffered(schedulingSettings.isIsWSGramPreferred());
+ return hostSchedulingSettings;
+ }
+
+ public static WorkflowOutputDataSettings
getWorkflowOutputDataSettingsObject(org.apache.airavata.experiment.execution.WorkflowOutputDataSettings
wfods) {
+ WorkflowOutputDataSettings wfOutDataSettings = new
WorkflowOutputDataSettingsImpl();
+ List<org.apache.airavata.experiment.execution.OutputDataSettings>
dataSettingsList = wfods.getOutputDataSettingsList();
+ for (org.apache.airavata.experiment.execution.OutputDataSettings
outPutDSettng : dataSettingsList) {
+ OutputDataSettings outputDataSettings = new
ApplicationOutputDataSettingsImpl(outPutDSettng.getNodeID());
+
outputDataSettings.setDataPersistent(outPutDSettng.isIsdataPersisted());
+
outputDataSettings.setDataRegistryUrl(outPutDSettng.getDataRegURL());
+
outputDataSettings.setOutputDataDirectory(outPutDSettng.getOutputdataDir());
+ wfOutDataSettings.addNewOutputDataSettings(outputDataSettings);
+ }
+ return wfOutDataSettings;
+ }
+
+
+
+}
Modified:
airavata/trunk/modules/xbaya-gui/src/main/resources/airavata-client.properties
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/resources/airavata-client.properties?rev=1541649&r1=1541648&r2=1541649&view=diff
==============================================================================
---
airavata/trunk/modules/xbaya-gui/src/main/resources/airavata-client.properties
(original)
+++
airavata/trunk/modules/xbaya-gui/src/main/resources/airavata-client.properties
Wed Nov 13 18:22:07 2013
@@ -66,3 +66,19 @@ registry.service.wsdl=http://localhost:$
#class.project.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
#class.user.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
#class.published.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry
+
+
+############### ------------ FOR AMBER ----------------------
####################
+#Host name (resource) where you want to run amber job
+host.name=bigred2.uits.iu.edu
+ssh.username=cgateway
+ssh.password=the science gateways group
+#public.ssh.key=/path to public key for ssh
+#ssh.username=username for ssh connection
+#private.ssh.key=/path to private key file for ssh
+#ssh.keypass=passphrase for the private key
+
+###################################################################################
+# Thrift configuration
+###################################################################################
+thrift.server.port=6060
