This is an automated email from the ASF dual-hosted git repository.

dimuthuupe pushed a change to branch helix-integration
in repository https://gitbox.apache.org/repos/asf/airavata.git.


    from 8632150  changing dev email address to devjobs
     new c9a1b06  Initial helix migration
     new ef94a5a  Building groovy map
     new b199bc2  Stabalizing DefaultJobSubmission Task
     new cb54e4d  Fixing env setup task
     new 7350b25  Implementing DataStaging tasks
     new 573dbab  Fixing bugs in pre workflow
     new 4e1c1b0  Standalone email monitor initial implementation
     new 42ff5f4  Implementing post workflow
     new ca45564  Configuring pre workflow manager to read from rabbitmq launch 
queue
     new 1c3a5d4  Improving status publishing
     new f51f1f1  Thread safe entity manager factory
     new 71075e0  Logging improvements
     new 782b0e8  Refactoring
     new e864db3  Adding deployment module to helix workflows
     new a726a98  Moving helix-spectator module to airavata-helix module
     new 0053413  Moving helix-spectator module to airavata-helix module
     new 71b294e  Refactoring

The 17 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "add" were already present in the repository and have only
been added to this reference.


Summary of changes:
 modules/airavata-helix-distribution/pom.xml        |  55 ++
 .../src/main/assembly/bin-assembly.xml             | 111 +++
 .../resources/bin/airavata-controller-start.sh     |  99 +++
 .../main/resources/bin/airavata-controller-stop.sh |  71 ++
 .../main/resources/bin/airavata-monitor-start.sh   |  99 +++
 .../resources/bin/airavata-participant-start.sh    |  99 +++
 .../resources/bin/airavata-participant-stop.sh     |  71 ++
 .../main/resources/bin/airavata-post-wm-start.sh   |  99 +++
 .../main/resources/bin/airavata-post-wm-stop.sh    |  71 ++
 .../main/resources/bin/airavata-pre-wm-start.sh    |  99 +++
 .../src/main/resources/bin/airavata-pre-wm-stop.sh |  71 ++
 .../src/main/resources/bin/setenv.sh               |   0
 .../main/resources/conf/airavata-server.properties | 345 ++++++++
 .../src/main/resources/conf/application.properties |   3 +
 .../src/main/resources/conf/cred_store.jks         | Bin 0 -> 499 bytes
 .../src/main/resources/conf/log4j.properties       |  13 +
 modules/airavata-helix/agent-api/pom.xml           |  47 ++
 .../apache/airavata/agents/api/AdaptorParams.java  |  26 +
 .../java/org/apache/airavata/agents/api/Agent.java |  10 +
 .../apache/airavata/agents/api/AgentAdaptor.java   |  27 +
 .../apache/airavata/agents/api/AgentException.java |  30 +
 .../org/apache/airavata/agents/api/AgentStore.java | 103 +++
 .../apache/airavata/agents/api/CommandOutput.java  |  16 +
 .../airavata/agents/api/JobSubmissionOutput.java   |  83 ++
 .../agents/api/StorageResourceAdaptor.java         |   7 +
 modules/airavata-helix/agent-impl/pom.xml          |  27 +
 .../airavata-helix/agent-impl/ssh-agent/pom.xml    |  73 ++
 .../helix/agent/local/LocalAgentAdaptor.java       |  52 ++
 .../airavata/helix/agent/ssh/SshAdaptorParams.java | 116 +++
 .../airavata/helix/agent/ssh/SshAgentAdaptor.java  | 576 ++++++++++++++
 .../helix/agent/ssh/StandardOutReader.java         |  51 ++
 .../agent/storage/StorageResourceAdaptorImpl.java  |  85 ++
 modules/airavata-helix/helix-spectator/pom.xml     |  69 ++
 .../helix/impl/controller/HelixController.java     |  91 +++
 .../helix/impl/participant/GlobalParticipant.java  |  77 ++
 .../airavata/helix/impl/task/AiravataTask.java     | 335 ++++++++
 .../airavata/helix/impl/task/TaskContext.java      | 883 +++++++++++++++++++++
 .../helix/impl/task/TaskOnFailException.java       |  27 +
 .../helix/impl/task/completing/CompletingTask.java |  29 +
 .../airavata/helix/impl/task/env/EnvSetupTask.java |  43 +
 .../helix/impl/task/staging/DataStagingTask.java   |  97 +++
 .../impl/task/staging/InputDataStagingTask.java    | 114 +++
 .../impl/task/staging/OutputDataStagingTask.java   | 202 +++++
 .../task/submission/DefaultJobSubmissionTask.java  | 200 +++++
 .../task/submission/ForkJobSubmissionTask.java     |  84 ++
 .../impl/task/submission/JobSubmissionTask.java    | 195 +++++
 .../task/submission/LocalJobSubmissionTask.java    |  87 ++
 .../task/submission/config/GroovyMapBuilder.java   | 406 ++++++++++
 .../impl/task/submission/config/GroovyMapData.java | 466 +++++++++++
 .../impl/task/submission/config/JobFactory.java    | 100 +++
 .../submission/config/JobManagerConfiguration.java |  29 +
 .../impl/task/submission/config/OutputParser.java  |  41 +
 .../task/submission/config/RawCommandInfo.java     |  22 +
 .../helix/impl/task/submission/config/Script.java  |  43 +
 .../impl/task/submission/config/ScriptTag.java     |  13 +
 .../task/submission/config/SubmissionUtil.java     |  10 +
 .../config/app/ForkJobConfiguration.java           | 113 +++
 .../impl/task/submission/config/app/JobUtil.java   |  58 ++
 .../submission/config/app/LSFJobConfiguration.java | 120 +++
 .../submission/config/app/PBSJobConfiguration.java | 122 +++
 .../config/app/SlurmJobConfiguration.java          | 117 +++
 .../submission/config/app/UGEJobConfiguration.java | 117 +++
 .../parser/AiravataCustomCommandOutputParser.java  |  56 ++
 .../config/app/parser/ForkOutputParser.java        |  58 ++
 .../config/app/parser/LSFOutputParser.java         | 132 +++
 .../config/app/parser/PBSOutputParser.java         | 142 ++++
 .../config/app/parser/SlurmOutputParser.java       | 137 ++++
 .../config/app/parser/UGEOutputParser.java         | 107 +++
 .../helix/impl/workflow/PostWorkflowManager.java   | 266 +++++++
 .../helix/impl/workflow/PreWorkflowManager.java    | 145 ++++
 .../src/main/resources/airavata-server.properties  | 270 +++++++
 .../src/main/resources/application.properties      |   3 +
 .../src/main/resources/log4j.properties            |  13 +
 modules/airavata-helix/pom.xml                     |  25 +
 modules/airavata-helix/task-api/pom.xml            |  41 +
 .../apache/airavata/helix/task/api/TaskHelper.java |  14 +
 .../helix/task/api/annotation/TaskDef.java         |  18 +
 .../helix/task/api/annotation/TaskOutPort.java     |  18 +
 .../helix/task/api/annotation/TaskParam.java       |  20 +
 .../helix/task/api/support/AdaptorSupport.java     |  19 +
 .../src/main/resources/application.properties      |   3 +
 .../task-api/src/main/resources/log4j.properties   |   9 +
 modules/airavata-helix/task-core/pom.xml           |  52 ++
 .../apache/airavata/helix/core/AbstractTask.java   | 118 +++
 .../org/apache/airavata/helix/core/OutPort.java    |  44 +
 .../helix/core/participant/HelixParticipant.java   | 172 ++++
 .../helix/core/support/AdaptorSupportImpl.java     |  46 ++
 .../helix/core/support/TaskHelperImpl.java         |  17 +
 .../airavata/helix/core/util/PropertyResolver.java |  44 +
 .../apache/airavata/helix/core/util/TaskUtil.java  | 106 +++
 modules/airavata-helix/workflow-impl/pom.xml       |  44 +
 .../airavata/helix/workflow/SimpleWorkflow.java    |  40 +
 .../airavata/helix/workflow/WorkflowManager.java   | 104 +++
 modules/job-monitor/pom.xml                        |  43 +
 .../airavata/job/monitor/EmailBasedMonitor.java    | 312 ++++++++
 .../monitor/kafka/JobStatusResultDeserializer.java |  34 +
 .../monitor/kafka/JobStatusResultSerializer.java   |  29 +
 .../job/monitor/kafka/MessageProducer.java         |  37 +
 .../monitor/parser/AiravataCustomMailParser.java   |  77 ++
 .../airavata/job/monitor/parser/EmailParser.java   |  34 +
 .../job/monitor/parser/JobStatusResult.java        |  63 ++
 .../job/monitor/parser/LSFEmailParser.java         |  78 ++
 .../job/monitor/parser/PBSEmailParser.java         | 105 +++
 .../job/monitor/parser/ResourceConfig.java         |  54 ++
 .../job/monitor/parser/SLURMEmailParser.java       |  83 ++
 .../job/monitor/parser/UGEEmailParser.java         | 109 +++
 .../src/main/resources/airavata-server.properties  | 334 ++++++++
 .../src/main/resources/email-config.yaml           |  20 +
 .../src/main/resources/log4j.properties            |   9 +
 .../core/app/catalog/util/AppCatalogJPAUtils.java  |  61 +-
 pom.xml                                            |   8 +-
 111 files changed, 10689 insertions(+), 29 deletions(-)
 create mode 100644 modules/airavata-helix-distribution/pom.xml
 create mode 100644 
modules/airavata-helix-distribution/src/main/assembly/bin-assembly.xml
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-controller-start.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-controller-stop.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-monitor-start.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-participant-start.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-participant-stop.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-post-wm-start.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-post-wm-stop.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-pre-wm-start.sh
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/bin/airavata-pre-wm-stop.sh
 copy modules/{distribution => 
airavata-helix-distribution}/src/main/resources/bin/setenv.sh (100%)
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/conf/airavata-server.properties
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/conf/application.properties
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/conf/cred_store.jks
 create mode 100644 
modules/airavata-helix-distribution/src/main/resources/conf/log4j.properties
 create mode 100644 modules/airavata-helix/agent-api/pom.xml
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AdaptorParams.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/Agent.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentAdaptor.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentException.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentStore.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/CommandOutput.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/JobSubmissionOutput.java
 create mode 100644 
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/StorageResourceAdaptor.java
 create mode 100644 modules/airavata-helix/agent-impl/pom.xml
 create mode 100644 modules/airavata-helix/agent-impl/ssh-agent/pom.xml
 create mode 100644 
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/local/LocalAgentAdaptor.java
 create mode 100644 
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/SshAdaptorParams.java
 create mode 100644 
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/SshAgentAdaptor.java
 create mode 100644 
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/StandardOutReader.java
 create mode 100644 
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/storage/StorageResourceAdaptorImpl.java
 create mode 100644 modules/airavata-helix/helix-spectator/pom.xml
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/controller/HelixController.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/AiravataTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/TaskContext.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/TaskOnFailException.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobManagerConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/OutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/RawCommandInfo.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/Script.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/SubmissionUtil.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/SlurmOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/resources/airavata-server.properties
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/resources/application.properties
 create mode 100644 
modules/airavata-helix/helix-spectator/src/main/resources/log4j.properties
 create mode 100644 modules/airavata-helix/pom.xml
 create mode 100644 modules/airavata-helix/task-api/pom.xml
 create mode 100644 
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/TaskHelper.java
 create mode 100644 
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskDef.java
 create mode 100644 
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskOutPort.java
 create mode 100644 
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskParam.java
 create mode 100644 
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/support/AdaptorSupport.java
 create mode 100644 
modules/airavata-helix/task-api/src/main/resources/application.properties
 create mode 100644 
modules/airavata-helix/task-api/src/main/resources/log4j.properties
 create mode 100644 modules/airavata-helix/task-core/pom.xml
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/AbstractTask.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/OutPort.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/participant/HelixParticipant.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/AdaptorSupportImpl.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/TaskHelperImpl.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/util/PropertyResolver.java
 create mode 100644 
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/util/TaskUtil.java
 create mode 100644 modules/airavata-helix/workflow-impl/pom.xml
 create mode 100644 
modules/airavata-helix/workflow-impl/src/main/java/org/apache/airavata/helix/workflow/SimpleWorkflow.java
 create mode 100644 
modules/airavata-helix/workflow-impl/src/main/java/org/apache/airavata/helix/workflow/WorkflowManager.java
 create mode 100644 modules/job-monitor/pom.xml
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/EmailBasedMonitor.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/kafka/JobStatusResultDeserializer.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/kafka/JobStatusResultSerializer.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/kafka/MessageProducer.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/AiravataCustomMailParser.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/EmailParser.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/JobStatusResult.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/LSFEmailParser.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/PBSEmailParser.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/ResourceConfig.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/SLURMEmailParser.java
 create mode 100644 
modules/job-monitor/src/main/java/org/apache/airavata/job/monitor/parser/UGEEmailParser.java
 create mode 100644 
modules/job-monitor/src/main/resources/airavata-server.properties
 create mode 100644 modules/job-monitor/src/main/resources/email-config.yaml
 create mode 100644 modules/job-monitor/src/main/resources/log4j.properties

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