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Posted to commits@airavata.apache.org by ch...@apache.org on 2015/09/24 17:57:28 UTC
airavata git commit: JPA issues and enabling gordon mpi jobs
Repository: airavata
Updated Branches:
refs/heads/master 819157476 -> d8cbbb139
JPA issues and enabling gordon mpi jobs
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d8cbbb13
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d8cbbb13
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d8cbbb13
Branch: refs/heads/master
Commit: d8cbbb1392c7482caad2c1ee3ee794b1480a8d86
Parents: 8191574
Author: Chathuri Wimalasena <ch...@apache.org>
Authored: Thu Sep 24 11:57:22 2015 -0400
Committer: Chathuri Wimalasena <ch...@apache.org>
Committed: Thu Sep 24 11:57:22 2015 -0400
----------------------------------------------------------------------
.../java/org/apache/airavata/gfac/core/GFacUtils.java | 4 +++-
.../java/org/apache/airavata/gfac/impl/SSHUtils.java | 4 +++-
.../experiment/catalog/impl/ExperimentRegistry.java | 2 +-
.../catalog/resources/ExperimentErrorResource.java | 5 ++++-
.../catalog/resources/ExperimentInputResource.java | 7 +++++--
.../catalog/resources/ExperimentOutputResource.java | 7 +++++--
.../catalog/resources/ExperimentResource.java | 7 +++++--
.../catalog/resources/ExperimentStatusResource.java | 7 +++++--
.../core/experiment/catalog/resources/JobResource.java | 7 +++++--
.../experiment/catalog/resources/JobStatusResource.java | 7 +++++--
.../catalog/resources/ProcessErrorResource.java | 7 +++++--
.../catalog/resources/ProcessInputResource.java | 7 +++++--
.../catalog/resources/ProcessOutputResource.java | 7 +++++--
.../experiment/catalog/resources/ProcessResource.java | 8 +++++---
.../resources/ProcessResourceScheduleResource.java | 7 +++++--
.../catalog/resources/ProcessStatusResource.java | 7 +++++--
.../experiment/catalog/resources/TaskErrorResource.java | 7 +++++--
.../core/experiment/catalog/resources/TaskResource.java | 7 +++++--
.../catalog/resources/TaskStatusResource.java | 7 +++++--
.../resources/UserConfigurationDataResource.java | 7 +++++--
.../experiment/catalog/ExperimentInputResourceTest.java | 2 +-
.../catalog/ExperimentOutputResourceTest.java | 2 +-
.../experiment/catalog/GatewayResourceTest.java | 12 +++++++-----
.../airavata/experiment/catalog/JobResourceTest.java | 2 +-
.../experiment/catalog/ProcessResourceTest.java | 2 +-
.../airavata/experiment/catalog/TaskResourceTest.java | 2 +-
.../experiment/catalog/UserConfigurationDataTest.java | 2 +-
.../multitenantedairavata/FrameworkBootstrapping.java | 2 +-
.../src/main/resources/test-framework.json | 2 +-
29 files changed, 106 insertions(+), 50 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
index 5ea1ea3..3275734 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java
@@ -811,13 +811,15 @@ public class GFacUtils {
ApplicationParallelismType parallelism = appDepDescription.getParallelism();
if (parallelism != null) {
if (parallelism == ApplicationParallelismType.MPI || parallelism == ApplicationParallelismType.OPENMP || parallelism == ApplicationParallelismType.OPENMP_MPI) {
- // FIXME this is wrong for BR2
+ // FIXME this needs to be fixed once parallaliasation retrieved by app catalog
if (appDepDescription.getComputeHostId().contains("stampede")){
jobDescriptor.setJobSubmitter("ibrun");
}else if (appDepDescription.getComputeHostId().contains("bigred2")){
jobDescriptor.setJobSubmitter("aprun -n");
}else if (appDepDescription.getComputeHostId().contains("comet")){
jobDescriptor.setJobSubmitter("mpiexec");
+ }else if (appDepDescription.getComputeHostId().contains("gordon")){
+ jobDescriptor.setJobSubmitter(" mpirun_rsh -hostfile $PBS_NODEFILE -np");
}else {
jobDescriptor.setJobSubmitter("ibrun");
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
index 6a100a9..8a590e0 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/SSHUtils.java
@@ -173,7 +173,9 @@ public class SSHUtils {
OutputStream out = channel.getOutputStream();
InputStream in = channel.getInputStream();
- channel.connect();
+ if (!channel.isClosed()){
+ channel.connect();
+ }
byte[] buf = new byte[1024];
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
index 12aebe2..d960986 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/impl/ExperimentRegistry.java
@@ -746,7 +746,7 @@ public class ExperimentRegistry {
}
}
} catch (Exception e) {
- logger.error("Error while updating experiment...", e);
+ logger.error("Error while updating process...", e);
throw new RegistryException(e);
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentErrorResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentErrorResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentErrorResource.java
index 6a049d3..7217599 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentErrorResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentErrorResource.java
@@ -128,7 +128,6 @@ public class ExperimentErrorResource extends AbstractExpCatResource {
EntityManager em = null;
try {
em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
ExperimentError experimentError;
if(experimentId == null || errorId == null){
throw new RegistryException("Does not have the experiment id or error id");
@@ -137,6 +136,10 @@ public class ExperimentErrorResource extends AbstractExpCatResource {
experimentErrorPK.setExperimentId(experimentId);
experimentErrorPK.setErrorId(errorId);
experimentError = em.find(ExperimentError.class, experimentErrorPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(experimentError == null){
experimentError = new ExperimentError();
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentInputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentInputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentInputResource.java
index e5dfa3f..2389b57 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentInputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentInputResource.java
@@ -180,6 +180,10 @@ public class ExperimentInputResource extends AbstractExpCatResource {
experimentInputPK.setExperimentId(experimentId);
experimentInputPK.setInputName(inputName);
experimentInput = em.find(ExperimentInput.class, experimentInputPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(experimentInput == null){
experimentInput = new ExperimentInput();
}
@@ -195,8 +199,7 @@ public class ExperimentInputResource extends AbstractExpCatResource {
experimentInput.setIsRequired(isRequired);
experimentInput.setRequiredToAddedToCmd(requiredToAddedToCmd);
experimentInput.setDataStaged(dataStaged);
- em.getTransaction().begin();
- em.persist(experimentInput);
+ em.merge(experimentInput);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentOutputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentOutputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentOutputResource.java
index b554174..57c28fd 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentOutputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentOutputResource.java
@@ -162,6 +162,10 @@ public class ExperimentOutputResource extends AbstractExpCatResource {
experimentOutputPK.setExperimentId(experimentId);
experimentOutputPK.setOutputName(outputName);
experimentOutput = em.find(ExperimentOutput.class, experimentOutputPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(experimentOutput == null){
experimentOutput = new ExperimentOutput();
}
@@ -175,8 +179,7 @@ public class ExperimentOutputResource extends AbstractExpCatResource {
experimentOutput.setDataMovement(dataMovement);
experimentOutput.setLocation(location);
experimentOutput.setSearchQuery(searchQuery);
- em.getTransaction().begin();
- em.persist(experimentOutput);
+ em.merge(experimentOutput);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
index 68f40c5..ad71f91 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentResource.java
@@ -437,6 +437,10 @@ public class ExperimentResource extends AbstractExpCatResource {
try {
em = ExpCatResourceUtils.getEntityManager();
Experiment experiment = em.find(Experiment.class, experimentId);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if (experiment == null) {
experiment = new Experiment();
}
@@ -452,8 +456,7 @@ public class ExperimentResource extends AbstractExpCatResource {
experiment.setGatewayExecutionId(gatewayExecutionId);
experiment.setEnableEmailNotification(enableEmailNotification);
experiment.setEmailAddresses(emailAddresses);
- em.getTransaction().begin();
- em.persist(experiment);
+ em.merge(experiment);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentStatusResource.java
index 103a69e..c7242c2 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ExperimentStatusResource.java
@@ -110,7 +110,6 @@ public class ExperimentStatusResource extends AbstractExpCatResource {
EntityManager em = null;
try {
em = ExpCatResourceUtils.getEntityManager();
- em.getTransaction().begin();
ExperimentStatus experimentStatus;
if(experimentId == null || statusId == null){
throw new RegistryException("Does not have the experiment id or status id");
@@ -119,6 +118,10 @@ public class ExperimentStatusResource extends AbstractExpCatResource {
experimentStatusPK.setStatusId(statusId);
experimentStatusPK.setExperimentId(experimentId);
experimentStatus = em.find(ExperimentStatus.class, experimentStatusPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(experimentStatus == null){
experimentStatus = new ExperimentStatus();
}
@@ -127,7 +130,7 @@ public class ExperimentStatusResource extends AbstractExpCatResource {
experimentStatus.setState(state);
experimentStatus.setReason(reason);
experimentStatus.setTimeOfStateChange(timeOfStateChange);
- em.persist(experimentStatus);
+ em.merge(experimentStatus);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
index 7fe29d3..abee18f 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobResource.java
@@ -278,6 +278,10 @@ public class JobResource extends AbstractExpCatResource {
jobPK.setJobId(jobId);
jobPK.setProcessId(processId);
Job job = em.find(Job.class, jobPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(job == null){
job = new Job();
}
@@ -298,8 +302,7 @@ public class JobResource extends AbstractExpCatResource {
job.setJobName(jobName);
job.setWorkingDir(workingDir);
job.setExitCode(exitCode);
- em.getTransaction().begin();
- em.persist(job);
+ em.merge(job);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
index c2ff7a5..3de163c 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/JobStatusResource.java
@@ -128,6 +128,10 @@ public class JobStatusResource extends AbstractExpCatResource {
jobStatusPK.setStatusId(statusId);
jobStatusPK.setProcessId(processId);
jobStatus = em.find(JobStatus.class, jobStatusPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(jobStatus == null){
jobStatus = new JobStatus();
}
@@ -136,8 +140,7 @@ public class JobStatusResource extends AbstractExpCatResource {
jobStatus.setProcessId(processId);
jobStatus.setState(state);
jobStatus.setReason(reason);
- em.getTransaction().begin();
- em.persist(jobStatus);
+ em.merge(jobStatus);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
index a7ba797..3faa9b5 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessErrorResource.java
@@ -137,6 +137,10 @@ public class ProcessErrorResource extends AbstractExpCatResource {
processErrorPK.setProcessId(processId);
processErrorPK.setErrorId(errorId);
processError = em.find(ProcessError.class, processErrorPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(processError == null){
processError = new ProcessError();
}
@@ -146,8 +150,7 @@ public class ProcessErrorResource extends AbstractExpCatResource {
processError.setUserFriendlyMessage(userFriendlyMessage);
processError.setRootCauseErrorIdList(rootCauseErrorIdList);
processError.setTransientOrPersistent(transientOrPersistent);
- em.persist(processError);
- em.getTransaction().begin();
+ em.merge(processError);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
index eec4878..8f0531f 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessInputResource.java
@@ -181,6 +181,10 @@ public class ProcessInputResource extends AbstractExpCatResource {
processInputPk.setProcessId(processId);
processInputPk.setInputName(inputName);
processInput = em.find(ProcessInput.class, processInputPk);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(processInput == null){
processInput = new ProcessInput();
}
@@ -196,8 +200,7 @@ public class ProcessInputResource extends AbstractExpCatResource {
processInput.setIsRequired(isRequired);
processInput.setRequiredToAddedToCmd(requiredToAddedToCmd);
processInput.setDataStaged(dataStaged);
- em.getTransaction().begin();
- em.persist(processInput);
+ em.merge(processInput);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
index b1953b6..9300cfe 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessOutputResource.java
@@ -163,6 +163,10 @@ public class ProcessOutputResource extends AbstractExpCatResource {
processOutputPK.setProcessId(processId);
processOutputPK.setOutputName(outputName);
processOutput = em.find(ProcessOutput.class, processOutputPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(processOutput == null){
processOutput = new ProcessOutput();
}
@@ -176,8 +180,7 @@ public class ProcessOutputResource extends AbstractExpCatResource {
processOutput.setDataMovement(dataMovement);
processOutput.setLocation(location);
processOutput.setSearchQuery(searchQuery);
- em.getTransaction().begin();
- em.persist(processOutput);
+ em.merge(processOutput);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
index 5aa8324..2cab3e9 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResource.java
@@ -471,8 +471,11 @@ public class ProcessResource extends AbstractExpCatResource {
EntityManager em = null;
try {
em = ExpCatResourceUtils.getEntityManager();
-
Process process = em.find(Process.class, processId);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if (process == null) {
process = new Process();
}
@@ -488,8 +491,7 @@ public class ProcessResource extends AbstractExpCatResource {
process.setGatewayExecutionId(gatewayExecutionId);
process.setEnableEmailNotification(enableEmailNotification);
process.setEmailAddresses(emailAddresses);
- em.getTransaction().begin();
- em.persist(process);
+ em.merge(process);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
index 65ac551..0e7c4f8 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessResourceScheduleResource.java
@@ -141,6 +141,10 @@ public class ProcessResourceScheduleResource extends AbstractExpCatResource {
ProcessResourceSchedule processResourceSchedule;
processResourceSchedule = em.find(ProcessResourceSchedule.class, processId);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(processResourceSchedule == null){
processResourceSchedule = new ProcessResourceSchedule();
}
@@ -152,8 +156,7 @@ public class ProcessResourceScheduleResource extends AbstractExpCatResource {
processResourceSchedule.setQueueName(queueName);
processResourceSchedule.setWallTimeLimit(wallTimeLimit);
processResourceSchedule.setTotalPhysicalMemory(totalPhysicalMemory);
- em.getTransaction().begin();
- em.persist(processResourceSchedule);
+ em.merge(processResourceSchedule);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
index 894e95b..285a81e 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/ProcessStatusResource.java
@@ -119,6 +119,10 @@ public class ProcessStatusResource extends AbstractExpCatResource {
processStatusPK.setStatusId(statusId);
processStatusPK.setProcessId(processId);
processStatus = em.find(ProcessStatus.class, processStatusPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(processStatus == null){
processStatus = new ProcessStatus();
}
@@ -126,8 +130,7 @@ public class ProcessStatusResource extends AbstractExpCatResource {
processStatus.setProcessId(processId);
processStatus.setState(state);
processStatus.setReason(reason);
- em.getTransaction().begin();
- em.persist(processStatus);
+ em.merge(processStatus);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskErrorResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskErrorResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskErrorResource.java
index d93712e..5d5730f 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskErrorResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskErrorResource.java
@@ -137,6 +137,10 @@ public class TaskErrorResource extends AbstractExpCatResource {
taskErrorPK.setTaskId(taskId);
taskErrorPK.setErrorId(errorId);
taskError = em.find(TaskError.class, taskErrorPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(taskError == null){
taskError = new TaskError();
}
@@ -147,8 +151,7 @@ public class TaskErrorResource extends AbstractExpCatResource {
taskError.setUserFriendlyMessage(userFriendlyMessage);
taskError.setRootCauseErrorIdList(rootCauseErrorIdList);
taskError.setTransientOrPersistent(transientOrPersistent);
- em.getTransaction().begin();
- em.persist(taskError);
+ em.merge(taskError);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
index d480597..3904283 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskResource.java
@@ -276,6 +276,10 @@ public class TaskResource extends AbstractExpCatResource {
em = ExpCatResourceUtils.getEntityManager();
Task task = em.find(Task.class, taskId);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(task == null){
task = new Task();
}
@@ -286,8 +290,7 @@ public class TaskResource extends AbstractExpCatResource {
task.setLastUpdateTime(lastUpdateTime);
task.setTaskDetail(taskDetail);
task.setSetSubTaskModel(subTaskModel);
- em.getTransaction().begin();
- em.persist(task);
+ em.merge(task);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskStatusResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskStatusResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskStatusResource.java
index 8f8f31f..7b3d085 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskStatusResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/TaskStatusResource.java
@@ -119,6 +119,10 @@ public class TaskStatusResource extends AbstractExpCatResource {
taskStatusPK.setTaskId(taskId);
taskStatusPK.setStatusId(statusId);
taskStatus = em.find(TaskStatus.class, taskStatusPK);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(taskStatus == null){
taskStatus = new TaskStatus();
}
@@ -127,8 +131,7 @@ public class TaskStatusResource extends AbstractExpCatResource {
taskStatus.setState(state);
taskStatus.setReason(reason);
taskStatus.setTimeOfStateChange(timeOfStateChange);
- em.getTransaction().begin();
- em.persist(taskStatus);
+ em.merge(taskStatus);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/UserConfigurationDataResource.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/UserConfigurationDataResource.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/UserConfigurationDataResource.java
index 49c9de3..f7c2090 100644
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/UserConfigurationDataResource.java
+++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/experiment/catalog/resources/UserConfigurationDataResource.java
@@ -195,6 +195,10 @@ public class UserConfigurationDataResource extends AbstractExpCatResource {
throw new RegistryException("Does not have the experiment id");
}
userConfigurationData = em.find(UserConfigurationData.class, experimentId);
+ em.close();
+
+ em = ExpCatResourceUtils.getEntityManager();
+ em.getTransaction().begin();
if(userConfigurationData == null){
userConfigurationData = new UserConfigurationData();
}
@@ -212,8 +216,7 @@ public class UserConfigurationDataResource extends AbstractExpCatResource {
userConfigurationData.setQueueName(queueName);
userConfigurationData.setWallTimeLimit(wallTimeLimit);
userConfigurationData.setTotalPhysicalMemory(totalPhysicalMemory);
- em.getTransaction().begin();
- em.persist(userConfigurationData);
+ em.merge(userConfigurationData);
em.getTransaction().commit();
em.close();
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentInputResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentInputResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentInputResourceTest.java
index 0ebaecb..ac7c5bb 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentInputResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentInputResourceTest.java
@@ -34,7 +34,7 @@ import static org.junit.Assert.assertTrue;
public class ExperimentInputResourceTest extends AbstractResourceTest {
private ExperimentResource experimentResource;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID2";
ExperimentInputResource experimentInputResource;
@Override
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentOutputResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentOutputResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentOutputResourceTest.java
index 937c7d8..b25e5f1 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentOutputResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ExperimentOutputResourceTest.java
@@ -34,7 +34,7 @@ import static org.junit.Assert.assertTrue;
public class ExperimentOutputResourceTest extends AbstractResourceTest {
private ExperimentResource experimentResource;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID1";
ExperimentOutputResource outputResource;
@Override
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/GatewayResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/GatewayResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/GatewayResourceTest.java
index 12343d6..309df99 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/GatewayResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/GatewayResourceTest.java
@@ -40,6 +40,7 @@ public class GatewayResourceTest extends AbstractResourceTest {
private UserResource userResource;
private WorkerResource workerResource;
private ExperimentResource experimentResource;
+ private String testExpID = "testExpID3";
@Override
@@ -61,7 +62,8 @@ public class GatewayResourceTest extends AbstractResourceTest {
experimentResource = (ExperimentResource) gatewayResource.create(ResourceType.EXPERIMENT);
- experimentResource.setExperimentId("testExpID");
+
+ experimentResource.setExperimentId(testExpID);
experimentResource.setUserName(getWorkerResource().getUser());
experimentResource.setProjectId(getProjectResource().getId());
experimentResource.setCreationTime(currentDate);
@@ -91,13 +93,13 @@ public class GatewayResourceTest extends AbstractResourceTest {
@Test
public void testIsExists() throws Exception {
assertTrue(gatewayResource.isExists(ResourceType.GATEWAY_WORKER, ServerSettings.getDefaultUser()));
- assertTrue(gatewayResource.isExists(ResourceType.EXPERIMENT, "testExpID"));
+ assertTrue(gatewayResource.isExists(ResourceType.EXPERIMENT, testExpID));
}
@Test
public void testGet() throws Exception {
assertNotNull(gatewayResource.get(ResourceType.GATEWAY_WORKER, ServerSettings.getDefaultUser()));
- assertNotNull(gatewayResource.get(ResourceType.EXPERIMENT, "testExpID"));
+ assertNotNull(gatewayResource.get(ResourceType.EXPERIMENT, testExpID));
}
@Test
@@ -109,8 +111,8 @@ public class GatewayResourceTest extends AbstractResourceTest {
@Test
public void testRemove() throws Exception {
- gatewayResource.remove(ResourceType.EXPERIMENT, "testExpID");
- assertFalse(gatewayResource.isExists(ResourceType.EXPERIMENT, "testExpID"));
+ gatewayResource.remove(ResourceType.EXPERIMENT, testExpID);
+ assertFalse(gatewayResource.isExists(ResourceType.EXPERIMENT, testExpID));
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/JobResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/JobResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/JobResourceTest.java
index 1bbf7d7..ede0278 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/JobResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/JobResourceTest.java
@@ -40,7 +40,7 @@ public class JobResourceTest extends AbstractResourceTest{
private ProcessResource processResource;
private TaskResource taskResource;
private JobResource jobResource;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID4";
private String processId = "processID";
private String taskId = "taskID";
private String jobId = "jobID";
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ProcessResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ProcessResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ProcessResourceTest.java
index 6349007..0474cf0 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ProcessResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/ProcessResourceTest.java
@@ -34,7 +34,7 @@ public class ProcessResourceTest extends AbstractResourceTest{
private ExperimentResource experimentResource;
private ProcessResource processResource;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID5";
private String processId = "processID";
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/TaskResourceTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/TaskResourceTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/TaskResourceTest.java
index 85d3501..5821a06 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/TaskResourceTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/TaskResourceTest.java
@@ -38,7 +38,7 @@ public class TaskResourceTest extends AbstractResourceTest{
private ExperimentResource experimentResource;
private ProcessResource processResource;
private TaskResource taskResource;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID6";
private String processId = "processID";
private String taskId = "taskID";
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/UserConfigurationDataTest.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/UserConfigurationDataTest.java b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/UserConfigurationDataTest.java
index 6387aa8..0d0072d 100644
--- a/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/UserConfigurationDataTest.java
+++ b/modules/registry/registry-core/src/test/java/org/apache/airavata/experiment/catalog/UserConfigurationDataTest.java
@@ -37,7 +37,7 @@ import static org.junit.Assert.assertTrue;
public class UserConfigurationDataTest extends AbstractResourceTest {
private ExperimentResource experimentResource;
private UserConfigurationDataResource userConfigurationData;
- private String experimentID = "testExpID";
+ private String experimentID = "testExpID7";
@Override
@Before
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
index 3f6c73f..d3068d8 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/FrameworkBootstrapping.java
@@ -60,7 +60,7 @@ public class FrameworkBootstrapping {
logger.info("Applications registered for each each gateway...");
experimentExecution = new ExperimentExecution(setup.getAiravata(), tokens, properties);
experimentExecution.createEchoExperiment();
- experimentExecution.createAmberExperiment();
+// experimentExecution.createAmberExperiment();
experimentExecution.launchExperiments();
experimentExecution.monitorExperiments();
}else if (regApps){
http://git-wip-us.apache.org/repos/asf/airavata/blob/d8cbbb13/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
----------------------------------------------------------------------
diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json b/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
index 6f9183c..5b674f9 100644
--- a/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
+++ b/modules/test-suite/multi-tenanted-airavata/src/main/resources/test-framework.json
@@ -32,7 +32,7 @@
],
"applications": [
{
- "name": "amber_sander",
+ "name": "Amber_Sander",
"inputs": {
"Heat-Restart-File": "/Users/chathuri/dev/airavata/source/php/inputs/AMBER_FILES1/02_Heat.rst",
"Parameter-Topology-File": "/Users/chathuri/dev/airavata/source/php/inputs/AMBER_FILES1/03_Prod.in",