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Posted to commits@airavata.apache.org by ya...@apache.org on 2026/03/25 21:32:15 UTC
(airavata) branch feat/svclayer-services updated (dd9da642fa -> 2fb23e7b4d)
This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch feat/svclayer-services
in repository https://gitbox.apache.org/repos/asf/airavata.git
discard dd9da642fa feat(services): add service layer, domain models, and legacy cleanup
add 2fb23e7b4d refactor: remove legacy modules, Thrift stubs, and dev-tools
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Summary of changes:
{conf => .devcontainer}/keycloak/keycloak.conf | 3 +-
airavata-api/.dockerignore | 27 -
airavata-api/.mvn/extensions.xml | 8 -
airavata-api/.mvn/jvm.config | 2 -
airavata-api/.mvn/maven-build-cache-config.xml | 14 -
airavata-api/.mvn/wrapper/maven-wrapper.properties | 3 -
airavata-api/README.md | 428 --
airavata-api/examples/hello-world-experiment.sh | 223 -
airavata-api/modules/airavata-api/pom.xml | 585 --
.../accounting/entity/AllocationProjectEntity.java | 127 -
.../entity/CredentialAllocationProjectEntity.java | 91 -
.../entity/CredentialAllocationProjectPK.java | 82 -
.../accounting/mapper/AllocationProjectMapper.java | 36 -
.../accounting/model/AllocationProject.java | 116 -
.../model/CredentialAllocationProject.java | 87 -
.../repository/AllocationProjectRepository.java | 65 -
.../CredentialAllocationProjectRepository.java | 82 -
.../service/AllocationProjectService.java | 53 -
.../service/DefaultAllocationProjectService.java | 250 -
.../org/apache/airavata/agent/UserContext.java | 53 -
.../agent/entity/AgentDeploymentInfoEntity.java | 77 -
.../agent/entity/AgentExecutionStatusEntity.java | 100 -
.../agent/entity/ExperimentStorageCacheEntity.java | 96 -
.../repository/AgentDeploymentInfoRepository.java | 27 -
.../agent/repository/AgentExecutionRepository.java | 27 -
.../repository/AgentExecutionStatusRepository.java | 27 -
.../ExperimentStorageCacheRepository.java | 35 -
.../agent/service/AgentConnectionService.java | 98 -
.../agent/service/AgentManagementService.java | 418 --
.../apache/airavata/agent/service/PlanHandler.java | 55 -
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.../provider/ComputeProviderConfiguration.java | 121 -
.../compute/provider/aws/AwsComputeProvider.java | 619 --
.../airavata/compute/provider/aws/AwsJobSpec.java | 78 -
.../airavata/compute/provider/aws/AwsTaskUtil.java | 150 -
.../provider/local/LocalComputeProvider.java | 76 -
.../provider/slurm/SlurmComputeProvider.java | 638 --
.../resource/adapter/ComputeResourceAdapter.java | 164 -
.../resource/adapter/ResourceProfileAdapter.java | 210 -
.../resource/entity/ResourceBindingEntity.java | 191 -
.../compute/resource/entity/ResourceEntity.java | 198 -
.../resource/entity/ResourcePreferenceEntity.java | 152 -
.../resource/mapper/ResourceBindingMapper.java | 41 -
.../compute/resource/mapper/ResourceMapper.java | 44 -
.../compute/resource/model/ComputeCapability.java | 108 -
.../airavata/compute/resource/model/Job.java | 174 -
.../compute/resource/model/PreferenceKeys.java | 388 -
.../compute/resource/model/PreferenceLevel.java | 130 -
.../resource/model/PreferenceResourceType.java | 151 -
.../resource/model/PreferenceValueType.java | 79 -
.../airavata/compute/resource/model/Resource.java | 164 -
.../compute/resource/model/ResourceBinding.java | 153 -
.../resource/model/ResourceCapabilities.java | 71 -
.../resource/model/ResourceJobManagerType.java | 53 -
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.../service/DefaultCredentialEntityService.java | 335 -
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.../airavata/iam/exception/AuthExceptions.java | 60 -
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.../iam/keycloak/KeycloakGatewayManagement.java | 673 --
.../airavata/iam/keycloak/KeycloakRestClient.java | 626 --
.../apache/airavata/iam/mapper/DomainMapper.java | 74 -
.../airavata/iam/mapper/SharingUserMapper.java | 80 -
.../org/apache/airavata/iam/mapper/UserMapper.java | 87 -
.../org/apache/airavata/iam/model/AuthzToken.java | 84 -
.../airavata/iam/model/ClientRepresentation.java | 158 -
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.../iam/service/DefaultIamAdminService.java | 581 --
.../service/DefaultKeycloakAdminTokenResolver.java | 221 -
.../iam/service/DefaultKeycloakLogoutService.java | 203 -
.../iam/service/DefaultSharingService.java | 2065 ------
.../airavata/iam/service/DefaultUserService.java | 564 --
.../iam/service/GatewayGroupsInitializer.java | 114 -
.../apache/airavata/iam/service/GroupService.java | 68 -
.../airavata/iam/service/IamAdminService.java | 76 -
.../iam/service/KeycloakRequestAuthenticator.java | 285 -
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.../airavata/iam/util/ServiceOperationHelper.java | 130 -
.../airavata/protocol/DefaultAdapterSupport.java | 114 -
.../org/apache/airavata/protocol/FileTransfer.java | 439 --
.../airavata/protocol/ssh/PoolingSSHJClient.java | 446 --
.../airavata/protocol/ssh/SSHJAgentAdapter.java | 657 --
.../org/apache/airavata/protocol/ssh/SSHUtil.java | 183 -
.../application/adapter/ApplicationAdapter.java | 269 -
.../application/entity/ApplicationEntity.java | 220 -
.../entity/ApplicationInstallationEntity.java | 190 -
.../mapper/ApplicationInstallationMapper.java | 37 -
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.../research/application/model/Application.java | 215 -
.../model/ApplicationDeploymentDescription.java | 188 -
.../application/model/ApplicationField.java | 104 -
.../application/model/ApplicationInstallation.java | 160 -
.../application/model/InstallationStatus.java | 30 -
.../ApplicationInstallationRepository.java | 44 -
.../repository/ApplicationRepository.java | 44 -
.../service/ApplicationInstallationService.java | 39 -
.../application/service/ApplicationService.java | 58 -
.../DefaultApplicationInstallationService.java | 88 -
.../service/DefaultApplicationService.java | 70 -
.../artifact/entity/ArtifactStarEntity.java | 72 -
.../artifact/entity/ModelArtifactEntity.java | 57 -
.../artifact/entity/ResearchArtifactEntity.java | 193 -
.../research/artifact/mapper/ArtifactMapper.java | 89 -
.../research/artifact/model/ArtifactResponse.java | 42 -
.../artifact/model/CreateArtifactRequest.java | 127 -
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.../repository/ArtifactStarRepository.java | 39 -
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.../artifact/repository/TagRepository.java | 42 -
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.../artifact/service/DefaultArtifactService.java | 381 -
.../experiment/entity/ExperimentEntity.java | 269 -
.../experiment/entity/ExperimentInputEntity.java | 182 -
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.../experiment/exception/ExperimentExceptions.java | 76 -
.../experiment/mapper/ExperimentMapper.java | 205 -
.../experiment/mapper/ExperimentSummaryMapper.java | 56 -
.../experiment/mapper/NotificationMapper.java | 70 -
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airavata-api/pom.xml | 1396 ++--
airavata-api/scripts/README.md | 16 -
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.../api/server/handler/AiravataServerHandler.java | 7655 ++++++++++++++++++++
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.../ClusterStatusMonitorJobScheduler.java | 68 +
.../airavata/common/context/RequestContext.java} | 58 +-
.../airavata/common/context/WorkflowContext.java | 84 +
.../exception/AiravataConfigurationException.java} | 24 +-
.../common/exception/AiravataException.java} | 21 +-
.../exception/AiravataStartupException.java} | 27 +-
.../exception/ApplicationSettingsException.java} | 23 +-
.../apache/airavata/common/logging/Exception.java | 64 +
.../airavata/common/logging/MDCConstants.java} | 28 +-
.../apache/airavata/common/logging/MDCUtil.java} | 39 +-
.../airavata/common/utils/AiravataJobState.java | 115 +
.../airavata/common/utils/AiravataUtils.java} | 41 +-
.../airavata/common/utils/ApplicationSettings.java | 381 +
.../apache/airavata/common/utils/Constants.java | 51 +
.../common/utils/DBEventManagerConstants.java | 82 +
.../airavata/common/utils/DBEventService.java} | 26 +-
.../airavata/common/utils/DBInitConfig.java} | 20 +-
.../airavata/common/utils/DBInitializer.java | 72 +
.../org/apache/airavata/common/utils/DBUtil.java | 342 +
.../airavata/common/utils/DatabaseCreator.java | 381 +
.../airavata/common/utils/DatabaseTestCases.java | 123 +
.../utils/DefaultKeyStorePasswordCallback.java} | 40 +-
.../apache/airavata/common/utils/DerbyUtil.java | 112 +
.../airavata/common/utils/ExecutionMode.java} | 9 +-
.../org/apache/airavata/common/utils/IOUtil.java | 206 +
.../org/apache/airavata/common/utils/IServer.java | 59 +
.../apache/airavata/common/utils/JDBCConfig.java} | 18 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 102 +
.../org/apache/airavata/common/utils/JSONUtil.java | 148 +
.../common/utils/KeyStorePasswordCallback.java | 68 +
.../common/utils/LocalEventPublisher.java} | 35 +-
.../airavata/common/utils/NameValidator.java | 67 +
.../org/apache/airavata/common/utils/Pair.java | 76 +
.../airavata/common/utils}/SecurityUtil.java | 34 +-
.../airavata/common/utils/ServerSettings.java | 329 +
.../apache/airavata/common/utils/StringUtil.java | 479 ++
.../apache/airavata/common/utils/SwingUtil.java | 356 +
.../airavata/common/utils/ThriftClientPool.java | 237 +
.../apache/airavata/common/utils/ThriftUtils.java | 67 +
.../org/apache/airavata/common/utils/Version.java | 123 +
.../apache/airavata/common/utils/WSConstants.java | 181 +
.../apache/airavata/common/utils/ZkConstants.java} | 28 +-
.../ComputationalResourceMonitoringService.java | 129 +
.../monitoring/job/ComputeResourceMonitor.java | 146 +
.../resource/monitoring/job/MonitoringJob.java | 224 +
.../monitoring/job/output/OutputParser.java} | 18 +-
.../monitoring/job/output/OutputParserImpl.java | 62 +
.../resource/monitoring/utils/Constants.java | 34 +
.../store/client/CredentialStoreClientFactory.java | 44 +
.../credential/store/client/TestSSLClient.java | 139 +
.../credential/store/credential/AuditInfo.java} | 30 +-
.../store/credential}/CommunityUser.java | 57 +-
.../credential/store/credential/Credential.java | 81 +
.../store/credential/CredentialOwnerType.java} | 9 +-
.../impl/certificate/CertificateAuditInfo.java | 98 +
.../impl/certificate/CertificateCredential.java | 98 +
.../impl/password/PasswordCredential.java} | 31 +-
.../store/credential/impl/ssh/SSHCredential.java | 83 +
.../store/notifier/CredentialStoreNotifier.java | 59 +
.../store/notifier/NotificationMessage.java} | 26 +-
.../store/notifier/NotifierBootstrap.java | 133 +
.../notifier/impl/EmailNotificationMessage.java} | 43 +-
.../store/notifier/impl/EmailNotifier.java | 67 +
.../notifier/impl/EmailNotifierConfiguration.java | 73 +
.../store/server/CredentialStoreServer.java | 148 +
.../store/server/CredentialStoreServerHandler.java | 580 ++
.../credential/store/store/CredentialReader.java | 114 +
.../store/store/CredentialReaderFactory.java | 53 +
.../store/store}/CredentialStoreException.java | 14 +-
.../credential/store/store/CredentialWriter.java} | 21 +-
.../store/impl/CertificateCredentialWriter.java | 120 +
.../store/store/impl/CredentialReaderImpl.java | 186 +
.../store/store/impl/SSHCredentialWriter.java | 83 +
.../store/store/impl/db/CommunityUserDAO.java | 250 +
.../store/store/impl/db/CredentialsDAO.java | 495 ++
.../credential/store/store/impl/db/ParentDAO.java} | 18 +-
.../impl/util/CredentialStoreDBInitConfig.java} | 26 +-
.../store/impl/util/CredentialStoreJDBCConfig.java | 72 +
.../credential/store/util/ConfigurationReader.java | 116 +
.../store/util/CredentialStoreConstants.java} | 25 +-
.../credential/store/util/PrivateKeyStore.java | 65 +
.../credential/store/util/TokenGenerator.java} | 39 +-
.../airavata/credential/store/util/Utility.java | 105 +
.../db/event/manager/DBEventManagerRunner.java | 139 +
.../messaging/DBEventManagerException.java} | 14 +-
.../messaging/DBEventManagerMessagingFactory.java | 73 +
.../messaging/impl/DBEventMessageHandler.java | 112 +
.../db/event/manager/utils/Constants.java} | 11 +-
.../event/manager/utils/DbEventManagerZkUtils.java | 126 +
.../airavata/helix/adaptor/PoolingSSHJClient.java | 467 ++
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 821 +++
.../airavata/helix/adaptor/SSHJStorageAdaptor.java | 117 +
.../adaptor/wrapper/SCPFileTransferWrapper.java | 106 +
.../helix/adaptor/wrapper/SFTPClientWrapper.java | 50 +
.../helix/adaptor/wrapper/SSHClientWrapper.java} | 27 +-
.../helix/adaptor/wrapper/SessionWrapper.java | 194 +
.../apache/airavata/helix/agent/ssh/SSHUtil.java | 69 +
.../airavata/helix/agent/ssh/SshAdaptorParams.java | 134 +
.../airavata/helix/agent/ssh/SshAgentAdaptor.java | 710 ++
.../helix/agent/ssh/StandardOutReader.java | 68 +
.../agent/storage/StorageResourceAdaptorImpl.java | 89 +
.../apache/airavata/helix/core/AbstractTask.java | 247 +
.../org/apache/airavata/helix/core/OutPort.java} | 46 +-
.../helix/core/participant/HelixParticipant.java | 238 +
.../helix/core/support/TaskHelperImpl.java} | 24 +-
.../core/support/adaptor/AdaptorSupportImpl.java | 229 +
.../helix/core/support/adaptor/AgentStore.java | 152 +
.../airavata/helix/core/util/MonitoringUtil.java | 67 +
.../airavata/helix/core/util/PropertyResolver.java | 63 +
.../apache/airavata/helix/core/util/TaskUtil.java | 150 +
.../helix/impl/controller/HelixController.java | 131 +
.../impl/controller/WorkflowCleanupAgent.java | 94 +
.../helix/impl/participant/GlobalParticipant.java | 98 +
.../airavata/helix/impl/task/AWSTaskFactory.java | 73 +
.../airavata/helix/impl/task/AiravataTask.java | 680 ++
.../helix/impl/task/HelixTaskFactory.java} | 20 +-
.../airavata/helix/impl/task/SlurmTaskFactory.java | 84 +
.../airavata/helix/impl/task/TaskContext.java | 1088 +++
.../airavata/helix/impl/task/TaskFactory.java} | 35 +-
.../helix/impl/task/TaskOnFailException.java} | 6 +-
.../helix/impl/task/aws/AWSCompletingTask.java | 49 +
.../helix/impl/task/aws/AWSJobSubmissionTask.java | 339 +
.../impl/task/aws/AWSProcessContextManager.java | 138 +
.../helix/impl/task/aws/CreateEC2InstanceTask.java | 168 +
.../helix/impl/task/aws/NoOperationTask.java} | 34 +-
.../helix/impl/task/aws/utils/AWSTaskUtil.java | 125 +
.../task/aws/utils/ExponentialBackoffWaiter.java | 102 +
.../impl/task/cancel/CancelCompletingTask.java | 68 +
.../task/cancel/RemoteJobCancellationTask.java | 200 +
.../impl/task/cancel/WorkflowCancellationTask.java | 168 +
.../helix/impl/task/completing/CompletingTask.java | 65 +
.../airavata/helix/impl/task/env/EnvSetupTask.java | 67 +
.../airavata/helix/impl/task/mock/MockTask.java} | 28 +-
.../helix/impl/task/parsing/DataParsingTask.java | 546 ++
.../impl/task/parsing/ParsingTriggeringTask.java | 95 +
.../task/parsing/ProcessCompletionMessage.java} | 32 +-
.../ProcessCompletionMessageDeserializer.java | 43 +
.../kafka/ProcessCompletionMessageSerializer.java} | 26 +-
.../task/parsing/models/ParsingTaskInput.java} | 48 +-
.../task/parsing/models/ParsingTaskInputs.java} | 46 +-
.../task/parsing/models/ParsingTaskOutput.java} | 40 +-
.../task/parsing/models/ParsingTaskOutputs.java} | 47 +-
.../helix/impl/task/staging/ArchiveTask.java | 196 +
.../helix/impl/task/staging/DataStagingTask.java | 530 ++
.../impl/task/staging/InputDataStagingTask.java | 123 +
.../impl/task/staging/JobVerificationTask.java | 132 +
.../impl/task/staging/OutputDataStagingTask.java | 367 +
.../task/submission/DefaultJobSubmissionTask.java | 289 +
.../task/submission/ForkJobSubmissionTask.java | 105 +
.../impl/task/submission/JobSubmissionTask.java | 299 +
.../task/submission/LocalJobSubmissionTask.java | 95 +
.../task/submission/config/GroovyMapBuilder.java | 529 ++
.../impl/task/submission/config/GroovyMapData.java | 598 ++
.../impl/task/submission/config/JobFactory.java | 166 +
.../submission/config/JobManagerConfiguration.java | 49 +
.../impl/task/submission/config/OutputParser.java} | 12 +-
.../task/submission/config}/RawCommandInfo.java | 2 +-
.../impl/task/submission/config/ScriptTag.java} | 29 +-
.../config/app/CloudJobManagerConfiguration.java | 107 +
.../config/app/ForkJobConfiguration.java} | 74 +-
.../config/app/HTCondorJobConfiguration.java} | 95 +-
.../impl/task/submission/config/app/JobUtil.java} | 16 +-
.../submission/config/app/LSFJobConfiguration.java | 126 +
.../submission/config/app/PBSJobConfiguration.java | 132 +
.../config/app/SlurmJobConfiguration.java | 133 +
.../submission/config/app/UGEJobConfiguration.java | 124 +
.../parser/AiravataCustomCommandOutputParser.java} | 28 +-
.../config/app/parser/ForkOutputParser.java} | 21 +-
.../config/app/parser/HTCondorOutputParser.java | 167 +
.../config/app/parser/LSFOutputParser.java | 132 +
.../config/app/parser/PBSOutputParser.java | 140 +
.../config/app/parser}/SlurmOutputParser.java | 58 +-
.../config/app/parser/UGEOutputParser.java | 106 +
.../helix/impl/workflow/ParserWorkflowManager.java | 475 ++
.../helix/impl/workflow/PostWorkflowManager.java | 429 ++
.../helix/impl/workflow/PreWorkflowManager.java | 387 +
.../helix/impl/workflow/WorkflowManager.java | 193 +
.../airavata/helix/task/api/TaskHelper.java} | 21 +-
.../airavata/helix/task/api/TaskParamType.java} | 13 +-
.../helix/task/api/annotation/TaskDef.java} | 27 +-
.../helix/task/api/annotation/TaskOutPort.java} | 27 +-
.../helix/task/api/annotation/TaskParam.java} | 28 +-
.../helix/task/api/support/AdaptorSupport.java} | 26 +-
.../airavata/helix/workflow/QueueOperator.java | 204 +
.../airavata/helix/workflow/WorkflowOperator.java | 146 +
.../messaging/client/RabbitMQListener.java | 247 +
.../airavata/messaging/client/TestReader.java | 67 +
.../airavata/messaging/core/MessageContext.java | 89 +
.../airavata/messaging/core/MessageHandler.java} | 12 +-
.../messaging/core/MessagingConstants.java} | 23 +-
.../airavata/messaging/core/MessagingFactory.java | 194 +
.../apache/airavata/messaging/core/Publisher.java} | 30 +-
.../messaging/core/RabbitMQProperties.java | 124 +
.../apache/airavata/messaging/core/Subscriber.java | 46 +
.../apache/airavata/messaging/core/TestClient.java | 69 +
.../org/apache/airavata/messaging/core/Type.java} | 9 +-
.../messaging/core/impl/ExperimentConsumer.java | 123 +
.../messaging/core/impl/MessageConsumer.java | 90 +
.../messaging/core/impl/ProcessConsumer.java | 121 +
.../messaging/core/impl/RabbitMQPublisher.java | 161 +
.../messaging/core/impl/RabbitMQSubscriber.java | 191 +
.../messaging/core/impl/StatusConsumer.java | 140 +
.../messaging/core/stats/CountWriterTask.java | 52 +
.../messaging/core/stats/LatencyWriterTask.java | 53 +
.../airavata/messaging/core/stats/StatCounter.java | 99 +
.../messaging/core/util/DBEventPublisherUtils.java | 122 +
.../metascheduler/core/api/ProcessScheduler.java} | 24 +-
.../engine/ComputeResourceSelectionPolicy.java} | 30 +-
.../metascheduler/core/engine/DataAnalyzer.java} | 9 +-
.../metascheduler/core/engine/ProcessScanner.java} | 16 +-
.../metascheduler/core/engine/ReScheduler.java} | 20 +-
.../airavata/metascheduler/core/utils/Utils.java | 155 +
.../metadata/analyzer/DataInterpreterService.java | 113 +
.../metadata/analyzer/impl/DataAnalyzerImpl.java | 93 +
.../metadata/analyzer/utils/Constants.java} | 20 +-
.../scheduling/api/ProcessSchedulerImpl.java | 140 +
.../ComputeResourceSelectionPolicyImpl.java | 48 +
.../DefaultComputeResourceSelectionPolicy.java | 88 +
.../selection/MultipleComputeResourcePolicy.java | 91 +
.../rescheduler/ExponentialBackOffReScheduler.java | 185 +
.../rescheduler/ProcessReschedulingService.java | 116 +
.../engine/rescheduler/ProcessScannerImpl.java | 78 +
.../process/scheduling/utils/Constants.java} | 20 +-
.../airavata/model/util/AppDeploymentUtil.java | 48 +
.../airavata/model/util/AppInterfaceUtil.java | 70 +
.../apache/airavata/model/util/ExecutionType.java} | 9 +-
.../airavata/model/util/ExperimentModelUtil.java | 111 +
.../util/GroupComputeResourcePreferenceUtil.java | 58 +
.../airavata/model/util/ProjectModelUtil.java} | 28 +-
.../apache/airavata/monitor/AbstractMonitor.java | 132 +
.../apache/airavata/monitor/JobStateValidator.java | 92 +
.../apache/airavata/monitor/JobStatusResult.java | 70 +
.../airavata/monitor/MonitoringException.java} | 23 +-
.../airavata/monitor/email/EmailBasedMonitor.java | 314 +
.../email/parser/AiravataCustomMailParser.java | 79 +
.../monitor/email/parser/EmailParser.java} | 31 +-
.../monitor/email/parser/HTCondorEmailParser.java | 155 +
.../monitor/email/parser/LSFEmailParser.java | 82 +
.../monitor/email/parser/PBSEmailParser.java | 105 +
.../monitor/email/parser}/ResourceConfig.java | 4 +-
.../monitor/email/parser}/SLURMEmailParser.java | 53 +-
.../monitor/email/parser/UGEEmailParser.java | 110 +
.../monitor/kafka/JobStatusResultDeserializer.java | 45 +
.../monitor/kafka/JobStatusResultSerializer.java} | 33 +-
.../airavata/monitor/kafka/MessageProducer.java | 59 +
.../airavata/monitor/realtime/RealtimeMonitor.java | 99 +
.../realtime/parser/RealtimeJobStatusParser.java | 122 +
.../client/OrchestratorClientFactory.java | 43 +
.../core/OrchestratorConfiguration.java} | 31 +-
.../core/context/OrchestratorContext.java} | 53 +-
.../core/exception}/OrchestratorException.java | 6 +-
.../core/impl/GFACPassiveJobSubmitter.java | 159 +
.../orchestrator/core/job/JobSubmitter.java | 54 +
.../core/schedule/DefaultHostScheduler.java} | 21 +-
.../orchestrator/core/schedule/HostScheduler.java} | 31 +-
.../core/utils/OrchestratorConstants.java} | 17 +-
.../orchestrator/core/utils/OrchestratorUtils.java | 434 ++
.../core/validator/JobMetadataValidator.java | 43 +
.../core/validator/impl/BatchQueueValidator.java | 238 +
.../validator/impl/ExperimentStatusValidator.java | 55 +
.../impl/GroupResourceProfileValidator.java | 217 +
.../airavata/orchestrator/cpi/Orchestrator.java | 83 +
.../cpi/impl/AbstractOrchestrator.java | 102 +
.../cpi/impl/SimpleOrchestratorImpl.java | 918 +++
.../sample/OrchestratorClientSample.java | 142 +
.../orchestrator/server/OrchestratorServer.java | 237 +
.../server/OrchestratorServerHandler.java | 1099 +++
.../airavata/orchestrator/util/Constants.java} | 20 +-
.../util/OrchestratorServerThreadPoolExecutor.java | 53 +
.../orchestrator/util/OrchestratorUtils.java | 99 +
.../airavata/patform/monitoring/CountMonitor.java} | 36 +-
.../airavata/patform/monitoring/GaugeMonitor.java} | 29 +-
.../patform/monitoring/MonitoringServer.java | 55 +
.../api/client/RegistryServiceClientFactory.java | 43 +
.../registry/api/service/RegistryAPIServer.java | 192 +
.../api/service/handler/RegistryServerHandler.java | 5799 +++++++++++++++
.../messaging/RegistryServiceDBEventHandler.java | 235 +
.../RegistryServiceDBEventMessagingFactory.java | 96 +
.../registry/api/service/util/Constants.java} | 33 +-
.../airavata/registry/core/RegistryException.java} | 20 +-
.../AiravataWorkflowEntity.java | 164 +
.../AiravataWorkflowErrorEntity.java | 127 +
.../AiravataWorkflowErrorPK.java} | 42 +-
.../AiravataWorkflowStatusEntity.java | 104 +
.../AiravataWorkflowStatusPK.java} | 42 +-
.../ApplicationErrorEntity.java | 127 +
.../ApplicationErrorPK.java} | 42 +-
.../ApplicationStatusEntity.java | 104 +
.../ApplicationStatusPK.java} | 42 +-
.../HandlerErrorEntity.java | 130 +
.../airavataworkflowcatalog/HandlerErrorPK.java} | 42 +-
.../HandlerInputEntity.java} | 171 +-
.../airavataworkflowcatalog/HandlerInputPK.java} | 46 +-
.../HandlerOutputEntity.java} | 153 +-
.../airavataworkflowcatalog/HandlerOutputPK.java} | 46 +-
.../HandlerStatusEntity.java | 105 +
.../airavataworkflowcatalog/HandlerStatusPK.java} | 47 +-
.../WorkflowApplicationEntity.java | 210 +
.../WorkflowApplicationPK.java} | 42 +-
.../WorkflowConnectionEntity.java | 183 +
.../WorkflowConnectionPK.java} | 55 +-
.../WorkflowDataBlockEntity.java | 127 +
.../WorkflowHandlerEntity.java | 165 +
.../WorkflowHandlerPK.java} | 47 +-
.../AWSGroupComputeResourcePrefEntity.java | 75 +
.../entities/appcatalog/AppEnvironmentEntity.java | 96 +
.../entities/appcatalog/AppEnvironmentPK.java} | 53 +-
.../appcatalog/AppModuleMappingEntity.java | 84 +
.../entities/appcatalog/AppModuleMappingPK.java | 72 +
.../appcatalog/ApplicationDeploymentEntity.java | 300 +
.../appcatalog/ApplicationInputEntity.java} | 160 +-
.../entities/appcatalog/ApplicationInputPK.java | 72 +
.../appcatalog/ApplicationInterfaceEntity.java} | 134 +-
.../appcatalog/ApplicationModuleEntity.java | 117 +
.../appcatalog/ApplicationOutputEntity.java} | 149 +-
.../entities/appcatalog/ApplicationOutputPK.java | 72 +
.../core/entities/appcatalog/BatchQueueEntity.java | 203 +
.../core/entities/appcatalog/BatchQueuePK.java | 72 +
.../appcatalog/BatchQueueResourcePolicyEntity.java | 133 +
.../appcatalog/CloudJobSubmissionEntity.java | 103 +
.../entities/appcatalog/ComputeResourceEntity.java | 262 +
.../ComputeResourceFileSystemEntity.java | 85 +
.../appcatalog/ComputeResourceFileSystemPK.java | 74 +
.../appcatalog/ComputeResourcePolicyEntity.java | 109 +
.../ComputeResourcePreferenceEntity.java | 259 +
.../appcatalog/ComputeResourcePreferencePK.java | 76 +
.../ComputeResourceReservationEntity.java | 128 +
.../appcatalog/DataMovementInterfaceEntity.java | 118 +
.../appcatalog/DataMovementInterfacePK.java | 72 +
.../entities/appcatalog/GatewayGroupsEntity.java} | 51 +-
.../entities/appcatalog/GatewayProfileEntity.java | 133 +
.../appcatalog/GlobusGkEndpointEntity.java} | 39 +-
.../entities/appcatalog/GlobusGkEndpointPK.java | 72 +
.../appcatalog/GlobusSubmissionEntity.java | 71 +
.../appcatalog/GridftpDataMovementEntity.java | 82 +
.../entities/appcatalog/GridftpEndpointEntity.java | 94 +
.../entities/appcatalog/GridftpEndpointPK.java | 72 +
.../appcatalog/GroupComputeResourcePrefEntity.java | 160 +
.../appcatalog/GroupComputeResourcePrefPK.java | 71 +
.../appcatalog/GroupResourceProfileEntity.java | 158 +
.../GroupSSHAccountProvisionerConfig.java | 111 +
.../GroupSSHAccountProvisionerConfigPK.java | 88 +
.../entities/appcatalog/GsisshExportEntity.java} | 38 +-
.../core/entities/appcatalog/GsisshExportPK.java | 72 +
.../appcatalog/GsisshPostjobcommandEntity.java} | 40 +-
.../appcatalog/GsisshPostjobcommandPK.java | 72 +
.../appcatalog/GsisshPrejobcommandEntity.java} | 38 +-
.../entities/appcatalog/GsisshPrejobcommandPK.java | 72 +
.../appcatalog/GsisshSubmissionEntity.java | 94 +
.../appcatalog/JobManagerCommandEntity.java | 84 +
.../entities/appcatalog/JobManagerCommandPK.java | 73 +
.../appcatalog/JobSubmissionInterfaceEntity.java | 118 +
.../appcatalog/JobSubmissionInterfacePK.java | 72 +
.../appcatalog/LibraryApendPathEntity.java | 85 +
.../entities/appcatalog/LibraryAppendPathPK.java} | 49 +-
.../appcatalog/LibraryPrependPathEntity.java | 86 +
.../entities/appcatalog/LibraryPrependPathPK.java} | 50 +-
.../appcatalog/LocalDataMovementEntity.java} | 40 +-
.../entities/appcatalog/LocalSubmissionEntity.java | 105 +
.../entities/appcatalog/ModuleLoadCmdEntity.java | 85 +
.../core/entities/appcatalog/ModuleLoadCmdPK.java | 71 +
.../appcatalog/ParallelismCommandEntity.java | 84 +
.../entities/appcatalog/ParallelismCommandPK.java | 73 +
.../entities/appcatalog/ParserConnectorEntity.java | 127 +
.../appcatalog/ParserConnectorInputEntity.java | 121 +
.../core/entities/appcatalog/ParserEntity.java | 129 +
.../entities/appcatalog/ParserInputEntity.java | 97 +
.../entities/appcatalog/ParserOutputEntity.java | 97 +
.../entities/appcatalog/ParsingTemplateEntity.java | 96 +
.../appcatalog/ParsingTemplateInputEntity.java | 109 +
.../entities/appcatalog/PostjobCommandEntity.java | 85 +
.../core/entities/appcatalog/PostjobCommandPK.java | 71 +
.../entities/appcatalog/PrejobCommandEntity.java | 85 +
.../core/entities/appcatalog/PrejobCommandPK.java | 72 +
.../appcatalog/ResourceJobManagerEntity.java | 105 +
.../SSHAccountProvisionerConfiguration.java | 104 +
.../SSHAccountProvisionerConfigurationPK.java | 61 +
.../entities/appcatalog/ScpDataMovementEntity.java | 115 +
.../SlurmGroupComputeResourcePrefEntity.java | 146 +
.../appcatalog/SshJobSubmissionEntity.java | 129 +
.../appcatalog/StorageInterfaceEntity.java | 118 +
.../entities/appcatalog/StorageInterfacePK.java | 74 +
.../appcatalog/StoragePreferenceEntity.java | 104 +
.../entities/appcatalog/StoragePreferencePK.java | 71 +
.../entities/appcatalog/StorageResourceEntity.java | 118 +
.../appcatalog/UnicoreDatamovementEntity.java | 76 +
.../appcatalog/UnicoreSubmissionEntity.java | 71 +
.../UserComputeResourcePreferenceEntity.java | 193 +
.../UserComputeResourcePreferencePK.java | 84 +
.../appcatalog/UserResourceProfileEntity.java | 146 +
.../appcatalog/UserResourceProfilePK.java} | 55 +-
.../appcatalog/UserStoragePreferenceEntity.java | 115 +
.../appcatalog/UserStoragePreferencePK.java | 84 +
.../ComputationalResourceSchedulingEntity.java} | 139 +-
.../ComputationalResourceSchedulingPK.java | 79 +
.../core/entities/expcatalog/ExperimentEntity.java | 287 +
.../entities/expcatalog/ExperimentErrorEntity.java | 130 +
.../entities/expcatalog/ExperimentErrorPK.java | 71 +
.../expcatalog/ExperimentInputEntity.java} | 133 +-
.../entities/expcatalog/ExperimentInputPK.java | 71 +
.../expcatalog/ExperimentOutputEntity.java} | 78 +-
.../entities/expcatalog/ExperimentOutputPK.java | 71 +
.../expcatalog/ExperimentStatusEntity.java | 108 +
.../entities/expcatalog/ExperimentStatusPK.java | 71 +
.../expcatalog}/ExperimentSummaryEntity.java | 86 +-
.../core/entities/expcatalog/GatewayEntity.java | 247 +
.../GatewayUsageReportingCommandEntity.java} | 47 +-
.../expcatalog/GatewayUsageReportingPK.java} | 61 +-
.../entities/expcatalog/GatewayWorkerEntity.java} | 54 +-
.../core/entities/expcatalog/GatewayWorkerPK.java} | 65 +-
.../core/entities/expcatalog}/JobEntity.java | 151 +-
.../registry/core/entities/expcatalog/JobPK.java | 71 +
.../core/entities/expcatalog/JobStatusEntity.java | 123 +
.../core/entities/expcatalog/JobStatusPK.java | 83 +
.../entities/expcatalog}/NotificationEntity.java | 63 +-
.../core/entities/expcatalog/ProcessEntity.java | 379 +
.../entities/expcatalog/ProcessErrorEntity.java | 130 +
.../core/entities/expcatalog/ProcessErrorPK.java | 71 +
.../entities/expcatalog/ProcessInputEntity.java} | 135 +-
.../core/entities/expcatalog/ProcessInputPK.java | 71 +
.../entities/expcatalog/ProcessOutputEntity.java} | 84 +-
.../core/entities/expcatalog/ProcessOutputPK.java | 71 +
.../expcatalog/ProcessResourceScheduleEntity.java} | 135 +-
.../entities/expcatalog/ProcessStatusEntity.java | 108 +
.../core/entities/expcatalog/ProcessStatusPK.java | 71 +
.../entities/expcatalog/ProcessWorkflowEntity.java | 87 +
.../entities/expcatalog/ProcessWorkflowPK.java | 70 +
.../core/entities/expcatalog/ProjectEntity.java | 102 +
.../entities/expcatalog/ProjectUserEntity.java | 71 +
.../core/entities/expcatalog/ProjectUserPK.java | 71 +
.../entities/expcatalog/QueueStatusEntity.java | 105 +
.../core/entities/expcatalog/QueueStatusPK.java | 84 +
.../core/entities/expcatalog/TaskEntity.java | 172 +
.../core/entities/expcatalog/TaskErrorEntity.java | 130 +
.../core/entities/expcatalog/TaskErrorPK.java | 71 +
.../core/entities/expcatalog/TaskStatusEntity.java | 108 +
.../core/entities/expcatalog/TaskStatusPK.java | 71 +
.../expcatalog/UserConfigurationDataEntity.java | 317 +
.../core/entities/expcatalog/UserEntity.java} | 66 +-
.../registry/core/entities/expcatalog/UserPK.java} | 57 +-
.../replicacatalog/ConfigurationEntity.java} | 36 +-
.../entities/replicacatalog/ConfigurationPK.java | 71 +
.../entities/replicacatalog/DataProductEntity.java | 178 +
.../replicacatalog/DataProductMetadataEntity.java | 68 +
.../replicacatalog/DataProductMetadataPK.java | 71 +
.../replicacatalog/DataReplicaLocationEntity.java | 187 +
.../replicacatalog/DataReplicaMetadataEntity.java | 68 +
.../replicacatalog/DataReplicaMetadataPK.java | 70 +
.../workflowcatalog/ComponentStatusEntity.java | 94 +
.../core/entities/workflowcatalog/EdgeEntity.java | 105 +
.../core/entities/workflowcatalog/EdgePK.java | 71 +
.../core/entities/workflowcatalog/NodeEntity.java | 127 +
.../core/entities/workflowcatalog/NodePK.java | 71 +
.../core/entities/workflowcatalog/PortEntity.java | 105 +
.../core/entities/workflowcatalog/PortPK.java | 72 +
.../entities/workflowcatalog/WorkflowEntity.java | 169 +
.../workflowcatalog/WorkflowInputEntity.java} | 154 +-
.../entities/workflowcatalog/WorkflowInputPK.java | 75 +
.../workflowcatalog/WorkflowOutputEntity.java} | 152 +-
.../entities/workflowcatalog/WorkflowOutputPK.java | 72 +
.../workflowcatalog/WorkflowStatusEntity.java | 93 +
.../entities/workflowcatalog/WorkflowStatusPK.java | 71 +
.../core/repositories/AbstractRepository.java | 210 +
.../appcatalog/AppCatAbstractRepository.java} | 23 +-
.../ApplicationDeploymentRepository.java | 289 +
.../appcatalog/ApplicationInputRepository.java} | 25 +-
.../appcatalog/ApplicationInterfaceRepository.java | 324 +
.../appcatalog/ApplicationModuleRepository.java} | 24 +-
.../appcatalog/ApplicationOutputRepository.java} | 26 +-
.../appcatalog/BatchQueuePolicyRepository.java} | 23 +-
.../appcatalog/BatchQueueRepository.java} | 24 +-
.../ComputeResourcePolicyRepository.java} | 23 +-
.../appcatalog/ComputeResourcePrefRepository.java | 56 +
.../appcatalog/ComputeResourceRepository.java | 619 ++
.../appcatalog/DataMovementRepository.java | 43 +
.../appcatalog/GatewayGroupsRepository.java} | 24 +-
.../appcatalog/GroupResourceProfileRepository.java | 317 +
.../appcatalog/GrpComputePrefRepository.java | 88 +
.../appcatalog/GwyResourceProfileRepository.java | 225 +
.../JobSubmissionInterfaceRepository.java | 45 +
.../appcatalog/ParserInputRepository.java | 44 +
.../appcatalog/ParserOutputRepository.java | 44 +
.../repositories/appcatalog/ParserRepository.java | 76 +
.../appcatalog/ParsingTemplateRepository.java | 48 +
.../appcatalog/ResourceJobManagerRepository.java | 111 +
.../appcatalog/StoragePrefRepository.java} | 25 +-
.../appcatalog/StorageResourceRepository.java | 235 +
.../UserComputeResourcePreferenceRepository.java} | 20 +-
.../appcatalog/UserResourceProfileRepository.java | 240 +
.../UserStoragePreferenceRepository.java} | 16 +-
.../expcatalog/ExpCatAbstractRepository.java} | 23 +-
.../expcatalog/ExperimentErrorRepository.java | 75 +
.../expcatalog/ExperimentInputRepository.java | 73 +
.../expcatalog/ExperimentOutputRepository.java | 73 +
.../expcatalog/ExperimentRepository.java | 201 +
.../expcatalog/ExperimentStatusRepository.java | 126 +
.../expcatalog/ExperimentSummaryRepository.java | 589 ++
.../repositories/expcatalog/GatewayRepository.java | 105 +
.../GatewayUsageReportingCommandRepository.java | 75 +
.../repositories/expcatalog/JobRepository.java | 157 +
.../expcatalog/JobStatusRepository.java | 111 +
.../expcatalog/NotificationRepository.java | 102 +
.../expcatalog/ProcessErrorRepository.java | 73 +
.../expcatalog/ProcessInputRepository.java | 72 +
.../expcatalog/ProcessOutputRepository.java | 73 +
.../repositories/expcatalog/ProcessRepository.java | 230 +
.../expcatalog/ProcessStatusRepository.java | 131 +
.../expcatalog/ProcessWorkflowRepository.java | 72 +
.../repositories/expcatalog/ProjectRepository.java | 209 +
.../expcatalog/QueueStatusRepository.java | 69 +
.../expcatalog/TaskErrorRepository.java | 73 +
.../repositories/expcatalog/TaskRepository.java | 174 +
.../expcatalog/TaskStatusRepository.java | 99 +
.../repositories/expcatalog/UserRepository.java | 65 +
.../replicacatalog/DataProductRepository.java | 158 +
.../DataReplicaLocationRepository.java | 103 +
.../replicacatalog/RepCatAbstractRepository.java} | 23 +-
.../WorkflowCatAbstractRepository.java} | 23 +-
.../workflowcatalog/WorkflowRepository.java | 192 +
.../core/utils/AppCatalogDBInitConfig.java | 66 +
.../registry/core/utils/AppCatalogJDBCConfig.java | 65 +
.../registry/core/utils/AppCatalogUtils.java} | 22 +-
.../airavata/registry/core/utils/Committer.java} | 12 +-
.../registry/core/utils/CustomBeanFactory.java | 113 +
.../airavata/registry/core/utils/DBConstants.java | 202 +
.../utils/DozerConverter/CsvStringConverter.java | 53 +
.../DozerConverter/StorageDateConverter.java} | 45 +-
.../core/utils/ExpCatalogDBInitConfig.java | 84 +
.../registry/core/utils/ExpCatalogJDBCConfig.java | 65 +
.../registry/core/utils/ExpCatalogUtils.java} | 22 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 40 +
.../core/utils/JPAUtil/ExpCatalogJPAUtils.java} | 21 +-
.../core/utils/JPAUtil/RepCatalogJPAUtils.java | 40 +
.../utils/JPAUtil/WorkflowCatalogJPAUtils.java} | 29 +-
.../core/utils/ObjectMapperSingleton.java} | 28 +-
.../registry/core/utils/QueryConstants.java | 262 +
.../core/utils/ReplicaCatalogDBInitConfig.java} | 35 +-
.../core/utils/ReplicaCatalogJDBCConfig.java | 65 +
.../core/utils/WorkflowCatalogDBInitConfig.java} | 34 +-
.../core/utils/WorkflowCatalogJDBCConfig.java | 65 +
.../registry/core/utils/WorkflowCatalogUtils.java} | 16 +-
.../core/utils/migration/MappingToolRunner.java | 65 +
.../utils/migration/MigrationSchemaGenerator.java | 125 +
.../apache/airavata/registry/cpi/AppCatalog.java | 67 +
.../registry/cpi/AppCatalogException.java} | 14 +-
.../registry/cpi/ApplicationDeployment.java | 106 +
.../registry/cpi/ApplicationInterface.java | 165 +
.../airavata/registry/cpi/CompositeIdentifier.java | 68 +
.../airavata/registry/cpi/ComputeResource.java | 253 +
.../registry/cpi/DataProductInterface.java | 45 +
.../cpi/DataReplicaLocationInterface.java} | 20 +-
.../registry/cpi/ExpCatChildDataType.java} | 29 +-
.../registry/cpi/ExpCatParentDataType.java} | 20 +-
.../airavata/registry/cpi/ExperimentCatalog.java | 231 +
.../registry/cpi/ExperimentCatalogException.java} | 14 +-
.../registry/cpi/ExperimentCatalogModelType.java} | 33 +-
.../registry/cpi/GwyClientCredential.java} | 23 +-
.../airavata/registry/cpi/GwyResourceProfile.java | 91 +
.../apache/airavata/registry/cpi/Registry.java} | 16 +-
.../airavata/registry/cpi/RegistryException.java} | 14 +-
.../airavata/registry/cpi/ReplicaCatalog.java | 55 +
.../registry/cpi/ReplicaCatalogException.java} | 23 +-
.../airavata/registry/cpi/ResultOrderType.java | 48 +
.../airavata/registry/cpi/StorageResource.java | 92 +
.../airavata/registry/cpi/UsrResourceProfile.java | 148 +
.../airavata/registry/cpi/WorkflowCatalog.java | 43 +
.../registry/cpi/WorkflowCatalogException.java} | 14 +-
.../airavata/registry/cpi/utils}/Constants.java | 10 +-
.../airavata/registry/cpi/utils/StatusType.java} | 15 +-
.../airavata/security/AbstractAuthenticator.java | 143 +
.../security/AbstractDatabaseAuthenticator.java | 130 +
.../security}/AiravataSecurityException.java | 2 +-
.../security/AuthenticationException.java} | 15 +-
.../apache/airavata/security/Authenticator.java | 105 +
.../org/apache/airavata/security/Authoriser.java} | 25 +-
.../org/apache/airavata/security/UserStore.java | 67 +
.../airavata/security/UserStoreException.java} | 19 +-
.../AbstractConfigurationReader.java | 52 +
.../AuthenticatorConfigurationReader.java | 242 +
.../security/userstore/AbstractJDBCUserStore.java | 132 +
.../airavata/security/userstore/JDBCUserStore.java | 172 +
.../airavata/security/userstore/LDAPUserStore.java | 141 +
.../security/userstore/SessionDBUserStore.java | 132 +
.../airavata/security/util/PasswordDigester.java | 106 +
.../org/apache/airavata/server/ServerMain.java | 425 ++
.../client/ProfileServiceClientFactory.java | 100 +
.../commons/repositories/AbstractRepository.java | 123 +
.../commons/tenant/entities/GatewayEntity.java | 282 +
.../user/entities/CustomizedDashboardEntity.java | 321 +
.../user/entities/NSFDemographicsEntity.java | 106 +
.../commons/user/entities/UserProfileEntity.java | 351 +
.../service/profile/commons/utils/Committer.java} | 11 +-
.../profile/commons/utils/JPAConstants.java} | 28 +-
.../service/profile/commons/utils/JPAUtils.java | 52 +
.../commons/utils/ObjectMapperSingleton.java} | 28 +-
.../commons/utils/ProfileServiceJDBCConfig.java} | 36 +-
.../profile/commons/utils/QueryConstants.java | 52 +
.../service/profile/commons/utils/Utils.java | 99 +
.../handlers/GroupManagerServiceHandler.java | 436 ++
.../profile/handlers/IamAdminServicesHandler.java | 368 +
.../handlers/TenantProfileServiceHandler.java | 273 +
.../handlers/UserProfileServiceHandler.java | 263 +
.../core/impl/TenantManagementKeycloakImpl.java | 883 +++
.../interfaces/TenantManagementInterface.java} | 59 +-
.../profile/server/ProfileServiceServer.java | 190 +
.../core/repositories/TenantProfileRepository.java | 108 +
.../exceptions/UserProfileRegistryException.java} | 16 +-
.../core/repositories/UserProfileRepository.java | 126 +
.../utils/UserProfileCatalogDBInitConfig.java} | 26 +-
.../core/utils/UserProfileCatalogJDBCConfig.java} | 35 +-
.../service/security/AiravataSecurityManager.java} | 9 +-
.../service/security/GatewayGroupsInitializer.java | 193 +
.../service/security/IdentityContext.java} | 32 +-
.../service/security/KeyCloakSecurityManager.java | 452 ++
.../service/security/SecurityManagerFactory.java | 53 +
.../airavata/service/security}/UserInfo.java | 2 +-
.../service/security/authzcache/AuthzCache.java | 59 +
.../security/authzcache/AuthzCacheEntry.java | 62 +
.../security/authzcache/AuthzCacheIndex.java | 91 +
.../security/authzcache/AuthzCacheManager.java | 79 +
.../authzcache/AuthzCacheManagerFactory.java | 57 +
.../security/authzcache/AuthzCachedStatus.java} | 23 +-
.../authzcache/DefaultAuthzCacheManager.java | 105 +
.../security/interceptor/SecurityCheck.java} | 34 +-
.../security/interceptor/SecurityInterceptor.java | 83 +
.../security/interceptor/SecurityModule.java} | 28 +-
.../SharingRegistryServiceClientFactory.java | 45 +
.../registry/db/entities/DomainEntity.java} | 67 +-
.../registry/db/entities/EntityEntity.java} | 145 +-
.../sharing/registry/db/entities/EntityPK.java} | 31 +-
.../registry/db/entities/EntityTypeEntity.java} | 71 +-
.../registry/db/entities}/EntityTypePK.java | 6 +-
.../registry/db/entities/GroupAdminEntity.java | 98 +
.../registry/db/entities/GroupAdminPK.java} | 49 +-
.../db/entities/GroupMembershipEntity.java} | 91 +-
.../registry/db/entities/GroupMembershipPK.java} | 55 +-
.../db/entities/PermissionTypeEntity.java} | 68 +-
.../registry/db/entities}/PermissionTypePK.java | 6 +-
.../registry/db/entities/SharingEntity.java} | 101 +-
.../sharing/registry/db/entities}/SharingPK.java | 12 +-
.../sharing/registry/db/entities/UserEntity.java} | 79 +-
.../registry/db/entities/UserGroupEntity.java | 180 +
.../sharing/registry/db/entities}/UserGroupPK.java | 45 +-
.../sharing/registry/db/entities/UserPK.java} | 28 +-
.../db/repositories/AbstractRepository.java | 163 +
.../db/repositories/DomainRepository.java} | 26 +-
.../registry/db/repositories/EntityRepository.java | 191 +
.../db/repositories/EntityTypeRepository.java} | 18 +-
.../db/repositories/GroupAdminRepository.java} | 26 +-
.../db/repositories/GroupMembershipRepository.java | 120 +
.../db/repositories/PermissionTypeRepository.java | 52 +
.../db/repositories/SharingRepository.java | 120 +
.../db/repositories/UserGroupRepository.java | 108 +
.../registry/db/repositories/UserRepository.java | 92 +
.../sharing/registry/db/utils/Committer.java} | 12 +-
.../sharing/registry/db/utils/DBConstants.java} | 20 +-
.../sharing/registry/db/utils/JPAUtils.java} | 19 +-
.../registry/db/utils/ObjectMapperSingleton.java} | 28 +-
.../db/utils/SharingRegistryDBInitConfig.java} | 32 +-
.../db/utils/SharingRegistryJDBCConfig.java | 66 +
.../messaging/SharingServiceDBEventHandler.java | 392 +
.../SharingServiceDBEventMessagingFactory.java | 111 +
.../migrator/airavata/AiravataDataMigrator.java | 946 +++
.../migrator/airavata/ConnectionFactory.java | 65 +
.../sharing/registry/server/ServerMain.java | 106 +
.../registry/server/SharingRegistryServer.java | 183 +
.../server/SharingRegistryServerHandler.java | 1340 ++++
.../sharing/registry/utils/Constants.java} | 25 +-
.../registry/utils/ThriftDataModelConversion.java} | 29 +-
.../src/main/resources/META-INF/persistence.xml | 203 +
.../src/main/resources/airavata-server.properties | 199 +
.../main/resources/distribution/bin/controller.sh | 26 +
.../resources/distribution/bin/email-monitor.sh | 26 +
.../resources/distribution/bin/orchestrator.sh | 54 +
.../main/resources/distribution/bin/parser-wm.sh | 26 +
.../main/resources/distribution/bin/participant.sh | 26 +
.../src/main/resources/distribution/bin/post-wm.sh | 26 +
.../src/main/resources/distribution/bin/pre-wm.sh | 26 +
.../resources/distribution/bin/realtime-monitor.sh | 26 +
.../src/main/resources/distribution/bin/setenv.sh | 146 +
.../resources/distribution/bin/sharing-registry.sh | 26 +
.../src/main/resources/distribution/conf/.gitkeep | 0
airavata-api/src/main/resources/dozer_mapping.xml | 68 +
airavata-api/src/main/resources/email-config.yaml | 29 +
airavata-api/src/main/resources/log4j2.xml | 39 +
.../main/resources/templates/CLOUD_Groovy.template | 33 +
.../main/resources/templates/FORK_Groovy.template | 13 +
.../resources/templates/HTCONDOR_Groovy.template | 33 +
.../main/resources/templates/LSF_Groovy.template | 30 +
.../main/resources/templates/PBS_Groovy.template | 35 +
.../main/resources/templates/SLURM_Groovy.template | 0
.../main/resources/templates/UGE_Groovy.template | 31 +
.../SSHAccountProvisionerFactoryTest.java | 82 +
.../provisioner/TestSSHAccountProvisioner.java | 69 +
.../TestSSHAccountProvisionerProvider.java | 78 +
.../common/utils/ApplicationSettingsTest.java} | 15 +-
.../airavata/common/utils/DerbyTestUtil.java | 452 ++
.../airavata/common/utils/SecurityUtilTest.java | 78 +
.../common/utils/ThriftClientPoolTest.java | 223 +
.../store/cpi/SSHSummaryTest/SSHSummaryTest.java | 189 +
.../store/notifier/impl/EmailNotifierTest.java | 51 +
.../store/store/impl/db/CommunityUserDAOTest.java | 192 +
.../store/store/impl/db/CredentialsDAOTest.java | 464 ++
.../store/store/impl/db/SSHCredentialTest.java | 84 +
.../store/util/ConfigurationReaderTest.java | 58 +
.../credential/store/util/TokenGeneratorTest.java} | 18 +-
.../apache/airavata/helix/SFTPDeleteDirTest.java | 177 +
.../GroupComputeResourcePreferenceUtilTest.java | 141 +
.../client/OrchestratorClientFactoryTest.java | 75 +
.../orchestrator/core/BaseOrchestratorTest.java | 83 +
.../orchestrator/core/NewOrchestratorTest.java | 99 +
.../core/OrchestratorTestWithGRAM.java | 79 +
.../core/OrchestratorTestWithMyProxyAuth.java | 83 +
.../core/repositories/WorkspaceRepositoryTest.java | 175 +
.../ApplicationDeploymentRepositoryTest.java | 396 +
.../ApplicationInterfaceRepositoryTest.java | 641 ++
.../appcatalog/ComputeResourceRepositoryTest.java | 675 ++
.../appcatalog}/GatewayGroupsRepositoryTest.java | 69 +-
.../appcatalog/GatewayProfileRepositoryTest.java | 157 +
.../GroupResourceProfileRepositoryTest.java | 554 ++
.../JobSubmissionInterfaceRepositoryTest.java | 87 +
.../appcatalog/StorageResourceRepositoryTest.java | 140 +
.../UserResourceProfileRepositoryTest.java | 114 +
.../core/repositories/common/DerbyTestUtil.java | 454 ++
.../core/repositories/common/TestBase.java | 98 +
.../expcatalog/ExperimentErrorRepositoryTest.java | 97 +
.../expcatalog/ExperimentInputRepositoryTest.java | 108 +
.../expcatalog/ExperimentOutputRepositoryTest.java | 110 +
.../expcatalog/ExperimentRepositoryTest.java | 277 +
.../expcatalog/ExperimentStatusRepositoryTest.java | 113 +
.../ExperimentSummaryRepositoryTest.java | 325 +
.../expcatalog/GatewayRepositoryTest.java | 79 +
.../repositories/expcatalog/JobRepositoryTest.java | 139 +
.../expcatalog/JobStatusRepositoryTest.java | 132 +
.../expcatalog/NotificationRepositoryTest.java | 67 +
.../expcatalog/ProcessErrorRepositoryTest.java | 104 +
.../expcatalog/ProcessInputRepositoryTest.java | 110 +
.../expcatalog/ProcessOutputRepositoryTest.java | 110 +
.../expcatalog/ProcessRepositoryTest.java | 166 +
.../expcatalog/ProcessStatusRepositoryTest.java | 123 +
.../expcatalog/ProjectRepositoryTest.java | 103 +
.../expcatalog/QueueStatusRepositoryTest.java | 61 +
.../expcatalog/TaskErrorRepositoryTest.java | 115 +
.../expcatalog/TaskRepositoryTest.java | 122 +
.../expcatalog/TaskStatusRepositoryTest.java | 112 +
.../expcatalog}/UserRepositoryTest.java | 78 +-
.../replicacatalog/DataProductRepositoryTest.java | 143 +
.../DataReplicaLocationRepositoryTest.java | 115 +
.../workflowcatalog/WorkflowRepositoryTest.java | 171 +
.../registry/core/utils/CustomBeanFactoryTest.java | 58 +
.../core/utils/ObjectMapperSingletonTest.java | 69 +
.../AuthenticatorConfigurationReaderTest.java | 104 +
.../configurations/TestDBAuthenticator1.java | 55 +
.../configurations/TestDBAuthenticator2.java | 56 +
.../configurations/TestDBAuthenticator3.java | 55 +
.../security/configurations/TestUserStore.java} | 25 +-
.../security/userstore/JDBCUserStoreTest.java | 97 +
.../security/userstore/LDAPUserStoreTest.java | 64 +
.../security/userstore/SessionDBUserStoreTest.java | 93 +
.../admin/services/core/tests/SetupNewGateway.java | 169 +
.../security/GatewayGroupsInitializerTest.java | 131 +
.../security/KeyCloakSecurityManagerTest.java | 369 +
.../airavata/sharing/registry/CipresTest.java | 646 ++
.../registry/SharingRegistryServerHandlerTest.java | 486 ++
.../registry/SharingRegistryServiceTest.java | 432 ++
airavata-api/src/test/resources/PBSTemplate.xslt | 77 +
.../src/test/resources/airavata-server.properties | 72 +
airavata-api/src/test/resources/authenticators.xml | 88 +
.../src/test/resources/disabled-authenticator.xml | 84 +
.../src/test/resources/gsissh.properties | 20 +-
.../src/test/resources/jdbc-authenticator.xml | 39 +
.../src/test/resources/ldap-authenticator.xml | 41 +
airavata-api/src/test/resources/log4j2.xml | 52 +
.../src/test/resources/monitor.properties | 26 +-
.../src/test/resources/orchestrator.properties | 19 +-
.../src/test/resources/session-authenticator.xml | 44 +
airavata-api/src/test/resources/zoo.cfg | 22 +
...ader-java.txt => apache-license-header-java.txt | 0
...header-xml.txt => apache-license-header-xml.txt | 0
...license-header.txt => apache-license-header.txt | 0
conf/keycloak/setup-keycloak.sh | 429 --
.../models}/AgentAsyncCommandExecutionRequest.java | 2 +-
.../AgentAsyncCommandExecutionResponse.java | 2 +-
.../models}/AgentAsyncCommandListRequest.java | 2 +-
.../models}/AgentAsyncCommandListResponse.java | 2 +-
.../models}/AgentAsyncCommandTerminateRequest.java | 2 +-
.../AgentAsyncCommandTerminateResponse.java | 2 +-
.../service/models}/AgentCommandExecutionAck.java | 2 +-
.../models}/AgentCommandExecutionRequest.java | 2 +-
.../models}/AgentCommandExecutionResponse.java | 2 +-
.../service/models}/AgentEnvSetupAck.java | 2 +-
.../service/models}/AgentEnvSetupRequest.java | 2 +-
.../service/models}/AgentEnvSetupResponse.java | 2 +-
.../service/models}/AgentInfoResponse.java | 2 +-
.../service/models}/AgentJupyterExecutionAck.java | 2 +-
.../models}/AgentJupyterExecutionRequest.java | 2 +-
.../models}/AgentJupyterExecutionResponse.java | 2 +-
.../service/models}/AgentKernelRestartAck.java | 2 +-
.../service/models}/AgentKernelRestartRequest.java | 2 +-
.../models}/AgentKernelRestartResponse.java | 2 +-
.../service/models}/AgentLaunchRequest.java | 2 +-
.../service/models}/AgentLaunchResponse.java | 2 +-
.../service/models}/AgentPythonExecutionAck.java | 2 +-
.../models}/AgentPythonExecutionRequest.java | 2 +-
.../models}/AgentPythonExecutionResponse.java | 2 +-
.../service/models}/AgentTerminateResponse.java | 2 +-
.../connection/service/models}/AgentTunnelAck.java | 2 +-
.../service/models}/AgentTunnelCreateRequest.java | 2 +-
.../service/models}/AgentTunnelCreateResponse.java | 2 +-
.../models}/AgentTunnelTerminateRequest.java | 2 +-
.../connection/service/models}/AsyncCommand.java | 2 +-
.../connection/service/models}/DirectoryInfo.java | 2 +-
.../service/models}/ExperimentStorageResponse.java | 2 +-
.../agent/connection/service/models}/FileInfo.java | 12 +-
.../file/server}/model/AiravataDirectory.java | 5 +-
.../airavata/file/server}/model/AiravataFile.java | 9 +-
.../file/server}/model/FileUploadResponse.java | 2 +-
.../service/dto}/CreateProjectRequest.java | 10 +-
.../research/service/dto}/RedirectResponse.java | 2 +-
airavata-api/pom.xml => pom.xml | 639 +-
1236 files changed, 104304 insertions(+), 68319 deletions(-)
rename {conf => .devcontainer}/keycloak/keycloak.conf (77%)
delete mode 100644 airavata-api/.dockerignore
delete mode 100644 airavata-api/.mvn/extensions.xml
delete mode 100644 airavata-api/.mvn/jvm.config
delete mode 100644 airavata-api/.mvn/maven-build-cache-config.xml
delete mode 100644 airavata-api/.mvn/wrapper/maven-wrapper.properties
delete mode 100644 airavata-api/README.md
delete mode 100755 airavata-api/examples/hello-world-experiment.sh
delete mode 100644 airavata-api/modules/airavata-api/pom.xml
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/entity/AllocationProjectEntity.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/entity/CredentialAllocationProjectEntity.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/entity/CredentialAllocationProjectPK.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/mapper/AllocationProjectMapper.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/model/AllocationProject.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/model/CredentialAllocationProject.java
delete mode 100644 airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/accounting/repository/AllocationProjectRepository.java
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create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisioner.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisionerFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisionerProvider.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisionerProvider.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/agents/api/AdaptorParams.java} (55%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GranteeType.java => src/main/java/org/apache/airavata/agents/api/Agent.java} (84%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/protocol/AgentAdapter.java => src/main/java/org/apache/airavata/agents/api/AgentAdaptor.java} (59%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/AiravataSecurityException.java => src/main/java/org/apache/airavata/agents/api/AgentException.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/api/AgentUtils.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/agents/api/CommandOutput.java} (77%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/file/model/FileUploadResponse.java => src/main/java/org/apache/airavata/agents/api/FileMetadata.java} (67%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/api/JobSubmissionOutput.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/api/StorageResourceAdaptor.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandListResponse.java => src/main/java/org/apache/airavata/agents/streaming/TransferResult.java} (50%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/streaming/VirtualInputStream.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/streaming/VirtualOutputStream.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/agents/streaming/VirtualStreamProducer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/api/client/AiravataClientFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/api/server/AiravataAPIServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/api/server/util/Constants.java} (73%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/cluster/monitoring/ClusterStatusMonitorJob.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/cluster/monitoring/ClusterStatusMonitorJobScheduler.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/common/context/RequestContext.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/context/WorkflowContext.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentKernelRestartRequest.java => src/main/java/org/apache/airavata/common/exception/AiravataConfigurationException.java} (65%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/session/model/SessionStatus.java => src/main/java/org/apache/airavata/common/exception/AiravataException.java} (69%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/AiravataSecurityException.java => src/main/java/org/apache/airavata/common/exception/AiravataStartupException.java} (59%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/DirectoryInfo.java => src/main/java/org/apache/airavata/common/exception/ApplicationSettingsException.java} (68%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/logging/Exception.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/DirectoryInfo.java => src/main/java/org/apache/airavata/common/logging/MDCConstants.java} (67%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/config/ClusterApplicationConfiguration.java => src/main/java/org/apache/airavata/common/logging/MDCUtil.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/AiravataJobState.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/model/NotificationPriority.java => src/main/java/org/apache/airavata/common/utils/AiravataUtils.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/Constants.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DBEventManagerConstants.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RolesRepresentation.java => src/main/java/org/apache/airavata/common/utils/DBEventService.java} (66%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/SecurityProtocol.java => src/main/java/org/apache/airavata/common/utils/DBInitConfig.java} (79%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DBInitializer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DBUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DatabaseCreator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/util/EnumUtil.java => src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java} (50%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/Privacy.java => src/main/java/org/apache/airavata/common/utils/ExecutionMode.java} (88%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/IOUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/IServer.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/ResourceType.java => src/main/java/org/apache/airavata/common/utils/JDBCConfig.java} (79%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/JPAUtils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/JSONUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentEnvSetupResponse.java => src/main/java/org/apache/airavata/common/utils/LocalEventPublisher.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/NameValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/Pair.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/credential/util => src/main/java/org/apache/airavata/common/utils}/SecurityUtil.java (76%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/ServerSettings.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/StringUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/SwingUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/ThriftClientPool.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/Version.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/common/utils/WSConstants.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/common/utils/ZkConstants.java} (57%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/compute/resource/monitoring/ComputationalResourceMonitoringService.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/compute/resource/monitoring/job/ComputeResourceMonitor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/compute/resource/monitoring/job/MonitoringJob.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/service/KeycloakLogoutService.java => src/main/java/org/apache/airavata/compute/resource/monitoring/job/output/OutputParser.java} (67%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/compute/resource/monitoring/job/output/OutputParserImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/compute/resource/monitoring/utils/Constants.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/client/CredentialStoreClientFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMemberRole.java => src/main/java/org/apache/airavata/credential/store/credential/AuditInfo.java} (54%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/credential/model => src/main/java/org/apache/airavata/credential/store/credential}/CommunityUser.java (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/credential/Credential.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationScope.java => src/main/java/org/apache/airavata/credential/store/credential/CredentialOwnerType.java} (83%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/credential/impl/certificate/CertificateAuditInfo.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/credential/impl/certificate/CertificateCredential.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RoleRepresentation.java => src/main/java/org/apache/airavata/credential/store/credential/impl/password/PasswordCredential.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/notifier/CredentialStoreNotifier.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/SharingRegistryException.java => src/main/java/org/apache/airavata/credential/store/notifier/NotificationMessage.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/notifier/NotifierBootstrap.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/CredentialRepresentation.java => src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotificationMessage.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotifier.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotifierConfiguration.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/CredentialReader.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/CredentialReaderFactory.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/credential/exception => src/main/java/org/apache/airavata/credential/store/store}/CredentialStoreException.java (71%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/ComputeResourceType.java => src/main/java/org/apache/airavata/credential/store/store/CredentialWriter.java} (63%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/CertificateCredentialWriter.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/CredentialReaderImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/SSHCredentialWriter.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CommunityUserDAO.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CredentialsDAO.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/SecurityProtocol.java => src/main/java/org/apache/airavata/credential/store/store/impl/db/ParentDAO.java} (72%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreDBInitConfig.java} (60%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreJDBCConfig.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/util/ConfigurationReader.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/credential/store/util/CredentialStoreConstants.java} (59%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/util/PrivateKeyStore.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactType.java => src/main/java/org/apache/airavata/credential/store/util/TokenGenerator.java} (58%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/credential/store/util/Utility.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/db/event/manager/DBEventManagerRunner.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/OrchestratorException.java => src/main/java/org/apache/airavata/db/event/manager/messaging/DBEventManagerException.java} (71%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/db/event/manager/messaging/DBEventManagerMessagingFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/db/event/manager/messaging/impl/DBEventMessageHandler.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobSubmissionProtocol.java => src/main/java/org/apache/airavata/db/event/manager/utils/Constants.java} (81%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/db/event/manager/utils/DbEventManagerZkUtils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/PoolingSSHJClient.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/SSHJAgentAdaptor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/SSHJStorageAdaptor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SCPFileTransferWrapper.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SFTPClientWrapper.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/IamAdminServicesException.java => src/main/java/org/apache/airavata/helix/adaptor/wrapper/SSHClientWrapper.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SessionWrapper.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/agent/ssh/SSHUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/agent/ssh/SshAdaptorParams.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/agent/ssh/SshAgentAdaptor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/agent/ssh/StandardOutReader.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/agent/storage/StorageResourceAdaptorImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/AbstractTask.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/protocol/AdapterSupport.java => src/main/java/org/apache/airavata/helix/core/OutPort.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/participant/HelixParticipant.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/service/KeycloakLogoutService.java => src/main/java/org/apache/airavata/helix/core/support/TaskHelperImpl.java} (65%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/support/adaptor/AdaptorSupportImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/support/adaptor/AgentStore.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/util/MonitoringUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/util/PropertyResolver.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/core/util/TaskUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/controller/HelixController.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/controller/WorkflowCleanupAgent.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/AWSTaskFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/AiravataTask.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/submission/JobManagerSpec.java => src/main/java/org/apache/airavata/helix/impl/task/HelixTaskFactory.java} (58%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/SlurmTaskFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/TaskContext.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactType.java => src/main/java/org/apache/airavata/helix/impl/task/TaskFactory.java} (53%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/TaskFailureException.java => src/main/java/org/apache/airavata/helix/impl/task/TaskOnFailException.java} (86%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/AWSCompletingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/AWSJobSubmissionTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/AWSProcessContextManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/CreateEC2InstanceTask.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/TaskFailureException.java => src/main/java/org/apache/airavata/helix/impl/task/aws/NoOperationTask.java} (57%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/utils/AWSTaskUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/aws/utils/ExponentialBackoffWaiter.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/cancel/CancelCompletingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/cancel/RemoteJobCancellationTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/cancel/WorkflowCancellationTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/helix/impl/task/mock/MockTask.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/parsing/DataParsingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/parsing/ParsingTriggeringTask.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/workflow/model/WorkflowRunStepState.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/ProcessCompletionMessage.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/parsing/kafka/ProcessCompletionMessageDeserializer.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/mapper/JobMapper.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/kafka/ProcessCompletionMessageSerializer.java} (54%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/CredentialRepresentation.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskInput.java} (63%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentEnvSetupRequest.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskInputs.java} (52%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RoleRepresentation.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskOutput.java} (54%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentEnvSetupRequest.java => src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskOutputs.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/staging/ArchiveTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/staging/JobVerificationTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobManagerConfiguration.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/submission/JobOutputParser.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/OutputParser.java} (79%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/submission => src/main/java/org/apache/airavata/helix/impl/task/submission/config}/RawCommandInfo.java (94%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/DirectoryInfo.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java} (67%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/CloudJobManagerConfiguration.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/local/LocalJobSpec.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java} (57%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/slurm/SlurmJobSpec.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/HTCondorJobConfiguration.java} (50%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/submission/JobStateParser.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java} (81%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/local/LocalOutputParser.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java} (57%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/local/LocalOutputParser.java => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/HTCondorOutputParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/slurm => src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser}/SlurmOutputParser.java (65%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/workflow/ParserWorkflowManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/impl/workflow/WorkflowManager.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/helix/task/api/TaskHelper.java} (74%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupType.java => src/main/java/org/apache/airavata/helix/task/api/TaskParamType.java} (83%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMemberRole.java => src/main/java/org/apache/airavata/helix/task/api/annotation/TaskDef.java} (65%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMemberRole.java => src/main/java/org/apache/airavata/helix/task/api/annotation/TaskOutPort.java} (65%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/activity/JobStatusHandler.java => src/main/java/org/apache/airavata/helix/task/api/annotation/TaskParam.java} (61%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/protocol/AdapterSupport.java => src/main/java/org/apache/airavata/helix/task/api/support/AdaptorSupport.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/workflow/QueueOperator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/helix/workflow/WorkflowOperator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/client/RabbitMQListener.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/client/TestReader.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/MessageContext.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupCardinality.java => src/main/java/org/apache/airavata/messaging/core/MessageHandler.java} (83%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/monitoring/JobStatusResult.java => src/main/java/org/apache/airavata/messaging/core/MessagingConstants.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/MessagingFactory.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/monitoring/JobStatusResult.java => src/main/java/org/apache/airavata/messaging/core/Publisher.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/RabbitMQProperties.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/Subscriber.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/TestClient.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactState.java => src/main/java/org/apache/airavata/messaging/core/Type.java} (87%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/ExperimentConsumer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/MessageConsumer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/ProcessConsumer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQPublisher.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQSubscriber.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/impl/StatusConsumer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/stats/CountWriterTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/stats/LatencyWriterTask.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/stats/StatCounter.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/messaging/core/util/DBEventPublisherUtils.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMemberRole.java => src/main/java/org/apache/airavata/metascheduler/core/api/ProcessScheduler.java} (51%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/submission/JobManagerSpec.java => src/main/java/org/apache/airavata/metascheduler/core/engine/ComputeResourceSelectionPolicy.java} (57%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactState.java => src/main/java/org/apache/airavata/metascheduler/core/engine/DataAnalyzer.java} (86%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/model/SearchCondition.java => src/main/java/org/apache/airavata/metascheduler/core/engine/ProcessScanner.java} (77%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMemberRole.java => src/main/java/org/apache/airavata/metascheduler/core/engine/ReScheduler.java} (70%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/core/utils/Utils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/DataInterpreterService.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/impl/DataAnalyzerImpl.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobManagerCommand.java => src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/utils/Constants.java} (70%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/api/ProcessSchedulerImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/ComputeResourceSelectionPolicyImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/DefaultComputeResourceSelectionPolicy.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/MultipleComputeResourcePolicy.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ExponentialBackOffReScheduler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ProcessReschedulingService.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ProcessScannerImpl.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobManagerCommand.java => src/main/java/org/apache/airavata/metascheduler/process/scheduling/utils/Constants.java} (70%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/model/util/AppDeploymentUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/model/util/AppInterfaceUtil.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/status/model/EventKind.java => src/main/java/org/apache/airavata/model/util/ExecutionType.java} (87%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/model/util/ExperimentModelUtil.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/model/util/GroupComputeResourcePreferenceUtil.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/model/util/ProjectModelUtil.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/AbstractMonitor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/JobStateValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/JobStatusResult.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/AiravataSecurityException.java => src/main/java/org/apache/airavata/monitor/MonitoringException.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java} (55%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/slurm => src/main/java/org/apache/airavata/monitor/email/parser}/ResourceConfig.java (92%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/provider/slurm => src/main/java/org/apache/airavata/monitor/email/parser}/SLURMEmailParser.java (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/kafka/JobStatusResultDeserializer.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/entity/DatasetArtifactEntity.java => src/main/java/org/apache/airavata/monitor/kafka/JobStatusResultSerializer.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/kafka/MessageProducer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/realtime/RealtimeMonitor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/monitor/realtime/parser/RealtimeJobStatusParser.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactory.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/workflow/model/WorkflowEdgeMapping.java => src/main/java/org/apache/airavata/orchestrator/core/OrchestratorConfiguration.java} (53%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/orchestrator/core/context/OrchestratorContext.java} (53%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration => src/main/java/org/apache/airavata/orchestrator/core/exception}/OrchestratorException.java (87%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/job/JobSubmitter.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/service/JobService.java => src/main/java/org/apache/airavata/orchestrator/core/schedule/DefaultHostScheduler.java} (60%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/service/CrudService.java => src/main/java/org/apache/airavata/orchestrator/core/schedule/HostScheduler.java} (61%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/protocol/ResourceLookup.java => src/main/java/org/apache/airavata/orchestrator/core/utils/OrchestratorConstants.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/utils/OrchestratorUtils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/validator/JobMetadataValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/BatchQueueValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/ExperimentStatusValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/GroupResourceProfileValidator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/cpi/Orchestrator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/cpi/impl/SimpleOrchestratorImpl.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/sample/OrchestratorClientSample.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobManagerCommand.java => src/main/java/org/apache/airavata/orchestrator/util/Constants.java} (69%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorServerThreadPoolExecutor.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorUtils.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/UserContext.java => src/main/java/org/apache/airavata/patform/monitoring/CountMonitor.java} (50%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateResponse.java => src/main/java/org/apache/airavata/patform/monitoring/GaugeMonitor.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/patform/monitoring/MonitoringServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/api/client/RegistryServiceClientFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/api/service/RegistryAPIServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/api/service/messaging/RegistryServiceDBEventHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/api/service/messaging/RegistryServiceDBEventMessagingFactory.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AsyncCommand.java => src/main/java/org/apache/airavata/registry/api/service/util/Constants.java} (54%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/registry/core/RegistryException.java} (76%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowErrorEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowErrorPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowStatusEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowStatusPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationErrorEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationErrorPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationStatusEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationStatusPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerErrorEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerErrorPK.java} (52%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInput.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerInputEntity.java} (58%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/project/model/CreateProjectRequest.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerInputPK.java} (54%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationOutput.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerOutputEntity.java} (60%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/project/model/CreateProjectRequest.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerOutputPK.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerStatusEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RoleRepresentation.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerStatusPK.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowApplicationEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/storage/resource/model/StorageDirectoryInfo.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowApplicationPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowConnectionEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/AgentExecutionEntity.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowConnectionPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowDataBlockEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowHandlerEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RoleRepresentation.java => src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowHandlerPK.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AWSGroupComputeResourcePrefEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppEnvironmentEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/project/model/CreateProjectRequest.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppEnvironmentPK.java} (50%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppModuleMappingEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppModuleMappingPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationDeploymentEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInput.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInputEntity.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInputPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInterfaceDescription.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationModuleEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationOutput.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputEntity.java} (63%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueueEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueuePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueueResourcePolicyEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/CloudJobSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceFileSystemEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceFileSystemPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePolicyEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePreferenceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePreferencePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceReservationEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/DataMovementInterfaceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/DataMovementInterfacePK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/gateway/model/GatewayGroups.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GatewayGroupsEntity.java} (66%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GatewayProfileEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusGkEndpointEntity.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusGkEndpointPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpDataMovementEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpEndpointEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpEndpointPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupComputeResourcePrefEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupComputeResourcePrefPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupResourceProfileEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupSSHAccountProvisionerConfig.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupSSHAccountProvisionerConfigPK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/IamAdminServicesException.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshExportEntity.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshExportPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/credential/exception/CredentialStoreException.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPostjobcommandEntity.java} (50%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPostjobcommandPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/IamAdminServicesException.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPrejobcommandEntity.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPrejobcommandPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobManagerCommandEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobManagerCommandPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobSubmissionInterfaceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobSubmissionInterfacePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryApendPathEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/project/model/CreateProjectRequest.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryAppendPathPK.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryPrependPathEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/project/model/CreateProjectRequest.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryPrependPathPK.java} (50%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/entity/TagEntity.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java} (57%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ModuleLoadCmdEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ModuleLoadCmdPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParallelismCommandEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParallelismCommandPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserConnectorEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserConnectorInputEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserInputEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserOutputEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParsingTemplateEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParsingTemplateInputEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PostjobCommandEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PostjobCommandPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PrejobCommandEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PrejobCommandPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ResourceJobManagerEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SSHAccountProvisionerConfiguration.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SSHAccountProvisionerConfigurationPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ScpDataMovementEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SlurmGroupComputeResourcePrefEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SshJobSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageInterfaceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageInterfacePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StoragePreferenceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StoragePreferencePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageResourceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UnicoreDatamovementEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UnicoreSubmissionEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferenceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferencePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserResourceProfileEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserResourceProfilePK.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferenceEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferencePK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/ComputationalResourceScheduling.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ComputationalResourceSchedulingEntity.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ComputationalResourceSchedulingPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentErrorEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentErrorPK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInput.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentInputEntity.java} (63%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentInputPK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationOutput.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentOutputEntity.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentOutputPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentStatusPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/entity => src/main/java/org/apache/airavata/registry/core/entities/expcatalog}/ExperimentSummaryEntity.java (60%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/ComputeSubmissionTrackingEntity.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayUsageReportingCommandEntity.java} (55%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/UserGroupPK.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayUsageReportingPK.java} (50%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayWorkerEntity.java} (53%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/UserGroupPK.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayWorkerPK.java} (50%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/entity => src/main/java/org/apache/airavata/registry/core/entities/expcatalog}/JobEntity.java (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobStatusPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/entity => src/main/java/org/apache/airavata/registry/core/entities/expcatalog}/NotificationEntity.java (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessErrorEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessErrorPK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInput.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessInputEntity.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessInputPK.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationOutput.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessOutputEntity.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessOutputPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/ComputationalResourceScheduling.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessResourceScheduleEntity.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessStatusPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessWorkflowEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessWorkflowPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectUserEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectUserPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/QueueStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/QueueStatusPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskErrorEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskErrorPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskStatusPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserConfigurationDataEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserEntity.java} (53%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/entity/PlanEntity.java => src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserPK.java} (62%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/ConfigurationEntity.java} (53%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/ConfigurationPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductMetadataEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductMetadataPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaLocationEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaMetadataEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaMetadataPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/ComponentStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/EdgeEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/EdgePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/NodeEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/NodePK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/PortEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/PortPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationInput.java => src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowInputEntity.java} (62%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowInputPK.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationOutput.java => src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowOutputEntity.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowOutputPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowStatusEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowStatusPK.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/AbstractRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/mapper/JobMapper.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/AppCatAbstractRepository.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInputRepository.java} (58%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationModuleRepository.java} (62%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateResponse.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationOutputRepository.java} (58%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/BatchQueuePolicyRepository.java} (58%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/BatchQueueRepository.java} (61%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourcePolicyRepository.java} (59%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourcePrefRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourceRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/DataMovementRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GatewayGroupsRepository.java} (64%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GroupResourceProfileRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GrpComputePrefRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GwyResourceProfileRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/JobSubmissionInterfaceRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserInputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserOutputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParsingTemplateRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ResourceJobManagerRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/StoragePrefRepository.java} (58%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/StorageResourceRepository.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/service/KeycloakAdminTokenResolver.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserComputeResourcePreferenceRepository.java} (55%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandListRequest.java => src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserStoragePreferenceRepository.java} (56%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/mapper/JobMapper.java => src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExpCatAbstractRepository.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentErrorRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentInputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentOutputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentStatusRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentSummaryRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/GatewayRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/GatewayUsageReportingCommandRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobStatusRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/NotificationRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessErrorRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessInputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessOutputRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessStatusRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessWorkflowRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProjectRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/QueueStatusRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskErrorRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskStatusRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/UserRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataProductRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataReplicaLocationRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/mapper/JobMapper.java => src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/RepCatAbstractRepository.java} (56%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/mapper/JobMapper.java => src/main/java/org/apache/airavata/registry/core/repositories/workflowcatalog/WorkflowCatAbstractRepository.java} (55%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/repositories/workflowcatalog/WorkflowRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/AppCatalogDBInitConfig.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/AppCatalogJDBCConfig.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/registry/core/utils/AppCatalogUtils.java} (75%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupChildType.java => src/main/java/org/apache/airavata/registry/core/utils/Committer.java} (86%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/CustomBeanFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/DBConstants.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/DozerConverter/CsvStringConverter.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/model/NotificationPriority.java => src/main/java/org/apache/airavata/registry/core/utils/DozerConverter/StorageDateConverter.java} (50%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogDBInitConfig.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogJDBCConfig.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobState.java => src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogUtils.java} (75%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/AppCatalogJPAUtils.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandListRequest.java => src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/ExpCatalogJPAUtils.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/RepCatalogJPAUtils.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/WorkflowCatalogJPAUtils.java} (51%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/registry/core/utils/ObjectMapperSingleton.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/QueryConstants.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/entity/RepositoryArtifactEntity.java => src/main/java/org/apache/airavata/registry/core/utils/ReplicaCatalogDBInitConfig.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/ReplicaCatalogJDBCConfig.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/entity/NotebookArtifactEntity.java => src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogDBInitConfig.java} (52%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogJDBCConfig.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ModifyArtifactRequest.java => src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogUtils.java} (75%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/migration/MappingToolRunner.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/core/utils/migration/MigrationSchemaGenerator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/AppCatalog.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/OrchestratorException.java => src/main/java/org/apache/airavata/registry/cpi/AppCatalogException.java} (71%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ApplicationDeployment.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ApplicationInterface.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/CompositeIdentifier.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ComputeResource.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/DataProductInterface.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/ComputeSubmissionTrackingRepository.java => src/main/java/org/apache/airavata/registry/cpi/DataReplicaLocationInterface.java} (55%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/repository/PlanRepository.java => src/main/java/org/apache/airavata/registry/cpi/ExpCatChildDataType.java} (66%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/model/TaskState.java => src/main/java/org/apache/airavata/registry/cpi/ExpCatParentDataType.java} (79%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalog.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/OrchestratorException.java => src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalogException.java} (71%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/application/model/ApplicationScope.java => src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalogModelType.java} (59%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentKernelRestartRequest.java => src/main/java/org/apache/airavata/registry/cpi/GwyClientCredential.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/GwyResourceProfile.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ModifyArtifactRequest.java => src/main/java/org/apache/airavata/registry/cpi/Registry.java} (65%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/OrchestratorException.java => src/main/java/org/apache/airavata/registry/cpi/RegistryException.java} (71%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ReplicaCatalog.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/Tag.java => src/main/java/org/apache/airavata/registry/cpi/ReplicaCatalogException.java} (69%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/ResultOrderType.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/StorageResource.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/UsrResourceProfile.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/registry/cpi/WorkflowCatalog.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/orchestration/OrchestratorException.java => src/main/java/org/apache/airavata/registry/cpi/WorkflowCatalogException.java} (71%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/util => src/main/java/org/apache/airavata/registry/cpi/utils}/Constants.java (92%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GranteeType.java => src/main/java/org/apache/airavata/registry/cpi/utils/StatusType.java} (83%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/AbstractAuthenticator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/AbstractDatabaseAuthenticator.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception => src/main/java/org/apache/airavata/security}/AiravataSecurityException.java (96%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/exception/GroupManagerServiceException.java => src/main/java/org/apache/airavata/security/AuthenticationException.java} (70%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/Authenticator.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/execution/activity/JobStatusHandler.java => src/main/java/org/apache/airavata/security/Authoriser.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/UserStore.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/security/UserStoreException.java} (68%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/configurations/AbstractConfigurationReader.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/configurations/AuthenticatorConfigurationReader.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/userstore/AbstractJDBCUserStore.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/userstore/JDBCUserStore.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/userstore/LDAPUserStore.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/userstore/SessionDBUserStore.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/security/util/PasswordDigester.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/server/ServerMain.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/client/ProfileServiceClientFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/repositories/AbstractRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/tenant/entities/GatewayEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/user/entities/CustomizedDashboardEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/user/entities/NSFDemographicsEntity.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/user/entities/UserProfileEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactStatus.java => src/main/java/org/apache/airavata/service/profile/commons/utils/Committer.java} (85%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateResponse.java => src/main/java/org/apache/airavata/service/profile/commons/utils/JPAConstants.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/utils/JPAUtils.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/service/profile/commons/utils/ObjectMapperSingleton.java} (62%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentEnvSetupResponse.java => src/main/java/org/apache/airavata/service/profile/commons/utils/ProfileServiceJDBCConfig.java} (57%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/utils/QueryConstants.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/commons/utils/Utils.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/handlers/GroupManagerServiceHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/handlers/IamAdminServicesHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/handlers/TenantProfileServiceHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/handlers/UserProfileServiceHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/iam/admin/services/core/impl/TenantManagementKeycloakImpl.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/keycloak/GatewayManagement.java => src/main/java/org/apache/airavata/service/profile/iam/admin/services/core/interfaces/TenantManagementInterface.java} (76%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/server/ProfileServiceServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/tenant/core/repositories/TenantProfileRepository.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ModifyArtifactRequest.java => src/main/java/org/apache/airavata/service/profile/user/core/exceptions/UserProfileRegistryException.java} (73%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/profile/user/core/repositories/UserProfileRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/service/profile/user/core/utils/UserProfileCatalogDBInitConfig.java} (60%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentInfoResponse.java => src/main/java/org/apache/airavata/service/profile/user/core/utils/UserProfileCatalogJDBCConfig.java} (55%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/service/RequestAuthenticator.java => src/main/java/org/apache/airavata/service/security/AiravataSecurityManager.java} (88%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/GatewayGroupsInitializer.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/model/ArtifactType.java => src/main/java/org/apache/airavata/service/security/IdentityContext.java} (59%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/KeyCloakSecurityManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/SecurityManagerFactory.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model => src/main/java/org/apache/airavata/service/security}/UserInfo.java (97%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/AuthzCache.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/AuthzCacheEntry.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/AuthzCacheIndex.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/AuthzCacheManager.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/AuthzCacheManagerFactory.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/compute/resource/model/JobManagerCommand.java => src/main/java/org/apache/airavata/service/security/authzcache/AuthzCachedStatus.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/authzcache/DefaultAuthzCacheManager.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateResponse.java => src/main/java/org/apache/airavata/service/security/interceptor/SecurityCheck.java} (63%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/service/security/interceptor/SecurityInterceptor.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/core/exception/DuplicateEntryException.java => src/main/java/org/apache/airavata/service/security/interceptor/SecurityModule.java} (51%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/client/SharingRegistryServiceClientFactory.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/Domain.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/DomainEntity.java} (55%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/SharingEntity.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityEntity.java} (51%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/EntityTypePK.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityPK.java} (67%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/EntityType.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityTypeEntity.java} (51%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity => src/main/java/org/apache/airavata/sharing/registry/db/entities}/EntityTypePK.java (94%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupAdminEntity.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/PermissionTypePK.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupAdminPK.java} (59%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupMember.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupMembershipEntity.java} (53%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/GroupMemberPK.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupMembershipPK.java} (59%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/PermissionType.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/PermissionTypeEntity.java} (54%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity => src/main/java/org/apache/airavata/sharing/registry/db/entities}/PermissionTypePK.java (94%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/Sharing.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/SharingEntity.java} (56%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity => src/main/java/org/apache/airavata/sharing/registry/db/entities}/SharingPK.java (93%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/User.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/UserEntity.java} (58%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/entities/UserGroupEntity.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity => src/main/java/org/apache/airavata/sharing/registry/db/entities}/UserGroupPK.java (54%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/entity/EntityTypePK.java => src/main/java/org/apache/airavata/sharing/registry/db/entities/UserPK.java} (71%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/AbstractRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandTerminateRequest.java => src/main/java/org/apache/airavata/sharing/registry/db/repositories/DomainRepository.java} (61%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/EntityRepository.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandListRequest.java => src/main/java/org/apache/airavata/sharing/registry/db/repositories/EntityTypeRepository.java} (56%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentEnvSetupAck.java => src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupAdminRepository.java} (56%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/GroupChildType.java => src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java} (85%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/util/SharingDBConstants.java => src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java} (87%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentAsyncCommandListRequest.java => src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java} (54%)
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/agent/model/AgentCommandExecutionAck.java => src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java} (62%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/artifact/entity/DatasetArtifactEntity.java => src/main/java/org/apache/airavata/sharing/registry/db/utils/SharingRegistryDBInitConfig.java} (54%)
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/db/utils/SharingRegistryJDBCConfig.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/messaging/SharingServiceDBEventHandler.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/messaging/SharingServiceDBEventMessagingFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/migrator/airavata/AiravataDataMigrator.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/migrator/airavata/ConnectionFactory.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/server/ServerMain.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.java
create mode 100644 airavata-api/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServerHandler.java
copy airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/model/ResultOrderType.java => src/main/java/org/apache/airavata/sharing/registry/utils/Constants.java} (58%)
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/research/experiment/model/ResultOrderType.java => src/main/java/org/apache/airavata/sharing/registry/utils/ThriftDataModelConversion.java} (51%)
create mode 100644 airavata-api/src/main/resources/META-INF/persistence.xml
create mode 100644 airavata-api/src/main/resources/airavata-server.properties
create mode 100755 airavata-api/src/main/resources/distribution/bin/controller.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/email-monitor.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/orchestrator.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/parser-wm.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/participant.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/post-wm.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/pre-wm.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/realtime-monitor.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/setenv.sh
create mode 100755 airavata-api/src/main/resources/distribution/bin/sharing-registry.sh
copy airavata-python-sdk/__init__.py => airavata-api/src/main/resources/distribution/conf/.gitkeep (100%)
create mode 100644 airavata-api/src/main/resources/dozer_mapping.xml
create mode 100644 airavata-api/src/main/resources/email-config.yaml
create mode 100644 airavata-api/src/main/resources/log4j2.xml
create mode 100644 airavata-api/src/main/resources/templates/CLOUD_Groovy.template
create mode 100644 airavata-api/src/main/resources/templates/FORK_Groovy.template
create mode 100644 airavata-api/src/main/resources/templates/HTCONDOR_Groovy.template
create mode 100644 airavata-api/src/main/resources/templates/LSF_Groovy.template
create mode 100644 airavata-api/src/main/resources/templates/PBS_Groovy.template
rename airavata-api/{modules/airavata-api => }/src/main/resources/templates/SLURM_Groovy.template (100%)
create mode 100644 airavata-api/src/main/resources/templates/UGE_Groovy.template
create mode 100644 airavata-api/src/test/java/org/apache/airavata/accountprovisioning/SSHAccountProvisionerFactoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/accountprovisioning/provisioner/TestSSHAccountProvisioner.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/accountprovisioning/provisioner/TestSSHAccountProvisionerProvider.java
copy airavata-api/{modules/airavata-api/src/test/java/org/apache/airavata/config/ServerPropertiesTest.java => src/test/java/org/apache/airavata/common/utils/ApplicationSettingsTest.java} (72%)
create mode 100644 airavata-api/src/test/java/org/apache/airavata/common/utils/DerbyTestUtil.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/common/utils/SecurityUtilTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/common/utils/ThriftClientPoolTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/cpi/SSHSummaryTest/SSHSummaryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/notifier/impl/EmailNotifierTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/store/impl/db/CommunityUserDAOTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/store/impl/db/CredentialsDAOTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/store/impl/db/SSHCredentialTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/credential/store/util/ConfigurationReaderTest.java
rename airavata-api/{modules/airavata-api/src/test/java/org/apache/airavata/config/ServerPropertiesTest.java => src/test/java/org/apache/airavata/credential/store/util/TokenGeneratorTest.java} (67%)
create mode 100644 airavata-api/src/test/java/org/apache/airavata/helix/SFTPDeleteDirTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/model/util/GroupComputeResourcePreferenceUtilTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/orchestrator/core/BaseOrchestratorTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/orchestrator/core/NewOrchestratorTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithGRAM.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/orchestrator/core/OrchestratorTestWithMyProxyAuth.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/WorkspaceRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourceRepositoryTest.java
rename airavata-api/{modules/airavata-api/src/test/java/org/apache/airavata/gateway/repository => src/test/java/org/apache/airavata/registry/core/repositories/appcatalog}/GatewayGroupsRepositoryTest.java (56%)
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/GatewayProfileRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/GroupResourceProfileRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/JobSubmissionInterfaceRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/StorageResourceRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/common/DerbyTestUtil.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/common/TestBase.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentErrorRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentInputRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentOutputRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentStatusRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentSummaryRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/GatewayRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/JobStatusRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/NotificationRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessErrorRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessInputRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessOutputRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessStatusRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/ProjectRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/QueueStatusRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskErrorRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskStatusRepositoryTest.java
rename airavata-api/{modules/airavata-api/src/test/java/org/apache/airavata/iam/repository => src/test/java/org/apache/airavata/registry/core/repositories/expcatalog}/UserRepositoryTest.java (58%)
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataProductRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataReplicaLocationRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/repositories/workflowcatalog/WorkflowRepositoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/utils/CustomBeanFactoryTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/registry/core/utils/ObjectMapperSingletonTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/configurations/AuthenticatorConfigurationReaderTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/configurations/TestDBAuthenticator1.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/configurations/TestDBAuthenticator2.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/configurations/TestDBAuthenticator3.java
rename airavata-api/{modules/airavata-api/src/main/java/org/apache/airavata/iam/model/RolesRepresentation.java => src/test/java/org/apache/airavata/security/configurations/TestUserStore.java} (54%)
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/userstore/JDBCUserStoreTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/userstore/LDAPUserStoreTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/security/userstore/SessionDBUserStoreTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/service/profile/iam/admin/services/core/tests/SetupNewGateway.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/service/security/GatewayGroupsInitializerTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/service/security/KeyCloakSecurityManagerTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/sharing/registry/CipresTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/sharing/registry/SharingRegistryServerHandlerTest.java
create mode 100644 airavata-api/src/test/java/org/apache/airavata/sharing/registry/SharingRegistryServiceTest.java
create mode 100644 airavata-api/src/test/resources/PBSTemplate.xslt
create mode 100644 airavata-api/src/test/resources/airavata-server.properties
create mode 100644 airavata-api/src/test/resources/authenticators.xml
create mode 100644 airavata-api/src/test/resources/disabled-authenticator.xml
copy airavata-agent/Dockerfile => airavata-api/src/test/resources/gsissh.properties (72%)
create mode 100644 airavata-api/src/test/resources/jdbc-authenticator.xml
create mode 100644 airavata-api/src/test/resources/ldap-authenticator.xml
create mode 100644 airavata-api/src/test/resources/log4j2.xml
copy airavata-agent/Dockerfile => airavata-api/src/test/resources/monitor.properties (62%)
copy airavata-agent/Dockerfile => airavata-api/src/test/resources/orchestrator.properties (72%)
create mode 100644 airavata-api/src/test/resources/session-authenticator.xml
create mode 100644 airavata-api/src/test/resources/zoo.cfg
rename airavata-api/apache-license-header-java.txt => apache-license-header-java.txt (100%)
rename airavata-api/apache-license-header-xml.txt => apache-license-header-xml.txt (100%)
rename airavata-api/apache-license-header.txt => apache-license-header.txt (100%)
delete mode 100755 conf/keycloak/setup-keycloak.sh
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandExecutionRequest.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandExecutionResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandListRequest.java (94%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandListResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandTerminateRequest.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentAsyncCommandTerminateResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentCommandExecutionAck.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentCommandExecutionRequest.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentCommandExecutionResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentEnvSetupAck.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentEnvSetupRequest.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentEnvSetupResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentInfoResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentJupyterExecutionAck.java (93%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentJupyterExecutionRequest.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentJupyterExecutionResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentKernelRestartAck.java (93%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentKernelRestartRequest.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentKernelRestartResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentLaunchRequest.java (98%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentLaunchResponse.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentPythonExecutionAck.java (93%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentPythonExecutionRequest.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentPythonExecutionResponse.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentTerminateResponse.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentTunnelAck.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentTunnelCreateRequest.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentTunnelCreateResponse.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AgentTunnelTerminateRequest.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/AsyncCommand.java (95%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/DirectoryInfo.java (94%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/ExperimentStorageResponse.java (96%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/agent/model => modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models}/FileInfo.java (89%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/file => modules/file-server/src/main/java/org/apache/airavata/file/server}/model/AiravataDirectory.java (93%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/file => modules/file-server/src/main/java/org/apache/airavata/file/server}/model/AiravataFile.java (85%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/file => modules/file-server/src/main/java/org/apache/airavata/file/server}/model/FileUploadResponse.java (97%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/research/project/model => modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto}/CreateProjectRequest.java (89%)
rename {airavata-api/modules/airavata-api/src/main/java/org/apache/airavata/research/session/model => modules/research-framework/research-service/src/main/java/org/apache/airavata/research/service/dto}/RedirectResponse.java (95%)
copy airavata-api/pom.xml => pom.xml (59%)