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Thu, 24 Sep 2015 15:57:28 +0000 (UTC) Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: chathuri@apache.org To: commits@airavata.apache.org Message-Id: <39a911678bfb4f898824d3face1aee7f@git.apache.org> X-Mailer: ASF-Git Admin Mailer Subject: airavata git commit: JPA issues and enabling gordon mpi jobs Date: Thu, 24 Sep 2015 15:57:28 +0000 (UTC) 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 Authored: Thu Sep 24 11:57:22 2015 -0400 Committer: Chathuri Wimalasena 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",