From commits-return-19049-archive-asf-public=cust-asf.ponee.io@airavata.apache.org Mon Mar 12 16:21:11 2018 Return-Path: X-Original-To: archive-asf-public@cust-asf.ponee.io Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by mx-eu-01.ponee.io (Postfix) with SMTP id A415018067B for ; Mon, 12 Mar 2018 16:21:10 +0100 (CET) Received: (qmail 70995 invoked by uid 500); 12 Mar 2018 15:21:09 -0000 Mailing-List: contact commits-help@airavata.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@airavata.apache.org Delivered-To: mailing list commits@airavata.apache.org Received: (qmail 70981 invoked by uid 99); 12 Mar 2018 15:21:09 -0000 Received: from ec2-52-202-80-70.compute-1.amazonaws.com (HELO gitbox.apache.org) (52.202.80.70) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 12 Mar 2018 15:21:09 +0000 Received: by gitbox.apache.org (ASF Mail Server at gitbox.apache.org, from userid 33) id 16ECC807AF; Mon, 12 Mar 2018 15:21:09 +0000 (UTC) Date: Mon, 12 Mar 2018 15:21:09 +0000 To: "commits@airavata.apache.org" Subject: [airavata] 01/01: Merge branch 'helix-integration' into develop MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit From: dimuthuupe@apache.org In-Reply-To: <152086806895.18203.5310596656275030318@gitbox.apache.org> References: <152086806895.18203.5310596656275030318@gitbox.apache.org> X-Git-Host: gitbox.apache.org X-Git-Repo: airavata X-Git-Refname: refs/heads/develop X-Git-Reftype: branch X-Git-Rev: a03b8e538badec33acecf52b09597d9fffefa5be X-Git-NotificationType: diff X-Git-Multimail-Version: 1.5.dev Auto-Submitted: auto-generated Message-Id: <20180312152109.16ECC807AF@gitbox.apache.org> 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 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(-) -- To stop receiving notification emails like this one, please contact dimuthuupe@apache.org.