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From dimuthu...@apache.org
Subject [airavata] 01/01: Merge branch 'helix-integration' into develop
Date Mon, 12 Mar 2018 15:21:09 GMT
This is an automated email from the ASF dual-hosted git repository.

dimuthuupe pushed a commit to branch develop
in repository https://gitbox.apache.org/repos/asf/airavata.git

commit a03b8e538badec33acecf52b09597d9fffefa5be
Merge: 7124801 07e8984
Author: dimuthu <dimuthu.upeksha2@gmail.com>
AuthorDate: Mon Mar 12 11:12:45 2018 -0400

    Merge branch 'helix-integration' into develop

 modules/airavata-helix-distribution/pom.xml        |  76 ++
 .../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               |  46 ++
 .../main/resources/conf/airavata-server.properties | 275 +++++++
 .../src/main/resources/conf/cred_store.jks         | Bin 0 -> 499 bytes
 .../src/main/resources/conf/log4j.properties       |  29 +
 modules/airavata-helix/agent-api/pom.xml           |  68 ++
 .../apache/airavata/agents/api/AdaptorParams.java  |  45 +
 .../java/org/apache/airavata/agents/api/Agent.java |  29 +
 .../apache/airavata/agents/api/AgentAdaptor.java   |  46 ++
 .../apache/airavata/agents/api/AgentException.java |  49 ++
 .../org/apache/airavata/agents/api/AgentStore.java | 122 +++
 .../apache/airavata/agents/api/CommandOutput.java  |  35 +
 .../airavata/agents/api/JobSubmissionOutput.java   | 102 +++
 .../agents/api/StorageResourceAdaptor.java         |  26 +
 modules/airavata-helix/agent-impl/pom.xml          |  48 ++
 .../airavata-helix/agent-impl/ssh-agent/pom.xml    |  73 ++
 .../helix/agent/local/LocalAgentAdaptor.java       |  71 ++
 .../airavata/helix/agent/ssh/SshAdaptorParams.java | 135 +++
 .../airavata/helix/agent/ssh/SshAgentAdaptor.java  | 595 ++++++++++++++
 .../helix/agent/ssh/StandardOutReader.java         |  70 ++
 .../agent/storage/StorageResourceAdaptorImpl.java  | 104 +++
 modules/airavata-helix/helix-spectator/pom.xml     |  90 ++
 .../helix/impl/controller/HelixController.java     | 110 +++
 .../helix/impl/participant/GlobalParticipant.java  |  96 +++
 .../airavata/helix/impl/task/AiravataTask.java     | 412 ++++++++++
 .../airavata/helix/impl/task/TaskContext.java      | 902 +++++++++++++++++++++
 .../helix/impl/task/TaskOnFailException.java       |  46 ++
 .../helix/impl/task/completing/CompletingTask.java |  48 ++
 .../airavata/helix/impl/task/env/EnvSetupTask.java |  62 ++
 .../helix/impl/task/staging/DataStagingTask.java   | 116 +++
 .../impl/task/staging/InputDataStagingTask.java    | 133 +++
 .../impl/task/staging/OutputDataStagingTask.java   | 224 +++++
 .../task/submission/DefaultJobSubmissionTask.java  | 219 +++++
 .../task/submission/ForkJobSubmissionTask.java     | 103 +++
 .../impl/task/submission/JobSubmissionTask.java    | 213 +++++
 .../task/submission/LocalJobSubmissionTask.java    | 106 +++
 .../task/submission/config/GroovyMapBuilder.java   | 425 ++++++++++
 .../impl/task/submission/config/GroovyMapData.java | 485 +++++++++++
 .../impl/task/submission/config/JobFactory.java    | 119 +++
 .../submission/config/JobManagerConfiguration.java |  48 ++
 .../impl/task/submission/config/OutputParser.java  |  60 ++
 .../task/submission/config/RawCommandInfo.java     |  41 +
 .../helix/impl/task/submission/config/Script.java  |  62 ++
 .../impl/task/submission/config/ScriptTag.java     |  32 +
 .../task/submission/config/SubmissionUtil.java     |  29 +
 .../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   | 286 +++++++
 .../helix/impl/workflow/PreWorkflowManager.java    | 164 ++++
 .../src/main/resources/airavata-server.properties  | 275 +++++++
 .../src/main/resources/log4j.properties            |  29 +
 modules/airavata-helix/pom.xml                     |  46 ++
 modules/airavata-helix/task-api/pom.xml            |  62 ++
 .../apache/airavata/helix/task/api/TaskHelper.java |  32 +
 .../helix/task/api/annotation/TaskDef.java         |  37 +
 .../helix/task/api/annotation/TaskOutPort.java     |  37 +
 .../helix/task/api/annotation/TaskParam.java       |  39 +
 .../helix/task/api/support/AdaptorSupport.java     |  38 +
 .../src/main/resources/application.properties      |   3 +
 .../task-api/src/main/resources/log4j.properties   |   9 +
 modules/airavata-helix/task-core/pom.xml           |  73 ++
 .../apache/airavata/helix/core/AbstractTask.java   | 137 ++++
 .../org/apache/airavata/helix/core/OutPort.java    |  63 ++
 .../helix/core/participant/HelixParticipant.java   | 191 +++++
 .../helix/core/support/AdaptorSupportImpl.java     |  65 ++
 .../helix/core/support/TaskHelperImpl.java         |  36 +
 .../airavata/helix/core/util/PropertyResolver.java |  63 ++
 .../apache/airavata/helix/core/util/TaskUtil.java  | 128 +++
 modules/airavata-helix/workflow-impl/pom.xml       |  65 ++
 .../airavata/helix/workflow/WorkflowManager.java   | 123 +++
 modules/job-monitor/pom.xml                        |  64 ++
 .../airavata/job/monitor/EmailBasedMonitor.java    | 331 ++++++++
 .../monitor/kafka/JobStatusResultDeserializer.java |  53 ++
 .../monitor/kafka/JobStatusResultSerializer.java   |  48 ++
 .../job/monitor/kafka/MessageProducer.java         |  56 ++
 .../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                                            |   5 +-
 108 files changed, 11950 insertions(+), 29 deletions(-)

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