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
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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
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modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/OutputParser.java
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modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/RawCommandInfo.java
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modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/Script.java
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modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java
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modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/SubmissionUtil.java
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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
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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
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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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