You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by ch...@apache.org on 2014/11/05 19:30:24 UTC
[36/44] git commit: Ingegrated appCatalog thrift model with GSISSH
input and output handlers and inprove job execution context
Ingegrated appCatalog thrift model with GSISSH input and output handlers and inprove job execution context
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/5a28f745
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/5a28f745
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/5a28f745
Branch: refs/heads/gfac_appcatalog_int
Commit: 5a28f745193e0cbab43dac26e018cc31ded1d26d
Parents: 3f953e0
Author: shamrath <sh...@gmail.com>
Authored: Fri Oct 31 17:41:22 2014 -0400
Committer: Chathuri Wimalasena <ka...@gmail.com>
Committed: Wed Nov 5 11:23:05 2014 -0500
----------------------------------------------------------------------
.../model/workspace/experiment/JobDetails.java | 11 ++-
.../gfac/core/context/JobExecutionContext.java | 27 +++++-
.../airavata/gfac/core/cpi/BetterGfacImpl.java | 91 ++++++++++++++++----
.../handler/GSISSHDirectorySetupHandler.java | 7 +-
.../gfac/gsissh/handler/GSISSHInputHandler.java | 18 ++--
.../gsissh/handler/GSISSHOutputHandler.java | 53 +++---------
.../airavata/gsi/ssh/api/job/JobDescriptor.java | 7 ++
7 files changed, 143 insertions(+), 71 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/experiment/JobDetails.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/experiment/JobDetails.java b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/experiment/JobDetails.java
index d1cbe5e..c1034a0 100644
--- a/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/experiment/JobDetails.java
+++ b/airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/experiment/JobDetails.java
@@ -271,9 +271,14 @@ import org.slf4j.LoggerFactory;
}
}
- public String getJobDescription() {
- return this.jobDescription;
- }
+ /**
+ * this method is deprecated after we introduce new thirft model with appcatalog
+ * @return
+ */
+ @Deprecated
+ public String getJobDescription() {
+ return this.jobDescription;
+ }
public void setJobDescription(String jobDescription) {
this.jobDescription = jobDescription;
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/JobExecutionContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/JobExecutionContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/JobExecutionContext.java
index cade06b..dcae96a 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/JobExecutionContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/context/JobExecutionContext.java
@@ -33,6 +33,7 @@ import org.apache.airavata.gfac.SecurityContext;
import org.apache.airavata.gfac.core.cpi.GFac;
import org.apache.airavata.gfac.core.notification.GFacNotifier;
import org.apache.airavata.gfac.core.provider.GFacProvider;
+import org.apache.airavata.model.appcatalog.computeresource.DataMovementInterface;
import org.apache.airavata.model.appcatalog.computeresource.DataMovementProtocol;
import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
@@ -100,12 +101,20 @@ public class JobExecutionContext extends AbstractContext implements Serializable
private DataMovementProtocol preferredDataMovementProtocol;
/**
* List of job submission protocols sorted by priority order.
- */
+ */
private List<JobSubmissionInterface> hostPrioritizedJobSubmissionInterfaces;
/**
* use preferred job submission protocol.
*/
private JobSubmissionInterface preferredJobSubmissionInterface;
+ /**
+ * List of job submission protocols sorted by priority order.
+ */
+ private List<DataMovementInterface> hostPrioritizedDataMovementInterfaces;
+ /**
+ * use preferred job submission protocol.
+ */
+ private DataMovementInterface preferredDataMovementInterface;
// private ContextHeaderDocument.ContextHeader contextHeader;
@@ -434,4 +443,20 @@ public class JobExecutionContext extends AbstractContext implements Serializable
public String getHostName() {
return applicationContext.getComputeResourceDescription().getHostName();
}
+
+ public List<DataMovementInterface> getHostPrioritizedDataMovementInterfaces() {
+ return hostPrioritizedDataMovementInterfaces;
+ }
+
+ public void setHostPrioritizedDataMovementInterfaces(List<DataMovementInterface> hostPrioritizedDataMovementInterfaces) {
+ this.hostPrioritizedDataMovementInterfaces = hostPrioritizedDataMovementInterfaces;
+ }
+
+ public DataMovementInterface getPreferredDataMovementInterface() {
+ return preferredDataMovementInterface;
+ }
+
+ public void setPreferredDataMovementInterface(DataMovementInterface preferredDataMovementInterface) {
+ this.preferredDataMovementInterface = preferredDataMovementInterface;
+ }
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
index e8e4c66..656a291 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
@@ -52,8 +52,9 @@ import org.apache.airavata.messaging.core.PublisherFactory;
import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
import org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription;
import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription;
+import org.apache.airavata.model.appcatalog.computeresource.DataMovementInterface;
+import org.apache.airavata.model.appcatalog.computeresource.FileSystems;
import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface;
-import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference;
import org.apache.airavata.model.messaging.event.*;
import org.apache.airavata.model.workspace.experiment.*;
@@ -74,6 +75,7 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
+import java.util.Map;
import java.util.Properties;
/**
@@ -303,6 +305,7 @@ public class BetterGfacImpl implements GFac,Watcher {
jobExecutionContext.setZk(zk);
jobExecutionContext.setCredentialStoreToken(AiravataZKUtils.getExpTokenId(zk, experimentID, taskID));
+ // handle job submission protocol
List<JobSubmissionInterface> jobSubmissionInterfaces = computeResource.getJobSubmissionInterfaces();
if (jobSubmissionInterfaces != null && !jobSubmissionInterfaces.isEmpty()){
Collections.sort(jobSubmissionInterfaces, new Comparator<JobSubmissionInterface>() {
@@ -316,36 +319,92 @@ public class BetterGfacImpl implements GFac,Watcher {
}else {
throw new GFacException("Compute resource should have at least one job submission interface defined...");
}
+ // handle data movement protocol
+ List<DataMovementInterface> dataMovementInterfaces = computeResource.getDataMovementInterfaces();
+ if (dataMovementInterfaces != null && !dataMovementInterfaces.isEmpty()) {
+ Collections.sort(dataMovementInterfaces, new Comparator<DataMovementInterface>() {
+ @Override
+ public int compare(DataMovementInterface dataMovementInterface, DataMovementInterface dataMovementInterface2) {
+ return dataMovementInterface.getPriorityOrder() - dataMovementInterface2.getPriorityOrder();
+ }
+ });
+ jobExecutionContext.setHostPrioritizedDataMovementInterfaces(dataMovementInterfaces);
+ }
+
+ // set compute resource configuration as default preferred values, after that replace those with gateway user preferences.
+ populateDefaultComputeResourceConfiguration(jobExecutionContext, applicationInterface, computeResource);
+ // if gateway resource preference is set
if (gatewayResourcePreferences != null ) {
if (gatewayResourcePreferences.getScratchLocation() == null) {
gatewayResourcePreferences.setScratchLocation("/tmp");
}
+ setUpWorkingLocation(jobExecutionContext, applicationInterface, gatewayResourcePreferences.getScratchLocation());
- /**
- * Working dir
- */
- String workingDir = gatewayResourcePreferences.getScratchLocation() + File.separator + jobExecutionContext.getExperimentID();
- jobExecutionContext.setWorkingDir(workingDir);
+ jobExecutionContext.setPreferredJobSubmissionProtocol(gatewayResourcePreferences.getPreferredJobSubmissionProtocol());
+ if (gatewayResourcePreferences.getPreferredJobSubmissionProtocol() == null) {
+ jobExecutionContext.setPreferredJobSubmissionInterface(jobExecutionContext.getHostPrioritizedJobSubmissionInterfaces().get(0));
+ jobExecutionContext.setPreferredJobSubmissionProtocol(jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionProtocol());
+ } else {
+ for (JobSubmissionInterface jobSubmissionInterface : jobSubmissionInterfaces) {
+ if (gatewayResourcePreferences.getPreferredJobSubmissionProtocol() == jobSubmissionInterface.getJobSubmissionProtocol()) {
+ jobExecutionContext.setPreferredJobSubmissionInterface(jobSubmissionInterface);
+ break;
+ }
+ }
+ }
+
+ // set gatewayUserPreferred data movement protocol and interface
+ jobExecutionContext.setPreferredDataMovementProtocol(gatewayResourcePreferences.getPreferredDataMovementProtocol());
+ if (gatewayResourcePreferences.getPreferredJobSubmissionProtocol() == null) {
+ jobExecutionContext.setPreferredDataMovementInterface(jobExecutionContext.getHostPrioritizedDataMovementInterfaces().get(0));
+ jobExecutionContext.setPreferredDataMovementProtocol(jobExecutionContext.getPreferredDataMovementInterface().getDataMovementProtocol());
+ } else {
+ for (DataMovementInterface dataMovementInterface : dataMovementInterfaces) {
+ if (gatewayResourcePreferences.getPreferredDataMovementProtocol() == dataMovementInterface.getDataMovementProtocol()) {
+ jobExecutionContext.setPreferredDataMovementInterface(dataMovementInterface);
+ break;
+ }
+ }
+ }
+ }
+ return jobExecutionContext;
+ }
+
+ private void setUpWorkingLocation(JobExecutionContext jobExecutionContext, ApplicationInterfaceDescription applicationInterface, String scratchLocation) {
+
+ /**
+ * Working dir
+ */
+ String workingDir = scratchLocation + File.separator + jobExecutionContext.getExperimentID();
+ jobExecutionContext.setWorkingDir(workingDir);
/*
* Input and Output Directory
*/
- jobExecutionContext.setInputDir(workingDir + File.separator + Constants.INPUT_DATA_DIR_VAR_NAME);
- jobExecutionContext.setOutputDir(workingDir + File.separator + Constants.OUTPUT_DATA_DIR_VAR_NAME);
+ jobExecutionContext.setInputDir(workingDir + File.separator + Constants.INPUT_DATA_DIR_VAR_NAME);
+ jobExecutionContext.setOutputDir(workingDir + File.separator + Constants.OUTPUT_DATA_DIR_VAR_NAME);
/*
* Stdout and Stderr for Shell
*/
- jobExecutionContext.setStandardOutput(workingDir + File.separator + applicationInterface.getApplicationName().replaceAll("\\s+", "") + ".stdout");
- jobExecutionContext.setStandardError(workingDir + File.separator + applicationInterface.getApplicationName().replaceAll("\\s+", "") + ".stderr");
+ jobExecutionContext.setStandardOutput(workingDir + File.separator + applicationInterface.getApplicationName().replaceAll("\\s+", "") + ".stdout");
+ jobExecutionContext.setStandardError(workingDir + File.separator + applicationInterface.getApplicationName().replaceAll("\\s+", "") + ".stderr");
+ }
- jobExecutionContext.setPreferredJobSubmissionProtocol(gatewayResourcePreferences.getPreferredJobSubmissionProtocol());
- if (gatewayResourcePreferences.getPreferredJobSubmissionProtocol() == null) {
- jobExecutionContext.setPreferredJobSubmissionInterface(jobExecutionContext.getHostPrioritizedJobSubmissionInterfaces().get(0));
- jobExecutionContext.setPreferredJobSubmissionProtocol(jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionProtocol());
- }
+ private void populateDefaultComputeResourceConfiguration(JobExecutionContext jobExecutionContext, ApplicationInterfaceDescription applicationInterface, ComputeResourceDescription computeResource) {
+ Map<FileSystems, String> fileSystems = computeResource.getFileSystems();
+ String scratchLocation = fileSystems.get(FileSystems.SCRATCH);
+ if (scratchLocation != null) {
+ setUpWorkingLocation(jobExecutionContext, applicationInterface, scratchLocation);
+ }
+
+ jobExecutionContext.setPreferredJobSubmissionInterface(jobExecutionContext.getHostPrioritizedJobSubmissionInterfaces().get(0));
+ jobExecutionContext.setPreferredJobSubmissionProtocol(jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionProtocol());
+
+ if (jobExecutionContext.getHostPrioritizedDataMovementInterfaces() != null) {
+ jobExecutionContext.setPreferredDataMovementInterface(jobExecutionContext.getHostPrioritizedDataMovementInterfaces().get(0));
+ jobExecutionContext.setPreferredDataMovementProtocol(jobExecutionContext.getPreferredDataMovementInterface().getDataMovementProtocol());
}
- return jobExecutionContext;
}
private boolean submitJob(JobExecutionContext jobExecutionContext) throws GFacException {
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
index b87f99a..b2790c9 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
@@ -77,12 +77,11 @@ public class GSISSHDirectorySetupHandler extends AbstractRecoverableHandler {
} else {
log.info("Successfully retrieved the Security Context");
}
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
- String workingDirectory = app.getScratchWorkingDirectory();
+ String workingDirectory = jobExecutionContext.getWorkingDir();
cluster.makeDirectory(workingDirectory);
- cluster.makeDirectory(app.getInputDataDirectory());
- cluster.makeDirectory(app.getOutputDataDirectory());
+ cluster.makeDirectory(jobExecutionContext.getInputDir());
+ cluster.makeDirectory(jobExecutionContext.getOutputDir());
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
status.setTransferState(TransferState.DIRECTORY_SETUP);
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
index 5665b5b..b882be6 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
@@ -27,17 +27,18 @@ import org.apache.airavata.commons.gfac.type.MappingFactory;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.core.context.JobExecutionContext;
import org.apache.airavata.gfac.core.context.MessageContext;
-import org.apache.airavata.gfac.core.handler.AbstractHandler;
import org.apache.airavata.gfac.core.handler.AbstractRecoverableHandler;
import org.apache.airavata.gfac.core.handler.GFacHandlerException;
import org.apache.airavata.gfac.core.utils.GFacUtils;
import org.apache.airavata.gfac.gsissh.security.GSISecurityContext;
import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
import org.apache.airavata.gsi.ssh.api.Cluster;
-import org.apache.airavata.gsi.ssh.api.SSHApiException;
-import org.apache.airavata.model.workspace.experiment.*;
+import org.apache.airavata.model.workspace.experiment.CorrectiveAction;
+import org.apache.airavata.model.workspace.experiment.DataTransferDetails;
+import org.apache.airavata.model.workspace.experiment.ErrorCategory;
+import org.apache.airavata.model.workspace.experiment.TransferState;
+import org.apache.airavata.model.workspace.experiment.TransferStatus;
import org.apache.airavata.registry.cpi.ChildDataType;
-import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
import org.apache.airavata.schemas.gfac.URIArrayType;
import org.apache.airavata.schemas.gfac.URIParameterType;
import org.slf4j.Logger;
@@ -45,7 +46,11 @@ import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
/**
* Recoverability for this handler assumes the same input values will come in the second
@@ -171,11 +176,10 @@ public class GSISSHInputHandler extends AbstractRecoverableHandler {
}
private static String stageInputFiles(Cluster cluster, JobExecutionContext jobExecutionContext, String paramValue) throws IOException, GFacException {
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
int i = paramValue.lastIndexOf(File.separator);
String substring = paramValue.substring(i + 1);
try {
- String targetFile = app.getInputDataDirectory() + File.separator + substring;
+ String targetFile = jobExecutionContext.getInputDir() + File.separator + substring;
if (paramValue.startsWith("file")) {
paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
index ac9bf3c..a714099 100644
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
@@ -27,6 +27,7 @@ import java.util.*;
import net.schmizz.sshj.connection.ConnectionException;
import net.schmizz.sshj.transport.TransportException;
+import org.apache.aiaravata.application.catalog.data.impl.AppCatalogFactory;
import org.apache.airavata.common.exception.ApplicationSettingsException;
import org.apache.airavata.common.utils.Constants;
import org.apache.airavata.commons.gfac.type.ActualParameter;
@@ -46,6 +47,10 @@ import org.apache.airavata.gfac.gsissh.util.GFACGSISSHUtils;
import org.apache.airavata.gsi.ssh.api.Cluster;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
+import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol;
+import org.apache.airavata.model.appcatalog.computeresource.MonitorMode;
+import org.apache.airavata.model.appcatalog.computeresource.SSHJobSubmission;
+import org.apache.airavata.model.appcatalog.computeresource.SecurityProtocol;
import org.apache.airavata.model.messaging.event.TaskIdentifier;
import org.apache.airavata.model.messaging.event.TaskOutputChangeEvent;
import org.apache.airavata.model.workspace.experiment.*;
@@ -67,36 +72,6 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
int oldIndex = 0;
List<String> oldFiles = new ArrayList<String>();
StringBuffer data = new StringBuffer("|");
- if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GsisshHostType) { // this is because we don't have the right jobexecution context
- // so attempting to get it from the registry
- if (Constants.PUSH.equals(((GsisshHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getMonitorMode())) {
- log.warn("During the out handler chain jobExecution context came null, so trying to handler");
- ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
- TaskDetails taskData = null;
- try {
- taskData = (TaskDetails) jobExecutionContext.getRegistry().get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
- } catch (RegistryException e) {
- log.error("Error retrieving job details from Registry");
- throw new GFacHandlerException("Error retrieving job details from Registry", e);
- }
- JobDetails jobDetails = taskData.getJobDetailsList().get(0);
- String jobDescription = jobDetails.getJobDescription();
- if (jobDescription != null) {
- JobDescriptor jobDescriptor = null;
- try {
- jobDescriptor = JobDescriptor.fromXML(jobDescription);
- } catch (XmlException e1) {
- e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
- applicationDeploymentDescription.getType().setScratchWorkingDirectory(
- jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
- applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
- applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
- applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
- applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
- }
- }
- }
try {
if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
@@ -114,8 +89,6 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
- .getApplicationDeploymentDescription().getType();
Cluster cluster = null;
try {
@@ -174,7 +147,7 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
localStdOutFile = new File(outputDataDir + File.separator + timeStampedExperimentID + "stdout");
while(stdOutStr.isEmpty()){
try {
- cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
+ cluster.scpFrom(jobExecutionContext.getStandardOutput(), localStdOutFile.getAbsolutePath());
stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
} catch (Exception e) {
log.error(e.getLocalizedMessage());
@@ -192,7 +165,7 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
data.append(oldFiles.get(index++)).append(",");
} else {
localStdErrFile = new File(outputDataDir + File.separator + timeStampedExperimentID + "stderr");
- cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
+ cluster.scpFrom(jobExecutionContext.getStandardError(), localStdErrFile.getAbsolutePath());
StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
}
@@ -219,7 +192,7 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
List<String> outputList = null;
int retry=3;
while(retry>0){
- outputList = cluster.listDirectory(app.getOutputDataDirectory());
+ outputList = cluster.listDirectory(jobExecutionContext.getOutputDir());
if (outputList.size() == 1 && outputList.get(0).isEmpty()) {
Thread.sleep(10000);
} else if (outputList.size() > 0) {
@@ -229,7 +202,6 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
}
retry--;
if(retry==0){
-// log.info("Ohhhhhhh shitttttttOhhhhhhh shitttttttOhhhhhhh shitttttttOhhhhhhh shitttttttOhhhhhhh shitttttttOhhhhhhh shittttttt");
}
Thread.sleep(10000);
}
@@ -269,7 +241,7 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
outputFile = oldFiles.get(index);
data.append(oldFiles.get(index++)).append(",");
} else {
- cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
+ cluster.scpFrom(jobExecutionContext.getOutputDir() + File.separator + valueList, outputDataDir);
outputFile = outputDataDir + File.separator + valueList;
jobExecutionContext.addOutputFile(outputFile);
StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
@@ -296,9 +268,10 @@ public class GSISSHOutputHandler extends AbstractRecoverableHandler {
);
}
}
- app.setStandardError(localStdErrFile.getAbsolutePath());
- app.setStandardOutput(localStdOutFile.getAbsolutePath());
- app.setOutputDataDirectory(outputDataDir);
+ // Why we set following?
+// app.setStandardError(localStdErrFile.getAbsolutePath());
+// app.setStandardOutput(localStdOutFile.getAbsolutePath());
+// app.setOutputDataDirectory(outputDataDir);
status.setTransferState(TransferState.DOWNLOAD);
detail.setTransferStatus(status);
detail.setTransferDescription(outputDataDir);
http://git-wip-us.apache.org/repos/asf/airavata/blob/5a28f745/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
index 9a0639b..9b7102b 100644
--- a/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gsi/ssh/api/job/JobDescriptor.java
@@ -60,6 +60,13 @@ public class JobDescriptor {
return this.jobDescriptionDocument;
}
+ /**
+ * With new app catalog thrift object integration, we don't use this
+ * @param xml
+ * @return
+ * @throws XmlException
+ */
+ @Deprecated
public static JobDescriptor fromXML(String xml)
throws XmlException {
JobDescriptorDocument parse = JobDescriptorDocument.Factory