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Posted to commits@airavata.apache.org by sa...@apache.org on 2014/04/23 18:29:18 UTC
[1/2] git commit: fixing the double node entry issue and some
refactoring
Repository: airavata
Updated Branches:
refs/heads/master 71de72f83 -> b4e41646f
fixing the double node entry issue and some refactoring
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/dd3b3f19
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/dd3b3f19
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/dd3b3f19
Branch: refs/heads/master
Commit: dd3b3f1945ed2e0d2a65bb27f1d3214ac899b906
Parents: 49eea6f
Author: Saminda Wijeratne <sa...@gmail.com>
Authored: Wed Apr 23 09:28:06 2014 -0700
Committer: Saminda Wijeratne <sa...@gmail.com>
Committed: Wed Apr 23 09:28:06 2014 -0700
----------------------------------------------------------------------
.../org/apache/airavata/gfac/cpi/GFacImpl.java | 9 +++----
.../gfac/provider/impl/GSISSHProvider.java | 3 +--
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 26 ++++++++++++--------
.../AiravataExperimentStatusUpdator.java | 1 +
.../job/monitor/AiravataJobStatusUpdator.java | 3 +--
.../job/monitor/AiravataTaskStatusUpdator.java | 2 +-
.../AiravataWorkflowNodeStatusUpdator.java | 2 +-
.../registry/jpa/impl/ExperimentRegistry.java | 2 +-
.../apache/airavata/job/monitor/MonitorID.java | 8 ++----
9 files changed, 28 insertions(+), 28 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
index d6a61a3..4530d37 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
@@ -42,7 +42,6 @@ import org.apache.airavata.gfac.context.ApplicationContext;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
import org.apache.airavata.gfac.handler.GFacHandler;
import org.apache.airavata.gfac.handler.GFacHandlerConfig;
import org.apache.airavata.gfac.handler.GFacHandlerException;
@@ -457,7 +456,7 @@ public class GFacImpl implements GFac, AbstractActivityListener {
String sshPrivateKeyPass = configurationProperties.getProperty(Constants.SSH_PRIVATE_KEY_PASS);
String sshPassword = configurationProperties.getProperty(Constants.SSH_PASSWORD);
String sshPublicKey = configurationProperties.getProperty(Constants.SSH_PUBLIC_KEY);
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+// SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
AuthenticationInfo authenticationInfo = null;
// we give higher preference to the password over keypair ssh authentication
if (sshPassword != null) {
@@ -479,9 +478,9 @@ public class GFacImpl implements GFac, AbstractActivityListener {
} catch (SSHApiException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
- sshSecurityContext.setPbsCluster(pbsCluster);
- sshSecurityContext.setUsername(sshUserName);
- jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, sshSecurityContext);
+// sshSecurityContext.setPbsCluster(pbsCluster);
+// sshSecurityContext.setUsername(sshUserName);
+// jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT, sshSecurityContext);
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
index 69ad519..4da1bcb 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
@@ -25,7 +25,6 @@ import java.util.Map;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
import org.apache.airavata.gfac.notification.events.StartExecutionEvent;
import org.apache.airavata.gfac.provider.GFacProviderException;
import org.apache.airavata.gfac.utils.GFacUtils;
@@ -66,7 +65,7 @@ public class GSISSHProvider extends AbstractProvider{
if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
} else {
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
+// cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
}
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
index 221f6e1..be78570 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
@@ -20,6 +20,13 @@
*/
package org.apache.airavata.core.gfac.services.impl;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
import org.apache.airavata.commons.gfac.type.ActualParameter;
import org.apache.airavata.commons.gfac.type.ApplicationDescription;
import org.apache.airavata.commons.gfac.type.HostDescription;
@@ -31,7 +38,6 @@ import org.apache.airavata.gfac.context.ApplicationContext;
import org.apache.airavata.gfac.context.JobExecutionContext;
import org.apache.airavata.gfac.context.MessageContext;
import org.apache.airavata.gfac.context.security.GSISecurityContext;
-import org.apache.airavata.gfac.context.security.SSHSecurityContext;
import org.apache.airavata.gfac.cpi.GFacImpl;
import org.apache.airavata.gsi.ssh.api.Cluster;
import org.apache.airavata.gsi.ssh.api.SSHApiException;
@@ -42,18 +48,18 @@ import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo
import org.apache.airavata.gsi.ssh.util.CommonUtils;
import org.apache.airavata.model.workspace.experiment.TaskDetails;
import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
-import org.apache.airavata.schemas.gfac.*;
-import org.testng.annotations.AfterClass;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GsisshHostType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.InputParameterType;
+import org.apache.airavata.schemas.gfac.JobTypeType;
+import org.apache.airavata.schemas.gfac.OutputParameterType;
+import org.apache.airavata.schemas.gfac.ProjectAccountType;
+import org.apache.airavata.schemas.gfac.QueueType;
+import org.apache.airavata.schemas.gfac.StringParameterType;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
public class GSISSHProviderTestWithMyProxyAuth {
private JobExecutionContext jobExecutionContext;
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataExperimentStatusUpdator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataExperimentStatusUpdator.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataExperimentStatusUpdator.java
index f172e6c..7cb0489 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataExperimentStatusUpdator.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataExperimentStatusUpdator.java
@@ -52,6 +52,7 @@ public class AiravataExperimentStatusUpdator implements AbstractActivityListener
try {
String experimentID = experimentStatus.getIdentity().getExperimentID();
updateExperimentStatus(experimentID, state);
+ logger.debug("Experiment " + experimentStatus.getIdentity().getExperimentID() + " status updated to "+state.toString());
} catch (Exception e) {
logger.error("Error persisting data" + e.getLocalizedMessage(), e);
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataJobStatusUpdator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataJobStatusUpdator.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataJobStatusUpdator.java
index 0a56543..29ba766 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataJobStatusUpdator.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataJobStatusUpdator.java
@@ -76,7 +76,7 @@ public class AiravataJobStatusUpdator implements AbstractActivityListener{
} catch (Exception e) {
logger.error("Error persisting data" + e.getLocalizedMessage(), e);
}
- logger.info("Job ID:" + jobStatus.getIdentity().getJobId() + " is "+state.toString());
+ logger.debug("Job " + jobStatus.getIdentity().getJobId() + " status updated to "+state.toString());
switch (state) {
case COMPLETE: case UNKNOWN: case CANCELED:case FAILED:case SUSPENDED:
jobsToMonitor.remove(jobStatus.getMonitorID());
@@ -112,7 +112,6 @@ public class AiravataJobStatusUpdator implements AbstractActivityListener{
default:
break;
}
- logger.debug("Publishing Task Status "+state.toString());
monitorPublisher.publish(new TaskStatusChangeRequest(jobStatus.getIdentity(),state));
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataTaskStatusUpdator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataTaskStatusUpdator.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataTaskStatusUpdator.java
index 86ae26a..5eea71a 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataTaskStatusUpdator.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataTaskStatusUpdator.java
@@ -57,6 +57,7 @@ public class AiravataTaskStatusUpdator implements AbstractActivityListener{
try {
String taskID = taskStatus.getIdentity().getTaskId();
updateTaskStatus(taskID, state);
+ logger.debug("Task " + taskStatus.getIdentity().getTaskId() + " status updated to "+state.toString());
} catch (Exception e) {
logger.error("Error persisting data" + e.getLocalizedMessage(), e);
}
@@ -84,7 +85,6 @@ public class AiravataTaskStatusUpdator implements AbstractActivityListener{
default:
break;
}
- logger.debug("Publishing Experiment Status "+state.toString());
monitorPublisher.publish(new WorkflowNodeStatusChangeRequest(taskStatus.getIdentity(),state));
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataWorkflowNodeStatusUpdator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataWorkflowNodeStatusUpdator.java b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataWorkflowNodeStatusUpdator.java
index cd07a1d..ce4012c 100644
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataWorkflowNodeStatusUpdator.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/job/monitor/AiravataWorkflowNodeStatusUpdator.java
@@ -58,6 +58,7 @@ public class AiravataWorkflowNodeStatusUpdator implements AbstractActivityListen
try {
String workflowNodeID = workflowNodeStatus.getIdentity().getWorkflowNodeID();
updateWorkflowNodeStatus(workflowNodeID, state);
+ logger.debug("Workflow node " + workflowNodeStatus.getIdentity().getWorkflowNodeID() + " status updated to "+state.toString());
} catch (Exception e) {
logger.error("Error persisting data" + e.getLocalizedMessage(), e);
}
@@ -83,7 +84,6 @@ public class AiravataWorkflowNodeStatusUpdator implements AbstractActivityListen
default:
break;
}
- logger.debug("Publishing Experiment Status "+state.toString());
monitorPublisher.publish(new ExperimentStatusChangeRequest(nodeStatus.getIdentity(),state));
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
index 3fa7b5f..ad2b9bc 100644
--- a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
+++ b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java
@@ -703,7 +703,7 @@ public class ExperimentRegistry {
WorkflowNodeDetailResource workflowNode = experiment.getWorkflowNode(nodeId);
workflowNode.setNodeName(nodeDetails.getNodeName());
workflowNode.setCreationTime(AiravataUtils.getTime(nodeDetails.getCreationTime()));
- workflowNode.setNodeInstanceId(getNodeInstanceID(nodeDetails.getNodeName()));
+ workflowNode.setNodeInstanceId(nodeId);
workflowNode.save();
String expID = workflowNode.getExperimentResource().getExpID();
List<DataObjectType> nodeInputs = nodeDetails.getNodeInputs();
http://git-wip-us.apache.org/repos/asf/airavata/blob/dd3b3f19/tools/job-monitor/src/main/java/org/apache/airavata/job/monitor/MonitorID.java
----------------------------------------------------------------------
diff --git a/tools/job-monitor/src/main/java/org/apache/airavata/job/monitor/MonitorID.java b/tools/job-monitor/src/main/java/org/apache/airavata/job/monitor/MonitorID.java
index 241e3b0..ef03fbc 100644
--- a/tools/job-monitor/src/main/java/org/apache/airavata/job/monitor/MonitorID.java
+++ b/tools/job-monitor/src/main/java/org/apache/airavata/job/monitor/MonitorID.java
@@ -63,12 +63,7 @@ public class MonitorID {
private JobState state;
public MonitorID(HostDescription host, String jobID,String taskID, String workflowNodeID, String experimentID, String userName) {
- this.host = host;
- this.jobStartedTime = new Timestamp((new Date()).getTime());
- this.userName = userName;
- this.jobID = jobID;
- this.taskID = taskID;
- this.experimentID = experimentID;
+ this(host, jobID, taskID, workflowNodeID, experimentID, userName, null);
}
public MonitorID(HostDescription host, String jobID,String taskID, String workflowNodeID, String experimentID, String userName,AuthenticationInfo authenticationInfo) {
@@ -84,6 +79,7 @@ public class MonitorID {
}
this.jobID = jobID;
this.taskID = taskID;
+ this.workflowNodeID=workflowNodeID;
this.experimentID = experimentID;
}
public HostDescription getHost() {
[2/2] git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by sa...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b4e41646
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b4e41646
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b4e41646
Branch: refs/heads/master
Commit: b4e41646f946817b6baee5cbddc71c3984229837
Parents: dd3b3f1 71de72f
Author: Saminda Wijeratne <sa...@gmail.com>
Authored: Wed Apr 23 09:29:03 2014 -0700
Committer: Saminda Wijeratne <sa...@gmail.com>
Committed: Wed Apr 23 09:29:03 2014 -0700
----------------------------------------------------------------------
.../monitor/impl/pull/qstat/QstatMonitor.java | 44 +++++++++++---------
1 file changed, 24 insertions(+), 20 deletions(-)
----------------------------------------------------------------------