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 <[email protected]> Authored: Wed Apr 23 09:28:06 2014 -0700 Committer: Saminda Wijeratne <[email protected]> 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() {
