This is an automated email from the ASF dual-hosted git repository. dimuthuupe pushed a commit to branch helix-integration in repository https://gitbox.apache.org/repos/asf/airavata.git
commit 782b0e81242604961dba675fc02386698cce48b9 Author: dimuthu <[email protected]> AuthorDate: Mon Mar 5 23:18:03 2018 -0500 Refactoring --- .../airavata/helix/impl/participant/GlobalParticipant.java | 14 +++++++------- .../helix/impl/task/{ => completing}/CompletingTask.java | 4 +++- .../airavata/helix/impl/task/{ => env}/EnvSetupTask.java | 4 +++- .../helix/impl/task/{ => staging}/DataStagingTask.java | 4 +++- .../impl/task/{ => staging}/InputDataStagingTask.java | 4 +++- .../impl/task/{ => staging}/OutputDataStagingTask.java | 4 +++- .../submission/{task => }/DefaultJobSubmissionTask.java | 6 +++--- .../task/submission/{task => }/ForkJobSubmissionTask.java | 9 +++------ .../impl/task/submission/{task => }/JobSubmissionTask.java | 14 ++------------ .../task/submission/{task => }/LocalJobSubmissionTask.java | 9 ++++----- .../task/submission/{ => config}/GroovyMapBuilder.java | 2 +- .../impl/task/submission/{ => config}/GroovyMapData.java | 2 +- .../helix/impl/task/submission/config/JobFactory.java | 6 ++---- .../helix/impl/task/submission/{ => config}/Script.java | 2 +- .../helix/impl/task/submission/{ => config}/ScriptTag.java | 2 +- .../impl/task/submission/{ => config}/SubmissionUtil.java | 2 +- .../config/{imp => app}/ForkJobConfiguration.java | 2 +- .../impl/task/submission/config/{imp => app}/JobUtil.java | 2 +- .../config/{imp => app}/LSFJobConfiguration.java | 2 +- .../config/{imp => app}/PBSJobConfiguration.java | 2 +- .../config/{imp => app}/SlurmJobConfiguration.java | 2 +- .../config/{imp => app}/UGEJobConfiguration.java | 2 +- .../parser/AiravataCustomCommandOutputParser.java | 2 +- .../config/{imp => app}/parser/ForkOutputParser.java | 2 +- .../config/{imp => app}/parser/LSFOutputParser.java | 2 +- .../config/{imp => app}/parser/PBSOutputParser.java | 4 ++-- .../config/{imp => app}/parser/SlurmOutputParser.java | 4 ++-- .../config/{imp => app}/parser/UGEOutputParser.java | 3 +-- .../airavata/helix/impl/workflow/PostWorkflowManager.java | 6 ++---- .../airavata/helix/impl/workflow/PreWorkflowManager.java | 7 +++---- .../helix-spectator/src/main/resources/log4j.properties | 4 ++-- 31 files changed, 62 insertions(+), 72 deletions(-) diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java index fc3fbcb..4849934 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java @@ -15,13 +15,13 @@ import java.util.Map; public class GlobalParticipant extends HelixParticipant { private String[] taskClasses = { - "org.apache.airavata.helix.impl.task.EnvSetupTask", - "org.apache.airavata.helix.impl.task.InputDataStagingTask", - "org.apache.airavata.helix.impl.task.OutputDataStagingTask", - "org.apache.airavata.helix.impl.task.CompletingTask", - "org.apache.airavata.helix.impl.task.submission.task.ForkJobSubmissionTask", - "org.apache.airavata.helix.impl.task.submission.task.DefaultJobSubmissionTask", - "org.apache.airavata.helix.impl.task.submission.task.LocalJobSubmissionTask" + "org.apache.airavata.helix.impl.task.env.EnvSetupTask", + "org.apache.airavata.helix.impl.task.staging.InputDataStagingTask", + "org.apache.airavata.helix.impl.task.staging.OutputDataStagingTask", + "org.apache.airavata.helix.impl.task.completing.CompletingTask", + "org.apache.airavata.helix.impl.task.submission.ForkJobSubmissionTask", + "org.apache.airavata.helix.impl.task.submission.DefaultJobSubmissionTask", + "org.apache.airavata.helix.impl.task.submission.LocalJobSubmissionTask" }; public Map<String, TaskFactory> getTaskFactory() { diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/CompletingTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java similarity index 85% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/CompletingTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java index d036258..f32d019 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/CompletingTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java @@ -1,5 +1,7 @@ -package org.apache.airavata.helix.impl.task; +package org.apache.airavata.helix.impl.task.completing; +import org.apache.airavata.helix.impl.task.AiravataTask; +import org.apache.airavata.helix.impl.task.TaskContext; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.status.ProcessState; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/EnvSetupTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java similarity index 92% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/EnvSetupTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java index 0ad5698..6eb1722 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/EnvSetupTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java @@ -1,6 +1,8 @@ -package org.apache.airavata.helix.impl.task; +package org.apache.airavata.helix.impl.task.env; import org.apache.airavata.agents.api.AgentAdaptor; +import org.apache.airavata.helix.impl.task.AiravataTask; +import org.apache.airavata.helix.impl.task.TaskContext; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.status.ProcessState; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/DataStagingTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java similarity index 96% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/DataStagingTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java index 594cbc9..76b4cb3 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/DataStagingTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java @@ -1,9 +1,11 @@ -package org.apache.airavata.helix.impl.task; +package org.apache.airavata.helix.impl.task.staging; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.AgentException; import org.apache.airavata.agents.api.StorageResourceAdaptor; import org.apache.airavata.common.utils.ServerSettings; +import org.apache.airavata.helix.impl.task.AiravataTask; +import org.apache.airavata.helix.impl.task.TaskOnFailException; import org.apache.airavata.helix.task.api.support.AdaptorSupport; import org.apache.airavata.model.appcatalog.storageresource.StorageResourceDescription; import org.apache.airavata.model.task.DataStagingTaskModel; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/InputDataStagingTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java similarity index 96% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/InputDataStagingTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java index 2c885f4..de2aeac 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/InputDataStagingTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java @@ -1,8 +1,10 @@ -package org.apache.airavata.helix.impl.task; +package org.apache.airavata.helix.impl.task.staging; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.AgentException; import org.apache.airavata.agents.api.StorageResourceAdaptor; +import org.apache.airavata.helix.impl.task.TaskContext; +import org.apache.airavata.helix.impl.task.TaskOnFailException; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.appcatalog.storageresource.StorageResourceDescription; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/OutputDataStagingTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/OutputDataStagingTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java index 738d955..7d657cb 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/OutputDataStagingTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java @@ -1,8 +1,10 @@ -package org.apache.airavata.helix.impl.task; +package org.apache.airavata.helix.impl.task.staging; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.AgentException; import org.apache.airavata.agents.api.StorageResourceAdaptor; +import org.apache.airavata.helix.impl.task.TaskContext; +import org.apache.airavata.helix.impl.task.TaskOnFailException; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.appcatalog.storageresource.StorageResourceDescription; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/DefaultJobSubmissionTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/DefaultJobSubmissionTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java index 9b015bb..82316f0 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/DefaultJobSubmissionTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java @@ -1,11 +1,11 @@ -package org.apache.airavata.helix.impl.task.submission.task; +package org.apache.airavata.helix.impl.task.submission; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.JobSubmissionOutput; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.helix.impl.task.TaskContext; -import org.apache.airavata.helix.impl.task.submission.GroovyMapBuilder; -import org.apache.airavata.helix.impl.task.submission.GroovyMapData; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapBuilder; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapData; import org.apache.airavata.helix.impl.task.submission.config.RawCommandInfo; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/ForkJobSubmissionTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java similarity index 90% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/ForkJobSubmissionTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java index afce74e..06ce0ea 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/ForkJobSubmissionTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java @@ -1,21 +1,18 @@ -package org.apache.airavata.helix.impl.task.submission.task; +package org.apache.airavata.helix.impl.task.submission; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.JobSubmissionOutput; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.helix.impl.task.TaskContext; -import org.apache.airavata.helix.impl.task.submission.GroovyMapBuilder; -import org.apache.airavata.helix.impl.task.submission.GroovyMapData; -import org.apache.airavata.helix.impl.task.submission.SubmissionUtil; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapBuilder; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapData; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.job.JobModel; import org.apache.airavata.model.status.JobState; import org.apache.airavata.model.status.JobStatus; -import org.apache.commons.io.FileUtils; import org.apache.helix.task.TaskResult; -import java.io.File; import java.util.Arrays; @TaskDef(name = "Fork Job Submission") diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/JobSubmissionTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java similarity index 91% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/JobSubmissionTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java index 4fed22d..7bf5034 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/JobSubmissionTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission.task; +package org.apache.airavata.helix.impl.task.submission; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.CommandOutput; @@ -7,20 +7,11 @@ import org.apache.airavata.common.exception.ApplicationSettingsException; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.common.utils.ServerSettings; import org.apache.airavata.helix.impl.task.AiravataTask; -import org.apache.airavata.helix.impl.task.submission.GroovyMapData; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapData; import org.apache.airavata.helix.impl.task.submission.config.JobFactory; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.RawCommandInfo; import org.apache.airavata.messaging.core.MessageContext; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; -import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription; -import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface; -import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol; -import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; -import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile; -import org.apache.airavata.model.appcatalog.userresourceprofile.UserComputeResourcePreference; -import org.apache.airavata.model.appcatalog.userresourceprofile.UserResourceProfile; -import org.apache.airavata.model.commons.ErrorModel; import org.apache.airavata.model.job.JobModel; import org.apache.airavata.model.messaging.event.JobIdentifier; import org.apache.airavata.model.messaging.event.JobStatusChangeEvent; @@ -36,7 +27,6 @@ import org.apache.helix.HelixManager; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; import org.apache.zookeeper.CreateMode; -import org.apache.zookeeper.ZooDefs; import java.io.File; import java.security.SecureRandom; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/LocalJobSubmissionTask.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java similarity index 90% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/LocalJobSubmissionTask.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java index 3e51b4f..db582c3 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/task/LocalJobSubmissionTask.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java @@ -1,13 +1,12 @@ -package org.apache.airavata.helix.impl.task.submission.task; +package org.apache.airavata.helix.impl.task.submission; import org.apache.airavata.agents.api.AgentAdaptor; import org.apache.airavata.agents.api.JobSubmissionOutput; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.helix.impl.task.TaskContext; -import org.apache.airavata.helix.impl.task.submission.GroovyMapBuilder; -import org.apache.airavata.helix.impl.task.submission.GroovyMapData; -import org.apache.airavata.helix.impl.task.submission.SubmissionUtil; -import org.apache.airavata.helix.impl.task.submission.task.JobSubmissionTask; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapBuilder; +import org.apache.airavata.helix.impl.task.submission.config.GroovyMapData; +import org.apache.airavata.helix.impl.task.submission.config.SubmissionUtil; import org.apache.airavata.helix.task.api.TaskHelper; import org.apache.airavata.helix.task.api.annotation.TaskDef; import org.apache.airavata.model.job.JobModel; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapBuilder.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java similarity index 99% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapBuilder.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java index 2119755..8b226ed 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapBuilder.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission; +package org.apache.airavata.helix.impl.task.submission.config; import groovy.text.GStringTemplateEngine; import groovy.text.TemplateEngine; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapData.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java similarity index 99% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapData.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java index 6ebde21..5414a46 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/GroovyMapData.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission; +package org.apache.airavata.helix.impl.task.submission.config; import groovy.lang.Writable; import groovy.text.GStringTemplateEngine; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java index b04ffd8..4ac0f80 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java @@ -1,12 +1,10 @@ package org.apache.airavata.helix.impl.task.submission.config; -import org.apache.airavata.helix.impl.task.submission.config.imp.*; -import org.apache.airavata.helix.impl.task.submission.config.imp.parser.*; +import org.apache.airavata.helix.impl.task.submission.config.app.*; +import org.apache.airavata.helix.impl.task.submission.config.app.parser.*; import org.apache.airavata.model.appcatalog.computeresource.*; -import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory; import org.apache.airavata.registry.cpi.AppCatalog; import org.apache.airavata.registry.cpi.AppCatalogException; -import org.apache.airavata.registry.cpi.RegistryException; public class JobFactory { diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/Script.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/Script.java similarity index 95% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/Script.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/Script.java index 208e9e5..d68fa1b 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/Script.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/Script.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission; +package org.apache.airavata.helix.impl.task.submission.config; public enum Script { diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ScriptTag.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java similarity index 83% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ScriptTag.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java index c03c11f..44f6e22 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ScriptTag.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission; +package org.apache.airavata.helix.impl.task.submission.config; import java.lang.annotation.ElementType; import java.lang.annotation.Retention; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/SubmissionUtil.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/SubmissionUtil.java similarity index 69% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/SubmissionUtil.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/SubmissionUtil.java index e2cbfee..7846ac8 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/SubmissionUtil.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/SubmissionUtil.java @@ -1,4 +1,4 @@ -package org.apache.airavata.helix.impl.task.submission; +package org.apache.airavata.helix.impl.task.submission.config; import java.io.File; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/ForkJobConfiguration.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/ForkJobConfiguration.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java index d25f17f..22237bd 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/ForkJobConfiguration.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/JobUtil.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java similarity index 97% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/JobUtil.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java index 36bce60..655e338 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/JobUtil.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.model.status.JobState; import org.slf4j.Logger; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/LSFJobConfiguration.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/LSFJobConfiguration.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java index bccd7ee..bec46a3 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/LSFJobConfiguration.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/PBSJobConfiguration.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/PBSJobConfiguration.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java index aeedeb9..52c132e 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/PBSJobConfiguration.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/SlurmJobConfiguration.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/SlurmJobConfiguration.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java index fc431ce..42f5cfe 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/SlurmJobConfiguration.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/UGEJobConfiguration.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/UGEJobConfiguration.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java index 6a12966..2befbf9 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/UGEJobConfiguration.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp; +package org.apache.airavata.helix.impl.task.submission.config.app; import org.apache.airavata.helix.impl.task.submission.config.JobManagerConfiguration; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/AiravataCustomCommandOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java similarity index 96% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/AiravataCustomCommandOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java index c3a5a2e..d622b3e 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/AiravataCustomCommandOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; import org.apache.airavata.model.status.JobStatus; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/ForkOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java similarity index 96% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/ForkOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java index a4f48cc..2b67cff 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/ForkOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/LSFOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java similarity index 98% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/LSFOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java index 0bf812f..7f3638b 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/LSFOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java @@ -17,7 +17,7 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; import org.apache.airavata.model.status.JobState; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/PBSOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java similarity index 97% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/PBSOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java index 3be8c8a..d82673b 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/PBSOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java @@ -17,10 +17,10 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; -import org.apache.airavata.helix.impl.task.submission.config.imp.JobUtil; +import org.apache.airavata.helix.impl.task.submission.config.app.JobUtil; import org.apache.airavata.model.status.JobStatus; import org.slf4j.Logger; import org.slf4j.LoggerFactory; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/SlurmOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/SlurmOutputParser.java similarity index 97% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/SlurmOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/SlurmOutputParser.java index 3ebbcfd..459d4f7 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/SlurmOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/SlurmOutputParser.java @@ -17,10 +17,10 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; -import org.apache.airavata.helix.impl.task.submission.config.imp.JobUtil; +import org.apache.airavata.helix.impl.task.submission.config.app.JobUtil; import org.apache.airavata.model.status.JobState; import org.apache.airavata.model.status.JobStatus; import org.slf4j.Logger; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/UGEOutputParser.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java similarity index 96% rename from modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/UGEOutputParser.java rename to modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java index 0f457ff..b454ea5 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/imp/parser/UGEOutputParser.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java @@ -17,10 +17,9 @@ * specific language governing permissions and limitations * under the License. */ -package org.apache.airavata.helix.impl.task.submission.config.imp.parser; +package org.apache.airavata.helix.impl.task.submission.config.app.parser; import org.apache.airavata.helix.impl.task.submission.config.OutputParser; -import org.apache.airavata.helix.impl.task.submission.config.imp.parser.PBSOutputParser; import org.apache.airavata.model.status.JobState; import org.apache.airavata.model.status.JobStatus; import org.slf4j.Logger; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java index b4ffacf..b0de43a 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java @@ -6,8 +6,8 @@ import org.apache.airavata.common.utils.AiravataUtils; import org.apache.airavata.common.utils.ServerSettings; import org.apache.airavata.helix.core.OutPort; import org.apache.airavata.helix.impl.task.*; -import org.apache.airavata.helix.impl.task.submission.task.DefaultJobSubmissionTask; -import org.apache.airavata.helix.impl.task.submission.task.JobSubmissionTask; +import org.apache.airavata.helix.impl.task.completing.CompletingTask; +import org.apache.airavata.helix.impl.task.staging.OutputDataStagingTask; import org.apache.airavata.helix.workflow.WorkflowManager; import org.apache.airavata.job.monitor.kafka.JobStatusResultDeserializer; import org.apache.airavata.job.monitor.parser.JobStatusResult; @@ -17,7 +17,6 @@ import org.apache.airavata.messaging.core.Publisher; import org.apache.airavata.messaging.core.Type; import org.apache.airavata.messaging.core.impl.RabbitMQPublisher; import org.apache.airavata.model.experiment.ExperimentModel; -import org.apache.airavata.model.job.JobModel; import org.apache.airavata.model.messaging.event.JobIdentifier; import org.apache.airavata.model.messaging.event.JobStatusChangeEvent; import org.apache.airavata.model.messaging.event.MessageType; @@ -36,7 +35,6 @@ import org.apache.kafka.clients.consumer.Consumer; import org.apache.kafka.clients.consumer.ConsumerConfig; import org.apache.kafka.clients.consumer.ConsumerRecords; import org.apache.kafka.clients.consumer.KafkaConsumer; -import org.apache.kafka.common.serialization.LongDeserializer; import org.apache.kafka.common.serialization.StringDeserializer; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; diff --git a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java index 3030375..ac29c9d 100644 --- a/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java +++ b/modules/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java @@ -5,9 +5,9 @@ import org.apache.airavata.common.utils.ServerSettings; import org.apache.airavata.common.utils.ThriftUtils; import org.apache.airavata.helix.core.OutPort; import org.apache.airavata.helix.impl.task.AiravataTask; -import org.apache.airavata.helix.impl.task.EnvSetupTask; -import org.apache.airavata.helix.impl.task.InputDataStagingTask; -import org.apache.airavata.helix.impl.task.submission.task.DefaultJobSubmissionTask; +import org.apache.airavata.helix.impl.task.env.EnvSetupTask; +import org.apache.airavata.helix.impl.task.staging.InputDataStagingTask; +import org.apache.airavata.helix.impl.task.submission.DefaultJobSubmissionTask; import org.apache.airavata.helix.workflow.WorkflowManager; import org.apache.airavata.messaging.core.*; import org.apache.airavata.model.experiment.ExperimentModel; @@ -19,7 +19,6 @@ import org.apache.airavata.model.task.TaskTypes; import org.apache.airavata.registry.core.experiment.catalog.impl.RegistryFactory; import org.apache.airavata.registry.cpi.ExperimentCatalog; import org.apache.airavata.registry.cpi.ExperimentCatalogModelType; -import org.apache.airavata.registry.cpi.RegistryException; import org.apache.log4j.LogManager; import org.apache.log4j.Logger; import org.apache.thrift.TBase; diff --git a/modules/helix-spectator/src/main/resources/log4j.properties b/modules/helix-spectator/src/main/resources/log4j.properties index dba82a1..04aa72a 100644 --- a/modules/helix-spectator/src/main/resources/log4j.properties +++ b/modules/helix-spectator/src/main/resources/log4j.properties @@ -3,8 +3,8 @@ log4j.rootLogger=INFO, A1 log4j.category.org.apache.helix=WARN log4j.category.org.apache.zookeeper=WARN -log4j.category.org.apache.airavata.helix.impl.task.submission.GroovyMapData=TRACE -log4j.category.org.apache.airavata.helix.impl.task.submission.task.JobSubmissionTask=DEBUG +log4j.category.org.apache.airavata.helix.impl.task.submission.config.GroovyMapData=TRACE +log4j.category.org.apache.airavata.helix.impl.task.submission.JobSubmissionTask=DEBUG # A1 is set to be a ConsoleAppender. log4j.appender.A1=org.apache.log4j.ConsoleAppender -- To stop receiving notification emails like this one, please contact [email protected].
