Merge branch 'master' into develop
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7a779933 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7a779933 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7a779933 Branch: refs/heads/develop Commit: 7a779933e7e6b89d722f11ef5c80026210e63dd1 Parents: b37882a 10d7c02 Author: Marcus Christie <[email protected]> Authored: Fri Apr 28 11:20:49 2017 -0400 Committer: Marcus Christie <[email protected]> Committed: Fri Apr 28 11:20:49 2017 -0400 ---------------------------------------------------------------------- airavata-api/airavata-api-server/pom.xml | 31 +++-- .../airavata/api/server/AiravataAPIServer.java | 4 +- .../api/server/AiravataDerbyServer.java | 4 +- .../server/handler/AiravataServerHandler.java | 4 +- .../AiravataExperimentStatusUpdator.java | 6 +- .../listener/ExperimentStatusChangedEvent.java | 19 +++ .../security/AiravataSecurityManager.java | 3 +- .../DefaultAiravataSecurityManager.java | 3 +- .../api/server/security/IdentityContext.java | 4 +- .../airavata/api/server/security/Main.java | 5 +- .../server/security/SecurityManagerFactory.java | 3 +- .../server/security/authzcache/AuthzCache.java | 3 +- .../security/authzcache/AuthzCacheEntry.java | 3 +- .../security/authzcache/AuthzCacheIndex.java | 3 +- .../security/authzcache/AuthzCacheManager.java | 3 +- .../authzcache/AuthzCacheManagerFactory.java | 3 +- .../security/authzcache/AuthzCachedStatus.java | 3 +- .../authzcache/DefaultAuthzCacheManager.java | 3 +- .../security/interceptor/SecurityCheck.java | 3 +- .../interceptor/SecurityInterceptor.java | 3 +- .../security/interceptor/SecurityModule.java | 3 +- .../security/oauth/DefaultOAuthClient.java | 3 +- .../server/security/xacml/DefaultPAPClient.java | 3 +- .../server/security/xacml/DefaultXACMLPEP.java | 3 +- .../airavata/api/server/util/Constants.java | 4 +- .../api/server/util/ThriftClientPool.java | 5 +- airavata-api/airavata-api-stubs/pom.xml | 31 +++-- .../java/org/apache/airavata/api/Airavata.java | 28 ++-- .../airavata/api/airavata_apiConstants.java | 28 ++-- .../api/client/AiravataClientFactory.java | 4 +- .../airavata-cpp-sdk/pom.xml | 27 +++- .../src/main/assembly/bin-assembly.xml | 29 ++-- .../airavata-php-sdk/pom.xml | 27 +++- .../src/main/assembly/bin-assembly.xml | 29 ++-- .../airavata-python-sdk/pom.xml | 27 +++- .../src/main/assembly/bin-assembly.xml | 29 ++-- .../java-client-samples/pom.xml | 26 +++- .../client/samples/CancelExperiments.java | 4 +- .../client/samples/CreateLaunchBES.java | 3 +- .../client/samples/CreateLaunchExperiment.java | 4 +- .../samples/CreateLaunchExperimentUS3.java | 2 +- .../client/samples/ReplicaCatalogSample.java | 5 +- .../client/samples/SampleEchoExperiment.java | 4 +- .../client/OAuthAppRegisteringClient.java | 3 +- .../client/OAuthTokenRetrievalClient.java | 3 +- .../client/secure/client/Properties.java | 3 +- .../client/secure/client/SecureClient.java | 3 +- .../tools/RegisterOGCEUS3Application.java | 6 +- .../tools/RegisterSampleApplications.java | 5 +- .../tools/RegisterSampleApplicationsUtils.java | 19 +++ .../client/tools/RegisterUS3Application.java | 6 +- airavata-api/airavata-client-sdks/pom.xml | 26 +++- airavata-api/airavata-data-models/pom.xml | 31 +++-- .../apache/airavata/model/ComponentState.java | 28 ++-- .../apache/airavata/model/ComponentStatus.java | 28 ++-- .../org/apache/airavata/model/EdgeModel.java | 28 ++-- .../org/apache/airavata/model/NodeModel.java | 28 ++-- .../org/apache/airavata/model/PortModel.java | 28 ++-- .../apache/airavata/model/WorkflowModel.java | 28 ++-- .../apache/airavata/model/WorkflowState.java | 28 ++-- .../apache/airavata/model/WorkflowStatus.java | 28 ++-- .../ApplicationDeploymentDescription.java | 28 ++-- .../appdeployment/ApplicationModule.java | 28 ++-- .../appcatalog/appdeployment/CommandObject.java | 28 ++-- .../appcatalog/appdeployment/SetEnvPaths.java | 28 ++-- .../application_deployment_modelConstants.java | 28 ++-- .../ApplicationInterfaceDescription.java | 28 ++-- .../application_interface_modelConstants.java | 28 ++-- .../appcatalog/computeresource/BatchQueue.java | 28 ++-- .../computeresource/CloudJobSubmission.java | 28 ++-- .../ComputeResourceDescription.java | 28 ++-- .../appcatalog/computeresource/DMType.java | 28 ++-- .../appcatalog/computeresource/FileSystems.java | 28 ++-- .../computeresource/GlobusJobSubmission.java | 28 ++-- .../computeresource/JobManagerCommand.java | 28 ++-- .../computeresource/JobSubmissionInterface.java | 28 ++-- .../computeresource/JobSubmissionProtocol.java | 28 ++-- .../computeresource/LOCALSubmission.java | 28 ++-- .../appcatalog/computeresource/MonitorMode.java | 28 ++-- .../computeresource/ProviderName.java | 28 ++-- .../computeresource/ResourceJobManager.java | 28 ++-- .../computeresource/ResourceJobManagerType.java | 28 ++-- .../computeresource/SSHJobSubmission.java | 28 ++-- .../computeresource/UnicoreJobSubmission.java | 28 ++-- .../compute_resource_modelConstants.java | 28 ++-- .../ComputeResourcePreference.java | 28 ++-- .../gatewayprofile/DataStoragePreference.java | 28 ++-- .../gatewayprofile/GatewayResourceProfile.java | 28 ++-- .../gatewayprofile/StoragePreference.java | 28 ++-- .../StorageResourceDescription.java | 28 ++-- .../UserComputeResourcePreference.java | 28 ++-- .../UserResourceProfile.java | 28 ++-- .../UserStoragePreference.java | 28 ++-- .../airavata/model/application/io/DataType.java | 28 ++-- .../application/io/InputDataObjectType.java | 28 ++-- .../application/io/OutputDataObjectType.java | 28 ++-- .../airavata/model/commons/ErrorModel.java | 28 ++-- .../model/commons/ValidationResults.java | 28 ++-- .../airavata/model/commons/ValidatorResult.java | 28 ++-- .../commons/airavata_commonsConstants.java | 28 ++-- .../credential/store/CertificateCredential.java | 28 ++-- .../model/credential/store/CommunityUser.java | 28 ++-- .../credential/store/CredentialOwnerType.java | 28 ++-- .../credential/store/CredentialSummary.java | 28 ++-- .../credential/store/PasswordCredential.java | 28 ++-- .../model/credential/store/SSHCredential.java | 28 ++-- .../credential/store/SSHCredentialSummary.java | 28 ++-- .../model/credential/store/SummaryType.java | 28 ++-- .../credential_store_data_modelsConstants.java | 28 ++-- .../airavata/model/data/movement/DMType.java | 28 ++-- .../data/movement/DataMovementInterface.java | 28 ++-- .../data/movement/DataMovementProtocol.java | 28 ++-- .../data/movement/GridFTPDataMovement.java | 28 ++-- .../model/data/movement/LOCALDataMovement.java | 28 ++-- .../model/data/movement/SCPDataMovement.java | 28 ++-- .../model/data/movement/SecurityProtocol.java | 28 ++-- .../data/movement/UnicoreDataMovement.java | 28 ++-- .../model/data/replica/DataProductModel.java | 28 ++-- .../model/data/replica/DataProductType.java | 28 ++-- .../data/replica/DataReplicaLocationModel.java | 28 ++-- .../data/replica/ReplicaLocationCategory.java | 28 ++-- .../data/replica/ReplicaPersistentType.java | 28 ++-- .../model/error/AiravataClientException.java | 28 ++-- .../airavata/model/error/AiravataErrorType.java | 28 ++-- .../model/error/AiravataSystemException.java | 28 ++-- .../model/error/AuthenticationException.java | 28 ++-- .../model/error/AuthorizationException.java | 28 ++-- .../error/ExperimentNotFoundException.java | 28 ++-- .../model/error/InvalidRequestException.java | 28 ++-- .../model/error/LaunchValidationException.java | 28 ++-- .../model/error/ProjectNotFoundException.java | 28 ++-- .../airavata/model/error/TimedOutException.java | 28 ++-- .../airavata/model/error/ValidationResults.java | 28 ++-- .../airavata/model/error/ValidatorResult.java | 28 ++-- .../model/experiment/ExperimentModel.java | 28 ++-- .../experiment/ExperimentSearchFields.java | 28 ++-- .../model/experiment/ExperimentStatistics.java | 28 ++-- .../experiment/ExperimentSummaryModel.java | 28 ++-- .../model/experiment/ExperimentType.java | 28 ++-- .../model/experiment/ProjectSearchFields.java | 28 ++-- .../experiment/UserConfigurationDataModel.java | 28 ++-- .../apache/airavata/model/group/GroupModel.java | 28 ++-- .../model/group/ResourcePermissionType.java | 28 ++-- .../airavata/model/group/ResourceType.java | 28 ++-- .../org/apache/airavata/model/job/JobModel.java | 28 ++-- .../event/ExperimentStatusChangeEvent.java | 28 ++-- .../messaging/event/ExperimentSubmitEvent.java | 28 ++-- .../model/messaging/event/JobIdentifier.java | 28 ++-- .../messaging/event/JobStatusChangeEvent.java | 28 ++-- .../event/JobStatusChangeRequestEvent.java | 28 ++-- .../airavata/model/messaging/event/Message.java | 28 ++-- .../model/messaging/event/MessageLevel.java | 28 ++-- .../model/messaging/event/MessageType.java | 28 ++-- .../messaging/event/ProcessIdentifier.java | 28 ++-- .../event/ProcessStatusChangeEvent.java | 28 ++-- .../event/ProcessStatusChangeRequestEvent.java | 28 ++-- .../messaging/event/ProcessSubmitEvent.java | 28 ++-- .../messaging/event/ProcessTerminateEvent.java | 28 ++-- .../model/messaging/event/TaskIdentifier.java | 28 ++-- .../messaging/event/TaskOutputChangeEvent.java | 28 ++-- .../messaging/event/TaskStatusChangeEvent.java | 28 ++-- .../event/TaskStatusChangeRequestEvent.java | 28 ++-- .../model/messaging/event/TaskSubmitEvent.java | 28 ++-- .../messaging/event/TaskTerminateEvent.java | 28 ++-- .../event/messaging_eventsConstants.java | 28 ++-- .../parallelism/ApplicationParallelismType.java | 28 ++-- .../airavata/model/process/ProcessModel.java | 28 ++-- .../ComputationalResourceSchedulingModel.java | 28 ++-- .../airavata/model/security/AuthzToken.java | 28 ++-- .../airavata/model/status/ExperimentState.java | 28 ++-- .../airavata/model/status/ExperimentStatus.java | 28 ++-- .../apache/airavata/model/status/JobState.java | 28 ++-- .../apache/airavata/model/status/JobStatus.java | 28 ++-- .../airavata/model/status/ProcessState.java | 28 ++-- .../airavata/model/status/ProcessStatus.java | 28 ++-- .../airavata/model/status/QueueStatusModel.java | 28 ++-- .../apache/airavata/model/status/TaskState.java | 28 ++-- .../airavata/model/status/TaskStatus.java | 28 ++-- .../airavata/model/task/DataStageType.java | 28 ++-- .../model/task/DataStagingTaskModel.java | 28 ++-- .../model/task/EnvironmentSetupTaskModel.java | 28 ++-- .../model/task/JobSubmissionTaskModel.java | 28 ++-- .../airavata/model/task/MonitorTaskModel.java | 28 ++-- .../apache/airavata/model/task/TaskModel.java | 28 ++-- .../apache/airavata/model/task/TaskTypes.java | 28 ++-- .../airavata/model/user/NSFDemographics.java | 28 ++-- .../org/apache/airavata/model/user/Status.java | 28 ++-- .../airavata/model/user/USCitizenship.java | 28 ++-- .../apache/airavata/model/user/UserProfile.java | 28 ++-- .../apache/airavata/model/user/disability.java | 28 ++-- .../apache/airavata/model/user/ethnicity.java | 28 ++-- .../org/apache/airavata/model/user/race.java | 28 ++-- .../model/user/user_profile_modelConstants.java | 28 ++-- .../model/workflow_data_modelConstants.java | 28 ++-- .../airavata/model/workspace/Gateway.java | 28 ++-- .../model/workspace/GatewayApprovalStatus.java | 28 ++-- .../apache/airavata/model/workspace/Group.java | 28 ++-- .../airavata/model/workspace/Notification.java | 28 ++-- .../model/workspace/NotificationPriority.java | 28 ++-- .../airavata/model/workspace/Project.java | 28 ++-- .../apache/airavata/model/workspace/User.java | 28 ++-- airavata-api/airavata-model-utils/pom.xml | 31 +++-- .../airavata/model/util/AppDeploymentUtil.java | 4 +- .../airavata/model/util/AppInterfaceUtil.java | 4 +- .../model/util/ComputeResourceUtil.java | 4 +- .../airavata/model/util/ExecutionType.java | 4 +- .../model/util/ExperimentModelUtil.java | 4 +- .../airavata/model/util/ProjectModelUtil.java | 2 +- airavata-api/pom.xml | 26 +++- .../commons/tenant/entities/GatewayEntity.java | 2 +- .../commons/utils/ObjectMapperSingleton.java | 2 +- .../UserProfileRegistryException.java | 2 +- .../security/interceptor/SecurityModule.java | 2 +- dev-tools/ansible/airavata.yml | 20 +++ dev-tools/ansible/ansible.cfg | 2 +- dev-tools/ansible/dev_airavata_deploy.yml | 20 +++ dev-tools/ansible/dev_pga_deploy.yml | 20 +++ .../inventories/develop/group_vars/all.yml | 20 +++ .../develop/group_vars/dev-airavata.yml | 20 +++ .../inventories/develop/group_vars/dev-pga.yml | 20 +++ .../geogateway-dev/group_vars/pga/vars.yml | 22 ++- .../scigap/production/files/airavata.jks | 76 ++++++++++ .../scigap/production/files/airavata_sym.jks | 30 ++++ .../production/files/client_truststore.jks | 126 +++++++++++++++++ .../scigap/production/group_vars/all/vars.yml | 123 +++++++++++++++++ .../scigap/production/group_vars/all/vault.yml | 20 +++ .../ansible/inventories/scigap/production/hosts | 20 +++ .../production/pga_config/brandeis/vars.yml | 51 +++++++ .../production/pga_config/brandeis/vault.yml | 18 +++ .../production/pga_config/cinetvtech/vars.yml | 55 ++++++++ .../production/pga_config/cinetvtech/vault.yml | 18 +++ .../cornell-dnasequence/pga-ssl-vhost.conf.j2 | 31 +++++ .../pga_config/cornell-dnasequence/vars.yml | 63 +++++++++ .../pga_config/cornell-dnasequence/vault.yml | 18 +++ .../production/pga_config/georgiastate/vars.yml | 55 ++++++++ .../pga_config/georgiastate/vault.yml | 18 +++ .../production/pga_config/iugateway/vars.yml | 55 ++++++++ .../production/pga_config/iugateway/vault.yml | 18 +++ .../scigap/production/pga_config/lsu/vars.yml | 51 +++++++ .../scigap/production/pga_config/lsu/vault.yml | 18 +++ .../scigap/production/pga_config/nsg/vars.yml | 56 ++++++++ .../scigap/production/pga_config/nsg/vault.yml | 18 +++ .../production/pga_config/oiitandy/vars.yml | 55 ++++++++ .../production/pga_config/oiitandy/vault.yml | 18 +++ .../scigap/production/pga_config/oscer/vars.yml | 55 ++++++++ .../production/pga_config/oscer/vault.yml | 18 +++ .../production/pga_config/phasta/vars.yml | 55 ++++++++ .../production/pga_config/phasta/vault.yml | 18 +++ .../production/pga_config/scigap/vars.yml | 56 ++++++++ .../production/pga_config/scigap/vault.yml | 18 +++ .../production/pga_config/seagrid/vars.yml | 56 ++++++++ .../production/pga_config/seagrid/vault.yml | 18 +++ .../production/pga_config/simvascular/vars.yml | 55 ++++++++ .../production/pga_config/simvascular/vault.yml | 18 +++ .../production/pga_config/southdakota/vars.yml | 55 ++++++++ .../production/pga_config/southdakota/vault.yml | 18 +++ .../pga_config/southernillinois/vars.yml | 55 ++++++++ .../pga_config/southernillinois/vault.yml | 18 +++ .../production/pga_config/testdrive/vars.yml | 56 ++++++++ .../production/pga_config/testdrive/vault.yml | 18 +++ .../production/pga_config/ultrascan/vars.yml | 64 +++++++++ .../production/pga_config/ultrascan/vault.yml | 18 +++ .../scigap/production/pga_config/utah/vars.yml | 55 ++++++++ .../scigap/production/pga_config/utah/vault.yml | 18 +++ .../testing-0.17-scigap/group_vars/all/vars.yml | 20 +++ .../testing-0.17-scigap/group_vars/pga/vars.yml | 22 ++- .../group_vars/all/vars.yml | 20 +++ .../group_vars/pga/vars.yml | 25 +++- .../testing-0.17/group_vars/all/vars.yml | 20 +++ .../testing-0.17/group_vars/pga/vars.yml | 22 ++- dev-tools/ansible/local_airavata_deploy.yml | 20 +++ dev-tools/ansible/pga-scigap-prod.yml | 41 ++++++ dev-tools/ansible/pga-single-vhost.yml | 37 +++++ dev-tools/ansible/pga.yml | 20 +++ .../ansible/roles/airavata_build/tasks/main.yml | 20 +++ .../roles/airavata_deploy/defaults/main.yml | 20 +++ .../roles/airavata_deploy/handlers/main.yml | 20 +++ .../roles/airavata_deploy/tasks/main.yml | 20 +++ .../ansible/roles/api-orch/defaults/main.yml | 22 +++ .../ansible/roles/api-orch/handlers/main.yml | 20 +++ dev-tools/ansible/roles/api-orch/tasks/main.yml | 42 +++++- .../api-orch/templates/gfac-config.yaml.j2 | 6 + .../roles/api-orch/templates/logback.xml.j2 | 55 ++++++++ .../ansible/roles/common/defaults/main.yml | 20 +++ dev-tools/ansible/roles/common/tasks/main.yml | 20 +++ dev-tools/ansible/roles/common/vars/main.yml | 20 +++ .../ansible/roles/database/defaults/main.yml | 21 +++ .../ansible/roles/database/files/mysql-tmp.te | 9 ++ .../ansible/roles/database/handlers/main.yml | 20 +++ dev-tools/ansible/roles/database/tasks/main.yml | 70 +++++++++- .../roles/database/tasks/secure_install.yml | 20 +++ dev-tools/ansible/roles/database/vars/main.yml | 21 ++- .../ansible/roles/env_setup/tasks/main.yml | 20 +++ .../ansible/roles/env_setup/tasks/redhat.yml | 20 +++ dev-tools/ansible/roles/gfac/defaults/main.yml | 21 +++ dev-tools/ansible/roles/gfac/handlers/main.yml | 20 +++ dev-tools/ansible/roles/gfac/tasks/main.yml | 34 ++++- .../roles/gfac/templates/gfac-config.yaml.j2 | 7 + .../ansible/roles/gfac/templates/logback.xml.j2 | 55 ++++++++ dev-tools/ansible/roles/java/tasks/main.yml | 20 +++ dev-tools/ansible/roles/java/vars/main.yml | 20 +++ dev-tools/ansible/roles/pga/defaults/main.yml | 37 ++++- dev-tools/ansible/roles/pga/files/default.conf | 5 + dev-tools/ansible/roles/pga/handlers/main.yml | 24 +++- .../roles/pga/tasks/install_deps_CentOS_7.yml | 20 +++ .../roles/pga/tasks/install_deps_Ubuntu_14.yml | 20 +++ .../roles/pga/tasks/install_deps_Ubuntu_16.yml | 20 +++ dev-tools/ansible/roles/pga/tasks/main.yml | 137 +++++++++++++++---- .../roles/pga/templates/pga-ssl-vhost.conf.j2 | 29 ++++ .../roles/pga/templates/pga-vhost.conf.j2 | 3 + .../roles/pga/templates/pga_config.php.j2 | 16 +-- .../ansible/roles/pga_deploy/handlers/main.yml | 20 +++ .../ansible/roles/pga_deploy/tasks/main.yml | 20 +++ .../ansible/roles/rabbitmq/handlers/main.yml | 20 +++ dev-tools/ansible/roles/rabbitmq/tasks/main.yml | 20 +++ dev-tools/ansible/roles/rabbitmq/vars/main.yml | 20 +++ dev-tools/ansible/roles/registry/tasks/main.yml | 20 +++ dev-tools/ansible/roles/wso2_is/tasks/main.yml | 20 +++ dev-tools/ansible/roles/wso2_is/vars/main.yml | 20 +++ .../ansible/roles/zookeeper/handlers/main.yml | 20 +++ .../ansible/roles/zookeeper/tasks/main.yml | 20 +++ dev-tools/ansible/roles/zookeeper/vars/main.yml | 20 +++ dev-tools/ansible/site.yml | 20 +++ modules/cloud/cloud-provisioning/pom.xml | 5 - modules/cluster-monitoring/pom.xml | 25 +++- .../monitoring/ClusterStatusMonitorJob.java | 5 +- .../ClusterStatusMonitorJobScheduler.java | 5 +- modules/commons/pom.xml | 30 ++-- .../airavata/common/utils/BuildConstant.java | 4 +- .../airavata/common/context/RequestContext.java | 4 +- .../common/context/WorkflowContext.java | 4 +- .../AiravataConfigurationException.java | 4 +- .../common/exception/AiravataException.java | 4 +- .../exception/AiravataStartupException.java | 4 +- .../exception/ApplicationSettingsException.java | 4 +- .../airavata/common/logging/Exception.java | 3 +- .../airavata/common/logging/LogEntry.java | 3 +- .../airavata/common/logging/MDCConstants.java | 3 +- .../apache/airavata/common/logging/MDCUtil.java | 19 +++ .../airavata/common/logging/ServerId.java | 3 +- .../common/logging/kafka/KafkaAppender.java | 3 +- .../airavata/common/utils/AiravataJobState.java | 5 +- .../airavata/common/utils/AiravataUtils.java | 4 +- .../airavata/common/utils/AiravataZKUtils.java | 5 +- .../common/utils/ApplicationSettings.java | 4 +- .../airavata/common/utils/AwsMetadata.java | 3 +- .../airavata/common/utils/BrowserLauncher.java | 4 +- .../airavata/common/utils/ClientSettings.java | 4 +- .../apache/airavata/common/utils/Constants.java | 4 +- .../apache/airavata/common/utils/DBUtil.java | 4 +- .../common/utils/DatabaseTestCases.java | 4 +- .../utils/DefaultKeyStorePasswordCallback.java | 4 +- .../apache/airavata/common/utils/DerbyUtil.java | 4 +- .../airavata/common/utils/ExecutionMode.java | 4 +- .../apache/airavata/common/utils/IOUtil.java | 4 +- .../apache/airavata/common/utils/IServer.java | 4 +- .../apache/airavata/common/utils/JSONUtil.java | 4 +- .../common/utils/KeyStorePasswordCallback.java | 19 +++ .../common/utils/LocalEventPublisher.java | 5 +- .../airavata/common/utils/NameValidator.java | 4 +- .../org/apache/airavata/common/utils/Pair.java | 4 +- .../airavata/common/utils/SecurityUtil.java | 4 +- .../airavata/common/utils/ServerSettings.java | 4 +- .../airavata/common/utils/ServiceUtils.java | 19 +++ .../airavata/common/utils/StringUtil.java | 4 +- .../apache/airavata/common/utils/SwingUtil.java | 4 +- .../airavata/common/utils/ThriftUtils.java | 4 +- .../apache/airavata/common/utils/Version.java | 4 +- .../airavata/common/utils/WSConstants.java | 4 +- .../apache/airavata/common/utils/WSDLUtil.java | 4 +- .../airavata/common/utils/ZkConstants.java | 3 +- .../listener/AbstractActivityListener.java | 4 +- .../listener/AbstractStateChangeRequest.java | 4 +- .../common/utils/listener/PublisherMessage.java | 4 +- .../common/utils/ApplicationSettingsTest.java | 4 +- .../airavata/common/utils/SecurityUtilTest.java | 4 +- modules/configuration/client/pom.xml | 26 +++- modules/configuration/pom.xml | 26 +++- modules/configuration/server/pom.xml | 26 +++- .../src/main/resources/LSF_Groovy.template | 3 + .../src/main/resources/UGE_Groovy.template | 3 +- .../server/src/main/resources/log4j.properties | 48 ------- .../server/src/main/resources/logback.xml | 70 ++++++---- .../credential-store-service/pom.xml | 33 +++-- .../credential/store/credential/AuditInfo.java | 4 +- .../store/credential/CommunityUser.java | 4 +- .../credential/store/credential/Credential.java | 4 +- .../store/credential/CredentialOwnerType.java | 19 +++ .../impl/certificate/CertificateAuditInfo.java | 6 +- .../impl/certificate/CertificateCredential.java | 4 +- .../impl/password/PasswordCredential.java | 4 +- .../credential/impl/ssh/SSHCredential.java | 4 +- .../impl/ssh/SSHCredentialGenerator.java | 4 +- .../store/notifier/CredentialStoreNotifier.java | 19 +++ .../store/notifier/NotificationMessage.java | 4 +- .../store/notifier/NotifierBootstrap.java | 4 +- .../notifier/impl/EmailNotificationMessage.java | 4 +- .../store/notifier/impl/EmailNotifier.java | 4 +- .../impl/EmailNotifierConfiguration.java | 4 +- .../store/server/CredentialStoreServer.java | 3 +- .../server/CredentialStoreServerHandler.java | 3 +- .../store/servlet/CredentialBootstrapper.java | 4 +- .../servlet/CredentialStoreCallbackServlet.java | 4 +- .../servlet/CredentialStoreStartServlet.java | 4 +- .../store/store/CredentialReader.java | 4 +- .../store/store/CredentialReaderFactory.java | 4 +- .../store/store/CredentialStoreException.java | 4 +- .../store/store/CredentialWriter.java | 4 +- .../store/impl/CertificateCredentialWriter.java | 4 +- .../store/store/impl/CredentialReaderImpl.java | 4 +- .../store/store/impl/SSHCredentialWriter.java | 4 +- .../store/store/impl/db/CommunityUserDAO.java | 4 +- .../store/store/impl/db/CredentialsDAO.java | 4 +- .../store/store/impl/db/ParentDAO.java | 4 +- .../store/store/impl/util/ConnectionPool.java | 5 +- .../impl/util/CredentialStoreInitUtil.java | 5 +- .../store/store/impl/util/DatabaseCreator.java | 5 +- .../store/store/impl/util/JdbcStorage.java | 5 +- .../store/util/ConfigurationReader.java | 4 +- .../store/util/CredentialStoreConstants.java | 4 +- .../credential/store/util/PrivateKeyStore.java | 4 +- .../credential/store/util/TokenGenerator.java | 4 +- .../airavata/credential/store/util/Utility.java | 4 +- .../cpi/SSHSummaryTest/SSHSummaryTest.java | 19 +++ .../store/notifier/impl/EmailNotifierTest.java | 4 +- .../store/impl/db/CommunityUserDAOTest.java | 4 +- .../store/store/impl/db/CredentialsDAOTest.java | 4 +- .../store/store/impl/db/SSHCredentialTest.java | 4 +- .../store/util/ConfigurationReaderTest.java | 4 +- .../store/util/TokenGeneratorTest.java | 4 +- .../credential-store-stubs/pom.xml | 31 +++-- .../client/CredentialStoreClientFactory.java | 4 +- .../credential/store/client/TestSSLClient.java | 3 +- .../store/cpi/CredentialStoreService.java | 19 +++ .../cpi/credential_store_cpiConstants.java | 19 +++ .../exception/CredentialStoreException.java | 19 +++ modules/credential-store/pom.xml | 26 +++- .../db/event/manager/utils/Constants.java | 2 +- modules/distribution/pom.xml | 46 +++++-- .../src/main/assembly/bin-assembly.xml | 32 +++-- .../src/main/assembly/src-assembly.xml | 37 ++--- .../main/resources/bin/airavata-server-start.sh | 17 ++- .../gfac-application-specific-handlers/pom.xml | 31 +++-- .../gaussian/handler/GaussianHandler.java | 19 +++ modules/gfac/gfac-bes/pom.xml | 29 ++-- .../gfac/bes/handlers/AbstractSMSHandler.java | 19 +++ .../gfac/bes/handlers/SMSByteIOInHandler.java | 19 +++ .../gfac/bes/handlers/SMSByteIOOutHandler.java | 19 +++ .../gfac/bes/handlers/SMSDirectoryHandler.java | 19 +++ .../gfac/bes/provider/impl/BESProvider.java | 3 +- .../bes/security/UNICORESecurityContext.java | 19 +++ .../gfac/bes/security/X509SecurityContext.java | 5 +- .../airavata/gfac/bes/utils/ActivityInfo.java | 19 +++ .../gfac/bes/utils/ApplicationProcessor.java | 4 +- .../airavata/gfac/bes/utils/BESConstants.java | 19 +++ .../gfac/bes/utils/DataTransferrer.java | 4 +- .../airavata/gfac/bes/utils/FileDownloader.java | 4 +- .../gfac/bes/utils/FileTransferBase.java | 4 +- .../airavata/gfac/bes/utils/FileUploader.java | 4 +- .../airavata/gfac/bes/utils/JSDLGenerator.java | 3 +- .../airavata/gfac/bes/utils/JSDLUtils.java | 4 +- .../apache/airavata/gfac/bes/utils/Mode.java | 4 +- .../airavata/gfac/bes/utils/MyProxyLogon.java | 19 +++ .../airavata/gfac/bes/utils/OSRequirement.java | 4 +- .../apache/airavata/gfac/bes/utils/OSType.java | 4 +- .../gfac/bes/utils/ProcessorRequirement.java | 6 +- .../airavata/gfac/bes/utils/RangeValueType.java | 4 +- .../gfac/bes/utils/ResourceProcessor.java | 4 +- .../airavata/gfac/bes/utils/SPMDProcessor.java | 4 +- .../airavata/gfac/bes/utils/SPMDVariations.java | 4 +- .../airavata/gfac/bes/utils/SecurityUtils.java | 19 +++ .../airavata/gfac/bes/utils/StorageCreator.java | 4 +- .../gfac/bes/utils/UASDataStagingProcessor.java | 4 +- .../airavata/gfac/bes/utils/URIUtils.java | 4 +- .../impl/JSDLGeneratorTestWithMyProxyAuth.java | 4 +- modules/gfac/gfac-client/pom.xml | 31 +++-- .../airavata/gfac/client/GFACInstance.java | 5 +- .../airavata/gfac/client/GFacClientFactory.java | 5 +- .../apache/airavata/gfac/cpi/GfacService.java | 19 +++ .../airavata/gfac/cpi/gfac_cpiConstants.java | 19 +++ modules/gfac/gfac-impl/pom.xml | 26 +++- .../java/com/jcraft/jsch/ExtendedSession.java | 4 +- .../com/jcraft/jsch/GSISSHIdentityFile.java | 4 +- .../jcraft/jsch/GSISSHIdentityRepository.java | 4 +- .../java/com/jcraft/jsch/GSSContextX509.java | 4 +- .../UserAuthGSSAPIWithMICGSSCredentials.java | 4 +- .../apache/airavata/gfac/impl/AuroraUtils.java | 3 +- .../airavata/gfac/impl/BESRemoteCluster.java | 6 +- .../gfac/impl/DefaultHostScheduler.java | 3 +- .../org/apache/airavata/gfac/impl/Factory.java | 3 +- .../airavata/gfac/impl/GFacEngineImpl.java | 6 +- .../apache/airavata/gfac/impl/GFacWorker.java | 4 +- .../airavata/gfac/impl/HPCRemoteCluster.java | 5 +- .../apache/airavata/gfac/impl/HTTPUtils.java | 19 +++ .../airavata/gfac/impl/LocalCommandOutput.java | 3 +- .../airavata/gfac/impl/LocalRemoteCluster.java | 3 +- .../org/apache/airavata/gfac/impl/SSHUtils.java | 3 +- .../airavata/gfac/impl/StandardOutReader.java | 5 +- .../job/AiravataCustomCommandOutputParser.java | 6 +- .../gfac/impl/job/ForkJobConfiguration.java | 6 +- .../gfac/impl/job/ForkOutputParser.java | 6 +- .../apache/airavata/gfac/impl/job/JobUtil.java | 3 +- .../gfac/impl/job/LSFJobConfiguration.java | 5 +- .../airavata/gfac/impl/job/LSFOutputParser.java | 5 +- .../gfac/impl/job/PBSJobConfiguration.java | 5 +- .../airavata/gfac/impl/job/PBSOutputParser.java | 5 +- .../gfac/impl/job/SlurmJobConfiguration.java | 5 +- .../gfac/impl/job/SlurmOutputParser.java | 5 +- .../gfac/impl/job/UGEJobConfiguration.java | 5 +- .../airavata/gfac/impl/job/UGEOutputParser.java | 5 +- .../airavata/gfac/impl/task/ArchiveTask.java | 3 +- .../gfac/impl/task/AuroraJobSubmissionTask.java | 3 +- .../gfac/impl/task/BESJobSubmissionTask.java | 19 +++ .../airavata/gfac/impl/task/DataStageTask.java | 3 +- .../gfac/impl/task/DataStreamingTask.java | 6 +- .../impl/task/DefaultJobSubmissionTask.java | 6 +- .../gfac/impl/task/EnvironmentSetupTask.java | 3 +- .../gfac/impl/task/ForkJobSubmissionTask.java | 6 +- .../gfac/impl/task/LocalJobSubmissionTask.java | 6 +- .../gfac/impl/task/SCPDataStageTask.java | 3 +- .../airavata/gfac/impl/task/TaskUtils.java | 3 +- .../gfac/impl/task/utils/StreamData.java | 6 +- .../gfac/impl/task/utils/bes/ActivityInfo.java | 19 +++ .../task/utils/bes/ApplicationProcessor.java | 4 +- .../gfac/impl/task/utils/bes/BESConstants.java | 19 +++ .../impl/task/utils/bes/DataTransferrer.java | 4 +- .../impl/task/utils/bes/FileDownloader.java | 4 +- .../impl/task/utils/bes/FileTransferBase.java | 4 +- .../gfac/impl/task/utils/bes/FileUploader.java | 4 +- .../gfac/impl/task/utils/bes/JSDLGenerator.java | 3 +- .../gfac/impl/task/utils/bes/JSDLUtils.java | 4 +- .../airavata/gfac/impl/task/utils/bes/Mode.java | 4 +- .../gfac/impl/task/utils/bes/MyProxyLogon.java | 19 +++ .../gfac/impl/task/utils/bes/OSType.java | 4 +- .../task/utils/bes/ProcessorRequirement.java | 6 +- .../impl/task/utils/bes/RangeValueType.java | 4 +- .../impl/task/utils/bes/ResourceProcessor.java | 4 +- .../task/utils/bes/ResourceRequirement.java | 4 +- .../impl/task/utils/bes/SPMDVariations.java | 4 +- .../gfac/impl/task/utils/bes/SecurityUtils.java | 19 +++ .../impl/task/utils/bes/StorageCreator.java | 4 +- .../task/utils/bes/UASDataStagingProcessor.java | 4 +- .../task/utils/bes/UNICORESecurityContext.java | 19 +++ .../gfac/impl/task/utils/bes/URIUtils.java | 4 +- .../task/utils/bes/X509SecurityContext.java | 5 +- .../impl/watcher/CancelRequestWatcherImpl.java | 3 +- .../watcher/RedeliveryRequestWatcherImpl.java | 3 +- .../handler/LocalDirectorySetupHandler.java | 19 +++ .../gfac/local/handler/LocalInputHandler.java | 19 +++ .../gfac/local/provider/impl/LocalProvider.java | 19 +++ .../local/utils/InputStreamToFileWriter.java | 5 +- .../airavata/gfac/local/utils/InputUtils.java | 5 +- .../gfac/local/utils/LocalProviderUtil.java | 19 +++ .../gfac/monitor/cloud/AuroraJobMonitor.java | 3 +- .../gfac/monitor/email/EmailBasedMonitor.java | 5 +- .../email/parser/AiravataCustomMailParser.java | 5 +- .../monitor/email/parser/LSFEmailParser.java | 5 +- .../monitor/email/parser/PBSEmailParser.java | 5 +- .../monitor/email/parser/SLURMEmailParser.java | 5 +- .../monitor/email/parser/UGEEmailParser.java | 5 +- .../exception/AiravataMonitorException.java | 5 +- .../gfac/ssh/context/SSHAuthWrapper.java | 5 +- .../gfac/ssh/security/SSHSecurityContext.java | 3 +- .../gfac/ssh/security/TokenizedSSHAuthInfo.java | 5 +- .../services/impl/BigRed2TestWithSSHAuth.java | 19 +++ .../gfac/services/impl/CredentialStoreTest.java | 19 +++ .../impl/GSISSHProviderTestWithMyProxyAuth.java | 19 +++ .../gfac/services/impl/LocalProviderTest.java | 19 +++ .../impl/SSHProviderTestWithSSHAuth.java | 19 +++ .../GSISecurityContextTestWithMyProxyAuth.java | 19 +++ .../email/parser/PBSEmailParserTest.java | 19 +++ .../gfac/ssh/config/ConfigReaderTest.java | 19 +++ .../impl/DefaultSSHApiTestWithMyProxyAuth.java | 19 +++ .../gfac/ssh/impl/VanilaTestWithSSHAuth.java | 19 +++ .../apache/airavata/job/AMQPMonitorTest.java | 19 +++ .../job/QstatMonitorTestWithMyProxyAuth.java | 19 +++ modules/gfac/gfac-service/pom.xml | 31 +++-- .../apache/airavata/gfac/server/GfacServer.java | 5 +- .../airavata/gfac/server/GfacServerHandler.java | 5 +- .../gfac/client/GfacClientFactoryTest.java | 6 +- .../airavata/gfac/client/util/Initialize.java | 4 +- modules/gfac/pom.xml | 26 +++- modules/integration-tests/pom.xml | 26 +++- .../org/apache/airavata/integration/Man.java | 4 +- .../integration/AbstractIntegrationTest.java | 4 +- .../apache/airavata/integration/BaseCaseIT.java | 4 +- .../airavata/integration/DataRetrievalIT.java | 4 +- .../airavata/integration/ForEachCaseIT.java | 4 +- .../apache/airavata/integration/OsUtils.java | 4 +- .../integration/PasswordCallbackImpl.java | 19 +++ .../airavata/integration/SimpleEchoIT.java | 4 +- .../SingleAppIntegrationTestBase.java | 3 +- .../WorkflowIntegrationTestBase.java | 4 +- .../integration/WorkflowSamplesCaseIT.java | 4 +- .../integration/tools/DocumentCreatorNew.java | 5 +- .../integration/tools/DocumentCreatorUtils.java | 4 +- .../integration-tests/src/test/java/suite.xml | 30 ++-- modules/messaging/client/pom.xml | 26 +++- .../messaging/client/RabbitMQListener.java | 4 +- .../airavata/messaging/client/TestReader.java | 3 +- modules/messaging/core/pom.xml | 29 ++-- .../airavata/messaging/core/MessageContext.java | 4 +- .../airavata/messaging/core/MessageHandler.java | 4 +- .../messaging/core/MessagingConstants.java | 4 +- .../messaging/core/MessagingFactory.java | 3 +- .../airavata/messaging/core/Publisher.java | 4 +- .../messaging/core/PublisherFactory.java | 19 +++ .../messaging/core/RabbitMQProperties.java | 3 +- .../airavata/messaging/core/Subscriber.java | 4 +- .../airavata/messaging/core/TestClient.java | 4 +- .../apache/airavata/messaging/core/Type.java | 3 +- .../messaging/core/impl/ExperimentConsumer.java | 3 +- .../messaging/core/impl/ProcessConsumer.java | 3 +- .../impl/RabbitMQProcessLaunchConsumer.java | 19 +++ .../impl/RabbitMQProcessLaunchPublisher.java | 19 +++ .../messaging/core/impl/RabbitMQProducer.java | 19 +++ .../messaging/core/impl/RabbitMQPublisher.java | 3 +- .../core/impl/RabbitMQStatusPublisher.java | 19 +++ .../core/impl/RabbitMQStatusSubscriber.java | 19 +++ .../messaging/core/impl/RabbitMQSubscriber.java | 4 +- .../messaging/core/impl/StatusConsumer.java | 3 +- .../messaging/core/stats/CountWriterTask.java | 3 +- .../messaging/core/stats/LatencyWriterTask.java | 3 +- .../messaging/core/stats/StatCounter.java | 3 +- modules/messaging/pom.xml | 26 +++- modules/monitoring/pom.xml | 31 +++-- .../org/apache/airavata/monitoring/Main.java | 3 +- .../airavata/monitoring/MessageExtract.java | 3 +- .../org/apache/airavata/monitoring/Util.java | 3 +- .../monitoring/consumer/StatusConsumer.java | 3 +- .../monitoring/consumer/StatusReceiver.java | 3 +- .../monitoring/mailbox/GmailSMTPMailBox.java | 3 +- .../airavata/monitoring/mailbox/MailBox.java | 3 +- .../airavata/monitoring/mailbox/MailConfig.java | 3 +- .../producer/RabbitMQEmailPublisher.java | 3 +- .../monitoring/simulator/FetchPublish.java | 3 +- .../monitoring/simulator/Simulator.java | 3 +- modules/orchestrator/NULL | 1 - .../orchestrator/orchestrator-client/pom.xml | 31 +++-- .../client/OrchestratorClientFactory.java | 4 +- .../orchestrator/cpi/OrchestratorService.java | 19 +++ .../cpi/orchestrator_cpiConstants.java | 19 +++ .../sample/OrchestratorClientSample.java | 6 +- modules/orchestrator/orchestrator-core/pom.xml | 31 +++-- .../core/OrchestratorConfiguration.java | 5 +- .../core/context/OrchestratorContext.java | 5 +- .../core/exception/OrchestratorException.java | 5 +- .../core/impl/GFACPassiveJobSubmitter.java | 5 +- .../orchestrator/core/job/JobSubmitter.java | 5 +- .../core/utils/OrchestratorConstants.java | 5 +- .../core/utils/OrchestratorUtils.java | 5 +- .../core/validator/JobMetadataValidator.java | 5 +- .../validator/impl/BatchQueueValidator.java | 5 +- .../impl/ExperimentStatusValidator.java | 5 +- .../airavata/orchestrator/cpi/Orchestrator.java | 5 +- .../cpi/impl/AbstractOrchestrator.java | 5 +- .../cpi/impl/SimpleOrchestratorImpl.java | 5 +- .../orchestrator/core/BaseOrchestratorTest.java | 5 +- .../orchestrator/core/NewOrchestratorTest.java | 5 +- .../core/OrchestratorTestWithGRAM.java | 5 +- .../core/OrchestratorTestWithMyProxyAuth.java | 5 +- .../orchestrator/core/ValidatorTest.java | 19 +++ .../orchestrator/core/util/Initialize.java | 4 +- .../orchestrator/core/util/SecondValidator.java | 19 +++ .../orchestrator/core/util/TestValidator.java | 19 +++ .../orchestrator/orchestrator-service/pom.xml | 31 +++-- .../orchestrator/server/OrchestratorServer.java | 4 +- .../server/OrchestratorServerHandler.java | 4 +- .../airavata/orchestrator/util/Constants.java | 4 +- .../OrchestratorServerThreadPoolExecutor.java | 4 +- .../orchestrator/util/OrchestratorUtils.java | 3 +- .../client/OrchestratorClientFactoryTest.java | 6 +- .../orchestrator/client/util/Initialize.java | 4 +- modules/orchestrator/pom.xml | 26 +++- modules/registry/pom.xml | 26 +++- modules/registry/registry-core/pom.xml | 26 +++- .../core/app/catalog/impl/AppCatalogImpl.java | 4 +- .../catalog/impl/ApplicationDeploymentImpl.java | 4 +- .../catalog/impl/ApplicationInterfaceImpl.java | 4 +- .../app/catalog/impl/ComputeResourceImpl.java | 4 +- .../catalog/impl/GwyResourceProfileImpl.java | 4 +- .../app/catalog/impl/StorageResourceImpl.java | 4 +- .../catalog/impl/UsrResourceProfileImpl.java | 4 +- .../core/app/catalog/model/AppEnvironment.java | 4 +- .../app/catalog/model/AppEnvironment_PK.java | 4 +- .../core/app/catalog/model/AppInput_PK.java | 4 +- .../app/catalog/model/AppModuleMapping.java | 4 +- .../app/catalog/model/AppModuleMapping_PK.java | 4 +- .../core/app/catalog/model/AppOutput_PK.java | 4 +- .../catalog/model/ApplicationDeployment.java | 4 +- .../app/catalog/model/ApplicationIntInput.java | 4 +- .../app/catalog/model/ApplicationIntOutput.java | 4 +- .../app/catalog/model/ApplicationInterface.java | 4 +- .../app/catalog/model/ApplicationModule.java | 4 +- .../core/app/catalog/model/BatchQueue.java | 4 +- .../core/app/catalog/model/BatchQueue_PK.java | 4 +- .../app/catalog/model/CloudJobSubmission.java | 5 +- .../core/app/catalog/model/ComputeResource.java | 4 +- .../model/ComputeResourceFileSystem.java | 4 +- .../model/ComputeResourceFileSystem_PK.java | 4 +- .../model/ComputeResourcePreference.java | 4 +- .../model/ComputeResourcePreferencePK.java | 4 +- .../core/app/catalog/model/Configuration.java | 19 +++ .../app/catalog/model/Configuration_PK.java | 4 +- .../catalog/model/DataMovementInterface.java | 4 +- .../catalog/model/DataMovementInterface_PK.java | 4 +- .../app/catalog/model/DataStorageResource.java | 4 +- .../core/app/catalog/model/GSISSHExport.java | 4 +- .../core/app/catalog/model/GSISSHExportPK.java | 4 +- .../app/catalog/model/GSISSHSubmission.java | 4 +- .../core/app/catalog/model/GatewayProfile.java | 4 +- .../app/catalog/model/GlobusGKEndPointPK.java | 4 +- .../app/catalog/model/GlobusGKEndpoint.java | 4 +- .../app/catalog/model/GlobusJobSubmission.java | 4 +- .../app/catalog/model/GridftpDataMovement.java | 4 +- .../core/app/catalog/model/GridftpEndpoint.java | 4 +- .../app/catalog/model/GridftpEndpoint_PK.java | 4 +- .../core/app/catalog/model/HostAlias.java | 4 +- .../core/app/catalog/model/HostAliasPK.java | 4 +- .../core/app/catalog/model/HostIPAddress.java | 4 +- .../core/app/catalog/model/HostIPAddressPK.java | 4 +- .../app/catalog/model/JobManagerCommand.java | 4 +- .../app/catalog/model/JobManagerCommand_PK.java | 4 +- .../catalog/model/JobSubmissionInterface.java | 4 +- .../model/JobSubmissionInterface_PK.java | 4 +- .../app/catalog/model/LibraryApendPath.java | 4 +- .../app/catalog/model/LibraryApendPath_PK.java | 4 +- .../app/catalog/model/LibraryPrepandPath.java | 4 +- .../catalog/model/LibraryPrepandPath_PK.java | 4 +- .../app/catalog/model/LocalDataMovement.java | 4 +- .../core/app/catalog/model/LocalSubmission.java | 4 +- .../core/app/catalog/model/ModuleLoadCmd.java | 4 +- .../app/catalog/model/ModuleLoadCmd_PK.java | 4 +- .../catalog/model/ParallelismPrefixCommand.java | 4 +- .../model/ParallelismPrefixCommand_PK.java | 4 +- .../core/app/catalog/model/PostJobCommand.java | 4 +- .../app/catalog/model/PostJobCommandPK.java | 4 +- .../core/app/catalog/model/PreJobCommand.java | 4 +- .../core/app/catalog/model/PreJobCommandPK.java | 4 +- .../app/catalog/model/ResourceJobManager.java | 4 +- .../core/app/catalog/model/ScpDataMovement.java | 4 +- .../app/catalog/model/SshJobSubmission.java | 4 +- .../app/catalog/model/StorageInterface.java | 4 +- .../app/catalog/model/StorageInterface_PK.java | 4 +- .../app/catalog/model/StoragePreference.java | 4 +- .../app/catalog/model/StoragePreferencePK.java | 4 +- .../core/app/catalog/model/StorageResource.java | 4 +- .../app/catalog/model/UnicoreDataMovement.java | 6 +- .../app/catalog/model/UnicoreJobSubmission.java | 6 +- .../model/UserComputeResourcePreference.java | 4 +- .../model/UserComputeResourcePreferencePK.java | 4 +- .../app/catalog/model/UserResourceProfile.java | 4 +- .../catalog/model/UserResourceProfilePK.java | 4 +- .../catalog/model/UserStoragePreference.java | 4 +- .../catalog/model/UserStoragePreferencePK.java | 4 +- .../resources/AppCatAbstractResource.java | 4 +- .../catalog/resources/AppCatalogResource.java | 19 +++ .../resources/AppDeploymentResource.java | 4 +- .../resources/AppEnvironmentResource.java | 4 +- .../catalog/resources/AppInterfaceResource.java | 4 +- ...ppModuleMappingAppCatalogResourceAppCat.java | 4 +- .../catalog/resources/AppModuleResource.java | 4 +- .../resources/ApplicationInputResource.java | 2 +- .../resources/ApplicationOutputResource.java | 2 +- .../catalog/resources/BatchQueueResource.java | 4 +- .../resources/CloudSubmissionResource.java | 5 +- .../ComputeHostPreferenceResource.java | 4 +- .../ComputeResourceFileSystemResource.java | 4 +- .../resources/ComputeResourceResource.java | 4 +- .../DataMovementInterfaceResource.java | 4 +- .../catalog/resources/GSISSHExportResource.java | 2 +- .../resources/GSISSHSubmissionResource.java | 2 +- .../resources/GatewayProfileResource.java | 2 +- .../resources/GlobusGKEndpointResource.java | 2 +- .../resources/GlobusJobSubmissionResource.java | 2 +- .../resources/GridftpDataMovementResource.java | 2 +- .../resources/GridftpEndpointResource.java | 2 +- .../catalog/resources/HostAliasAppResource.java | 2 +- .../resources/HostIPAddressResource.java | 2 +- .../resources/JobManagerCommandResource.java | 4 +- .../JobSubmissionInterfaceResource.java | 4 +- .../resources/LibraryApendPathResource.java | 4 +- .../resources/LibraryPrepandPathResource.java | 4 +- .../resources/LocalDataMovementResource.java | 4 +- .../resources/LocalSubmissionResource.java | 4 +- .../resources/ModuleLoadCmdResource.java | 4 +- .../ParallelismPrefixCommandResource.java | 4 +- .../resources/PostJobCommandResource.java | 2 +- .../resources/PreJobCommandResource.java | 2 +- .../resources/ResourceJobManagerResource.java | 4 +- .../resources/ScpDataMovementResource.java | 2 +- .../resources/SshJobSubmissionResource.java | 2 +- .../resources/StorageInterfaceResource.java | 4 +- .../resources/StoragePreferenceResource.java | 4 +- .../resources/StorageResourceResource.java | 4 +- .../resources/UnicoreDataMovementResource.java | 6 +- .../resources/UnicoreJobSubmissionResource.java | 6 +- .../UserComputeHostPreferenceResource.java | 4 +- .../resources/UserResourceProfileResource.java | 2 +- .../UserStoragePreferenceResource.java | 4 +- .../app/catalog/util/AppCatalogJPAUtils.java | 4 +- .../catalog/util/AppCatalogQueryGenerator.java | 4 +- .../catalog/util/AppCatalogResourceType.java | 4 +- .../util/AppCatalogThriftConversion.java | 4 +- .../core/app/catalog/util/AppCatalogUtils.java | 4 +- .../experiment/catalog/ExpCatResourceUtils.java | 5 +- .../catalog/ExperimentCatResource.java | 5 +- .../core/experiment/catalog/JPAConstants.java | 4 +- .../core/experiment/catalog/ResourceType.java | 5 +- .../catalog/impl/ExperimentCatalogImpl.java | 4 +- .../catalog/impl/ExperimentRegistry.java | 4 +- .../catalog/impl/GatewayRegistry.java | 4 +- .../catalog/impl/NotificationRegistry.java | 4 +- .../catalog/impl/ProjectRegistry.java | 4 +- .../catalog/impl/RegistryFactory.java | 4 +- .../experiment/catalog/impl/UserRegistry.java | 4 +- .../experiment/catalog/model/Experiment.java | 5 +- .../catalog/model/ExperimentError.java | 5 +- .../catalog/model/ExperimentErrorPK.java | 5 +- .../catalog/model/ExperimentInput.java | 5 +- .../catalog/model/ExperimentInputPK.java | 5 +- .../catalog/model/ExperimentOutput.java | 5 +- .../catalog/model/ExperimentOutputPK.java | 5 +- .../catalog/model/ExperimentStatus.java | 5 +- .../catalog/model/ExperimentStatusPK.java | 5 +- .../catalog/model/ExperimentSummary.java | 5 +- .../core/experiment/catalog/model/Gateway.java | 5 +- .../experiment/catalog/model/GatewayWorker.java | 5 +- .../catalog/model/GatewayWorkerPK.java | 5 +- .../core/experiment/catalog/model/Job.java | 5 +- .../core/experiment/catalog/model/JobPK.java | 5 +- .../experiment/catalog/model/JobStatus.java | 5 +- .../experiment/catalog/model/JobStatusPK.java | 5 +- .../experiment/catalog/model/Notification.java | 5 +- .../core/experiment/catalog/model/Process.java | 5 +- .../experiment/catalog/model/ProcessError.java | 5 +- .../catalog/model/ProcessErrorPK.java | 5 +- .../experiment/catalog/model/ProcessInput.java | 5 +- .../catalog/model/ProcessInputPK.java | 5 +- .../experiment/catalog/model/ProcessOutput.java | 5 +- .../catalog/model/ProcessOutputPK.java | 5 +- .../catalog/model/ProcessResourceSchedule.java | 5 +- .../experiment/catalog/model/ProcessStatus.java | 5 +- .../catalog/model/ProcessStatusPK.java | 5 +- .../core/experiment/catalog/model/Project.java | 5 +- .../experiment/catalog/model/ProjectUser.java | 5 +- .../experiment/catalog/model/ProjectUserPK.java | 5 +- .../experiment/catalog/model/QueueStatus.java | 5 +- .../experiment/catalog/model/QueueStatusPK.java | 5 +- .../core/experiment/catalog/model/Task.java | 5 +- .../experiment/catalog/model/TaskError.java | 5 +- .../experiment/catalog/model/TaskErrorPK.java | 5 +- .../experiment/catalog/model/TaskStatus.java | 5 +- .../experiment/catalog/model/TaskStatusPK.java | 5 +- .../catalog/model/UserConfigurationData.java | 5 +- .../core/experiment/catalog/model/UserPK.java | 5 +- .../core/experiment/catalog/model/Users.java | 5 +- .../resources/AbstractExpCatResource.java | 3 +- .../resources/ExperimentErrorResource.java | 4 +- .../resources/ExperimentInputResource.java | 4 +- .../resources/ExperimentOutputResource.java | 4 +- .../catalog/resources/ExperimentResource.java | 4 +- .../resources/ExperimentStatisticsResource.java | 5 +- .../resources/ExperimentStatusResource.java | 4 +- .../resources/ExperimentSummaryResource.java | 5 +- .../catalog/resources/GatewayResource.java | 5 +- .../catalog/resources/JobResource.java | 4 +- .../catalog/resources/JobStatusResource.java | 4 +- .../catalog/resources/NotificationResource.java | 5 +- .../catalog/resources/ProcessErrorResource.java | 4 +- .../catalog/resources/ProcessInputResource.java | 4 +- .../resources/ProcessOutputResource.java | 4 +- .../catalog/resources/ProcessResource.java | 4 +- .../ProcessResourceScheduleResource.java | 4 +- .../resources/ProcessStatusResource.java | 4 +- .../catalog/resources/ProjectResource.java | 5 +- .../catalog/resources/ProjectUserResource.java | 4 +- .../catalog/resources/QueueStatusResource.java | 5 +- .../catalog/resources/TaskErrorResource.java | 4 +- .../catalog/resources/TaskResource.java | 4 +- .../catalog/resources/TaskStatusResource.java | 4 +- .../UserConfigurationDataResource.java | 4 +- .../catalog/resources/UserResource.java | 5 +- .../experiment/catalog/resources/Utils.java | 3 +- .../catalog/resources/WorkerResource.java | 9 +- .../catalog/utils/QueryGenerator.java | 4 +- .../utils/ThriftDataModelConversion.java | 19 +++ .../registry/core/impl/RegistryImpl.java | 6 +- .../catalog/impl/ReplicaCatalogImpl.java | 4 +- .../replica/catalog/model/Configuration.java | 19 +++ .../replica/catalog/model/Configuration_PK.java | 4 +- .../core/replica/catalog/model/DataProduct.java | 5 +- .../catalog/model/DataProductMetaData.java | 5 +- .../catalog/model/DataProductMetaData_PK.java | 5 +- .../catalog/model/DataReplicaLocation.java | 5 +- .../catalog/model/DataReplicaMetaData.java | 5 +- .../catalog/model/DataReplicaMetaData_PK.java | 5 +- .../catalog/utils/ReplicaCatalogConstants.java | 3 +- .../catalog/utils/ReplicaCatalogJPAUtils.java | 4 +- .../utils/ReplicaCatalogQueryGenerator.java | 4 +- .../utils/ThriftDataModelConversion.java | 19 +++ .../catalog/impl/WorkflowCatalogImpl.java | 4 +- .../workflow/catalog/model/ComponentStatus.java | 4 +- .../core/workflow/catalog/model/Edge.java | 4 +- .../core/workflow/catalog/model/Edge_PK.java | 4 +- .../core/workflow/catalog/model/Node.java | 4 +- .../core/workflow/catalog/model/Node_PK.java | 4 +- .../core/workflow/catalog/model/Port.java | 4 +- .../core/workflow/catalog/model/Port_PK.java | 4 +- .../core/workflow/catalog/model/Workflow.java | 4 +- .../workflow/catalog/model/WorkflowInput.java | 4 +- .../catalog/model/WorkflowInput_PK.java | 4 +- .../workflow/catalog/model/WorkflowOutput.java | 4 +- .../catalog/model/WorkflowOutput_PK.java | 4 +- .../workflow/catalog/model/WorkflowStatus.java | 4 +- .../catalog/model/WorkflowStatus_PK.java | 4 +- .../resources/ComponentStatusResource.java | 2 +- .../catalog/resources/EdgeResource.java | 2 +- .../catalog/resources/NodeResource.java | 2 +- .../catalog/resources/PortResource.java | 2 +- .../resources/WorkflowCatAbstractResource.java | 4 +- .../resources/WorkflowCatalogResource.java | 19 +++ .../resources/WorkflowInputResource.java | 2 +- .../resources/WorkflowOutputResource.java | 2 +- .../catalog/resources/WorkflowResource.java | 4 +- .../resources/WorkflowStatusResource.java | 2 +- .../catalog/utils/WorkflowCatalogJPAUtils.java | 4 +- .../utils/WorkflowCatalogQueryGenerator.java | 4 +- .../utils/WorkflowCatalogResourceType.java | 4 +- .../utils/WorkflowCatalogThriftConversion.java | 4 +- .../catalog/utils/WorkflowCatalogUtils.java | 4 +- .../airavata/app/catalog/AppDeploymentTest.java | 4 +- .../airavata/app/catalog/AppInterfaceTest.java | 4 +- ...puteAppCatalogExperimentCatResourceTest.java | 4 +- .../app/catalog/GatewayProfileTest.java | 4 +- .../catalog/StorageResourceAppCatalogTest.java | 4 +- .../app/catalog/UserResourceProfileTest.java | 4 +- .../airavata/app/catalog/util/Initialize.java | 4 +- .../catalog/AbstractResourceTest.java | 4 +- .../catalog/ExperimentInputResourceTest.java | 19 +++ .../catalog/ExperimentOutputResourceTest.java | 19 +++ .../catalog/ExperimentResourceTest.java | 19 +++ .../experiment/catalog/GatewayResourceTest.java | 19 +++ .../experiment/catalog/JobResourceTest.java | 2 +- .../experiment/catalog/ProcessResourceTest.java | 2 +- .../catalog/QueueStatusResourceTest.java | 19 +++ .../experiment/catalog/TaskResourceTest.java | 2 +- .../catalog/UserConfigurationDataTest.java | 4 +- .../experiment/catalog/UserResourceTest.java | 19 +++ .../experiment/catalog/util/Initialize.java | 4 +- .../replica/catalog/ReplicaCatalogTest.java | 5 +- .../replica/catalog/util/Initialize.java | 4 +- modules/registry/registry-cpi/pom.xml | 26 +++- .../airavata/registry/cpi/AppCatalog.java | 2 +- .../registry/cpi/AppCatalogException.java | 2 +- .../registry/cpi/ApplicationDeployment.java | 2 +- .../registry/cpi/ApplicationInterface.java | 2 +- .../registry/cpi/CompositeIdentifier.java | 4 +- .../airavata/registry/cpi/ComputeResource.java | 2 +- .../registry/cpi/ExpCatChildDataType.java | 2 +- .../registry/cpi/ExpCatParentDataType.java | 2 +- .../registry/cpi/ExperimentCatalog.java | 2 +- .../cpi/ExperimentCatalogException.java | 6 +- .../cpi/ExperimentCatalogModelType.java | 2 +- .../registry/cpi/GwyClientCredential.java | 2 +- .../registry/cpi/GwyResourceProfile.java | 2 +- .../apache/airavata/registry/cpi/Registry.java | 6 +- .../registry/cpi/RegistryException.java | 4 +- .../airavata/registry/cpi/ReplicaCatalog.java | 2 +- .../registry/cpi/ReplicaCatalogException.java | 2 +- .../airavata/registry/cpi/ResultOrderType.java | 19 +++ .../airavata/registry/cpi/StorageResource.java | 8 +- .../registry/cpi/UsrResourceProfile.java | 2 +- .../airavata/registry/cpi/WorkflowCatalog.java | 6 +- .../registry/cpi/WorkflowCatalogException.java | 2 +- .../airavata/registry/cpi/utils/Constants.java | 4 +- .../airavata/registry/cpi/utils/StatusType.java | 2 +- modules/registry/registry-server/pom.xml | 28 +++- .../registry-api-service/pom.xml | 21 +++ .../registry/api/service/RegistryAPIServer.java | 5 +- .../service/handler/RegistryServerHandler.java | 5 +- .../api/service/util/AppCatalogInitUtil.java | 19 +++ .../api/service/util/ConnectionPool.java | 6 +- .../registry/api/service/util/Constants.java | 4 +- .../api/service/util/DatabaseCreator.java | 5 +- .../service/util/ExperimentCatalogInitUtil.java | 19 +++ .../registry/api/service/util/JdbcStorage.java | 5 +- .../service/util/ReplicaCatalogInitUtil.java | 19 +++ .../service/util/WorkflowCatalogInitUtil.java | 19 +++ .../registry-server/registry-api-stubs/pom.xml | 21 +++ .../airavata/registry/api/RegistryService.java | 19 +++ .../client/RegistryServiceClientFactory.java | 4 +- .../api/exception/RegistryServiceException.java | 19 +++ .../registry/api/registry_apiConstants.java | 19 +++ modules/registry/registry-tools/jpa-gen/pom.xml | 26 +++- .../computeresource/BatchQueueGenerator.java | 4 +- .../ComputeResourceDescriptionGenerator.java | 4 +- .../DataMovementInterfaceGenerator.java | 4 +- .../computeresource/FileSystemsGenerator.java | 4 +- .../GridFTPDataMovementGenerator.java | 4 +- .../GridFTPEndpointsGenerator.java | 4 +- .../JobManagerCommandGenerator.java | 4 +- .../JobSubmissionInterfaceGenerator.java | 4 +- .../LocalDataMovementGenerator.java | 4 +- .../LocalSubmissionGenerator.java | 4 +- .../computeresource/ModuleCMDGenerator.java | 4 +- .../ResourceJobManagerGenerator.java | 4 +- .../SCPDataMovementGenerator.java | 4 +- .../SSHJobSubmissionGenerator.java | 4 +- .../main/java/generators/AbstractGenerator.java | 19 +++ .../main/java/generators/JPAClassGenerator.java | 19 +++ .../generators/JPAResourceClassGenerator.java | 19 +++ .../src/main/java/generators/SQLGenerator.java | 19 +++ .../src/main/java/model/JPAClassField.java | 19 +++ .../src/main/java/model/JPAClassModel.java | 19 +++ .../src/main/java/model/JPAPKClassModel.java | 19 +++ .../main/java/model/JPAResourceClassModel.java | 19 +++ .../jpa-gen/src/main/java/model/SQLData.java | 19 +++ .../jpa-gen/src/main/java/test/Test.java | 19 +++ modules/registry/registry-tools/pom.xml | 26 +++- .../registry-tools/registry-tool/pom.xml | 26 +++- .../airavata/registry/tool/DBMigrator.java | 4 +- .../DeltaScripts/appCatalog_schema_delta.sql | 20 +++ .../credentialStore_schema_delta.sql | 20 +++ .../DeltaScripts/expCatalog_schema_delta.sql | 20 +++ .../replicaCatalog_schema_delta.sql | 20 +++ .../DeltaScripts/workFlow_schema_delta.sql | 20 +++ modules/security/pom.xml | 30 ++-- .../security/AbstractAuthenticator.java | 4 +- .../security/AbstractDatabaseAuthenticator.java | 4 +- .../security/AiravataSecurityException.java | 3 +- .../security/AuthenticationException.java | 4 +- .../apache/airavata/security/Authenticator.java | 4 +- .../apache/airavata/security/Authoriser.java | 4 +- .../org/apache/airavata/security/UserStore.java | 4 +- .../airavata/security/UserStoreException.java | 4 +- .../AbstractConfigurationReader.java | 4 +- .../AuthenticatorConfigurationReader.java | 4 +- .../userstore/AbstractJDBCUserStore.java | 4 +- .../security/userstore/JDBCUserStore.java | 4 +- .../security/userstore/LDAPUserStore.java | 4 +- .../security/userstore/SessionDBUserStore.java | 4 +- .../security/util/PasswordDigester.java | 4 +- .../security/util/TrustStoreManager.java | 3 +- .../AuthenticatorConfigurationReaderTest.java | 4 +- .../configurations/TestDBAuthenticator1.java | 4 +- .../configurations/TestDBAuthenticator2.java | 4 +- .../configurations/TestDBAuthenticator3.java | 4 +- .../security/configurations/TestUserStore.java | 36 +++-- .../security/userstore/JDBCUserStoreTest.java | 36 +++-- .../security/userstore/LDAPUserStoreTest.java | 36 +++-- .../userstore/SessionDBUserStoreTest.java | 36 +++-- modules/server/pom.xml | 30 ++-- .../org/apache/airavata/server/ServerMain.java | 3 +- modules/sharing-registry/pom.xml | 21 +++ .../sharing-data-migrator/pom.xml | 21 +++ .../migrator/airavata/AiravataDataMigrator.java | 5 +- .../migrator/airavata/ConnectionFactory.java | 5 +- .../sharing-registry-distribution/pom.xml | 21 +++ .../src/main/assembly/bin-assembly.xml | 37 ++--- .../sharing-registry-server/pom.xml | 27 ++++ .../registry/db/entities/DomainEntity.java | 5 +- .../registry/db/entities/EntityEntity.java | 5 +- .../sharing/registry/db/entities/EntityPK.java | 5 +- .../registry/db/entities/EntityTypeEntity.java | 5 +- .../registry/db/entities/EntityTypePK.java | 5 +- .../db/entities/GroupMembershipEntity.java | 5 +- .../registry/db/entities/GroupMembershipPK.java | 5 +- .../db/entities/PermissionTypeEntity.java | 5 +- .../registry/db/entities/PermissionTypePK.java | 5 +- .../registry/db/entities/SharingEntity.java | 5 +- .../sharing/registry/db/entities/SharingPK.java | 5 +- .../registry/db/entities/UserEntity.java | 5 +- .../registry/db/entities/UserGroupEntity.java | 5 +- .../registry/db/entities/UserGroupPK.java | 5 +- .../sharing/registry/db/entities/UserPK.java | 5 +- .../db/repositories/AbstractRepository.java | 5 +- .../db/repositories/DomainRepository.java | 5 +- .../db/repositories/EntityRepository.java | 5 +- .../db/repositories/EntityTypeRepository.java | 5 +- .../repositories/GroupMembershipRepository.java | 5 +- .../repositories/PermissionTypeRepository.java | 5 +- .../db/repositories/SharingRepository.java | 5 +- .../db/repositories/UserGroupRepository.java | 5 +- .../db/repositories/UserRepository.java | 5 +- .../sharing/registry/db/utils/Committer.java | 5 +- .../registry/db/utils/ConnectionPool.java | 5 +- .../sharing/registry/db/utils/DBConstants.java | 5 +- .../registry/db/utils/DatabaseCreator.java | 5 +- .../sharing/registry/db/utils/JPAUtils.java | 5 +- .../sharing/registry/db/utils/JdbcStorage.java | 5 +- .../db/utils/ObjectMapperSingleton.java | 5 +- .../sharing/registry/server/ServerMain.java | 5 +- .../registry/server/SharingRegistryServer.java | 5 +- .../server/SharingRegistryServerHandler.java | 5 +- .../airavata/sharing/registry/CipresTest.java | 5 +- .../SharingRegistryServerHandlerTest.java | 5 +- .../registry/SharingRegistryServiceTest.java | 5 +- .../sharing/registry/util/Initialize.java | 4 +- .../sharing-registry-stubs/pom.xml | 21 +++ .../SharingRegistryServiceClientFactory.java | 5 +- .../sharing/registry/models/Domain.java | 19 +++ .../sharing/registry/models/Entity.java | 19 +++ .../registry/models/EntitySearchField.java | 19 +++ .../sharing/registry/models/EntityType.java | 19 +++ .../registry/models/GroupCardinality.java | 19 +++ .../sharing/registry/models/GroupChildType.java | 19 +++ .../registry/models/GroupMembership.java | 19 +++ .../sharing/registry/models/GroupType.java | 19 +++ .../sharing/registry/models/PermissionType.java | 19 +++ .../registry/models/SearchCondition.java | 19 +++ .../sharing/registry/models/SearchCriteria.java | 19 +++ .../sharing/registry/models/Sharing.java | 19 +++ .../models/SharingRegistryException.java | 19 +++ .../sharing/registry/models/SharingType.java | 19 +++ .../airavata/sharing/registry/models/User.java | 19 +++ .../sharing/registry/models/UserGroup.java | 19 +++ .../models/sharing_modelsConstants.java | 19 +++ .../service/cpi/SharingRegistryService.java | 19 +++ .../sharing-service-docs/api-docs/index.html | 21 +++ .../api-docs/sharing_cpi.html | 21 +++ .../api-docs/sharing_models.html | 21 +++ .../sharing-service-docs/api-docs/style.css | 22 ++- .../sharing-service-docs/index.html | 21 +++ .../sharing-service-docs/style.css | 22 ++- .../thrift_models/thrift-gen.sh | 20 +++ .../test-suite/multi-tenanted-airavata/pom.xml | 26 +++- .../multitenantedairavata/AiravataClient.java | 6 +- .../multitenantedairavata/AiravataIT.java | 6 +- .../ApplicationRegister.java | 6 +- .../ComputeResourceRegister.java | 6 +- .../ExperimentExecution.java | 6 +- .../FrameworkBootstrapping.java | 19 +++ .../multitenantedairavata/FrameworkSetup.java | 6 +- .../multitenantedairavata/GatewayRegister.java | 6 +- .../StorageResourceRegister.java | 19 +++ .../TestFrameworkProps.java | 6 +- .../utils/ApplicationProperties.java | 19 +++ .../utils/ComputeResourceProperties.java | 19 +++ .../utils/FrameworkUtils.java | 6 +- .../utils/PropertyFileType.java | 6 +- .../utils/PropertyReader.java | 6 +- .../utils/TestFrameworkConstants.java | 6 +- modules/test-suite/pom.xml | 26 +++- modules/user-profile-migration/pom.xml | 31 +++-- .../apache/airavata/ISLoginCredentialsDAO.java | 19 +++ .../apache/airavata/IdentityServerClient.java | 19 +++ .../org/apache/airavata/MigrationManager.java | 4 +- .../UserProfileAiravataThriftClient.java | 4 +- .../org/apache/airavata/UserProfileDAO.java | 4 +- modules/user-profile/pom.xml | 31 +++-- modules/user-profile/user-profile-core/pom.xml | 21 +++ .../core/UserProfileRegistryException.java | 2 +- .../core/entities/NSFDemographicsEntity.java | 2 +- .../core/entities/UserProfileEntity.java | 2 +- .../core/repositories/AbstractRepository.java | 2 +- .../repositories/UserProfileRepository.java | 2 +- .../user/registry/core/utils/Committer.java | 2 +- .../user/registry/core/utils/JPAUtils.java | 2 +- .../core/utils/ObjectMapperSingleton.java | 2 +- .../registry/core/utils/QueryConstants.java | 19 +++ .../user/registry/core/utils/Utils.java | 3 +- .../user-profile/user-profile-service/pom.xml | 21 +++ .../user/profile/server/UserProfileServer.java | 6 +- .../server/UserProfileServiceHandler.java | 5 +- modules/user-profile/user-profile-stubs/pom.xml | 31 +++-- .../userprofile/cpi/UserProfileService.java | 19 +++ .../client/UserProfileServiceClientFactory.java | 3 +- .../exception/UserProfileServiceException.java | 19 +++ .../cpi/user_profile_cpiConstants.java | 19 +++ modules/workflow-model/pom.xml | 26 +++- modules/workflow-model/workflow-engine/pom.xml | 26 +++- .../catalog/WorkflowCatalogFactory.java | 4 +- .../workflow/engine/WorkflowEngine.java | 4 +- .../engine/WorkflowEngineException.java | 4 +- .../workflow/engine/WorkflowEngineFactory.java | 4 +- .../workflow/engine/WorkflowEngineImpl.java | 4 +- .../airavata/workflow/engine/WorkflowUtils.java | 4 +- .../engine/concurrent/PredicatedExecutable.java | 5 +- .../engine/concurrent/PredicatedTaskRunner.java | 5 +- .../engine/core/amazon/AmazonCredential.java | 4 +- .../engine/core/amazon/EC2InstanceResult.java | 19 +++ .../engine/core/generators/XmlBeansFiler.java | 4 +- .../core/workflow/ParameterListModel.java | 4 +- .../engine/datadriven/WorkflowHarvester.java | 4 +- .../engine/file/XBayaPathConstants.java | 4 +- .../engine/gfac/GFacRegistryClient.java | 4 +- .../workflow/engine/gfac/SimpleWSClient.java | 4 +- .../engine/globus/FileTransferConstants.java | 4 +- .../globus/GridFTPFileTransferClient.java | 19 +++ .../engine/graph/controller/NodeController.java | 19 +++ .../engine/interpretor/DoWhileHandler.java | 3 +- .../engine/interpretor/HeaderConstants.java | 4 +- .../SSWorkflowInterpreterInteractorImpl.java | 4 +- .../interpretor/SystemComponentInvoker.java | 4 +- .../WorkFlowInterpreterException.java | 4 +- .../interpretor/WorkflowExecutionMessage.java | 4 +- .../engine/interpretor/WorkflowInterpreter.java | 4 +- .../WorkflowInterpreterConfiguration.java | 4 +- .../WorkflowInterpreterInteractor.java | 4 +- .../interpretor/WorkflowInterpreterInvoker.java | 4 +- .../WorkflowInterpreterSkeleton2.java | 19 +++ .../engine/invoker/AsynchronousInvoker.java | 4 +- .../workflow/engine/invoker/DynamicInvoker.java | 4 +- .../workflow/engine/invoker/Invoker.java | 4 +- .../invoker/MsgBoxWsaResponsesCorrelator.java | 19 +++ .../workflow/engine/invoker/SimpleInvoker.java | 4 +- .../engine/invoker/WorkflowInputUtil.java | 5 +- .../workflow/engine/util/AmazonUtil.java | 4 +- .../airavata/workflow/engine/util/Data.java | 4 +- .../workflow/engine/util/GOConstants.java | 4 +- .../workflow/engine/util/GlobusOnlineUtils.java | 19 +++ .../workflow/engine/util/InterpreterUtil.java | 3 +- .../engine/util/ProxyMonitorPublisher.java | 4 +- .../workflow/engine/util/RegistryConstants.java | 4 +- .../workflow/engine/util/TransferFile.java | 4 +- .../workflow/engine/util/XBayaUtil.java | 4 +- .../workflow/WorkflowEngineException.java | 4 +- .../engine/workflow/proxy/ProxyWSDL.java | 4 +- .../engine/workflow/proxy/WorkflowClient.java | 4 +- .../engine/workflow/proxy/WorkflowContext.java | 4 +- .../workflow/proxy/WorkflowProxyException.java | 4 +- .../interpreter/ComplexForEachWorkflowTest.java | 19 +++ .../xbaya/interpreter/ComplexMathService.java | 4 +- .../interpreter/ComplexMathWorkflowTest.java | 19 +++ .../interpreter/CrossProductWorkflowTest.java | 19 +++ .../airavata/xbaya/interpreter/EchoService.java | 3 +- .../xbaya/interpreter/ForEachWorkflowTest.java | 19 +++ .../interpreter/LevenshteinDistanceService.java | 4 +- .../airavata/xbaya/interpreter/Listener.java | 19 +++ .../xbaya/interpreter/NotificationSender.java | 19 +++ .../xbaya/interpreter/RegistryServiceTest.java | 19 +++ .../interpreter/SimpleForEachWorkflowTest.java | 19 +++ .../interpreter/SimpleMathWorkflowTest.java | 19 +++ .../xbaya/interpreter/WorkflowTest.java | 19 +++ .../xbaya/interpreter/WorkflowTrackingTest.java | 19 +++ .../xbaya/interpreter/XBayaClientTest.java | 5 +- .../interpreter/XBayaConsolidatedTestSuite.java | 19 +++ .../xbaya/interpreter/utils/ConfigKeys.java | 5 +- .../xbaya/interpreter/utils/TestUtilServer.java | 19 +++ .../interpreter/utils/WorkflowTestUtils.java | 19 +++ .../workflow-model-component/pom.xml | 26 +++- .../registry/JCRComponentReference.java | 4 +- .../registry/JCRComponentRegistry.java | 4 +- .../workflow-model/workflow-model-core/pom.xml | 26 +++- .../workflow/model/component/Component.java | 4 +- .../model/component/ComponentControlPort.java | 4 +- .../model/component/ComponentDataPort.java | 4 +- .../model/component/ComponentEPRPort.java | 4 +- .../model/component/ComponentException.java | 4 +- .../component/ComponentOperationReference.java | 4 +- .../workflow/model/component/ComponentPort.java | 4 +- .../model/component/ComponentReference.java | 4 +- .../model/component/ComponentRegistry.java | 4 +- .../component/ComponentRegistryException.java | 4 +- .../amazon/AmazonComponentRegistry.java | 4 +- .../component/amazon/InstanceComponent.java | 4 +- .../amazon/InstanceComponentDataPort.java | 4 +- .../amazon/TerminateInstanceComponent.java | 4 +- .../component/dynamic/DynamicComponent.java | 4 +- .../component/dynamic/DynamicComponentPort.java | 4 +- .../local/LocalComponentReference.java | 4 +- .../component/local/LocalComponentRegistry.java | 4 +- .../model/component/system/BlockComponent.java | 4 +- .../component/system/ConstantComponent.java | 4 +- .../system/DifferedInputComponent.java | 8 +- .../component/system/DoWhileComponent.java | 4 +- .../component/system/EndBlockComponent.java | 4 +- .../component/system/EndDoWhileComponent.java | 4 +- .../component/system/EndForEachComponent.java | 4 +- .../model/component/system/EndifComponent.java | 4 +- .../model/component/system/ExitComponent.java | 4 +- .../component/system/ForEachComponent.java | 4 +- .../model/component/system/IfComponent.java | 4 +- .../model/component/system/InputComponent.java | 4 +- .../model/component/system/MemoComponent.java | 4 +- .../model/component/system/OutputComponent.java | 4 +- .../component/system/ReceiveComponent.java | 4 +- .../component/system/S3InputComponent.java | 4 +- .../component/system/StreamSourceComponent.java | 4 +- .../component/system/SubWorkflowComponent.java | 4 +- .../model/component/system/SystemComponent.java | 4 +- .../system/SystemComponentDataPort.java | 4 +- .../system/SystemComponentReference.java | 4 +- .../system/SystemComponentRegistry.java | 4 +- .../component/url/URLComponentReference.java | 4 +- .../component/url/URLComponentRegistry.java | 4 +- .../component/web/WebComponentReference.java | 4 +- .../component/web/WebComponentRegistry.java | 4 +- .../model/component/ws/WSComponent.java | 4 +- .../component/ws/WSComponentApplication.java | 4 +- .../ws/WSComponentApplicationParameter.java | 4 +- .../model/component/ws/WSComponentFactory.java | 4 +- .../model/component/ws/WSComponentKey.java | 4 +- .../model/component/ws/WSComponentPort.java | 4 +- .../component/ws/WSComponentReference.java | 4 +- .../model/component/ws/WSComponentRegistry.java | 4 +- .../model/component/ws/WorkflowComponent.java | 4 +- .../exceptions/LazyLoadedDataException.java | 4 +- .../model/exceptions/UtilsException.java | 4 +- .../model/exceptions/WorkflowException.java | 4 +- .../exceptions/WorkflowRuntimeException.java | 4 +- .../airavata/workflow/model/gpel/DSCUtil.java | 4 +- .../workflow/model/gpel/script/BPELScript.java | 4 +- .../model/gpel/script/BPELScriptType.java | 4 +- .../model/gpel/script/WorkflowWSDL.java | 4 +- .../workflow/model/graph/ControlEdge.java | 4 +- .../workflow/model/graph/ControlPort.java | 4 +- .../airavata/workflow/model/graph/DataEdge.java | 4 +- .../airavata/workflow/model/graph/DataPort.java | 4 +- .../airavata/workflow/model/graph/EPRPort.java | 4 +- .../airavata/workflow/model/graph/Edge.java | 4 +- .../model/graph/ForEachExecutableNode.java | 5 +- .../airavata/workflow/model/graph/Graph.java | 4 +- .../workflow/model/graph/GraphException.java | 4 +- .../workflow/model/graph/GraphFactory.java | 4 +- .../workflow/model/graph/GraphPiece.java | 4 +- .../workflow/model/graph/GraphSchema.java | 4 +- .../airavata/workflow/model/graph/Node.java | 4 +- .../airavata/workflow/model/graph/Port.java | 4 +- .../model/graph/amazon/InstanceDataPort.java | 4 +- .../model/graph/amazon/InstanceNode.java | 4 +- .../model/graph/amazon/ResourceNode.java | 4 +- .../graph/amazon/TerminateInstanceNode.java | 4 +- .../model/graph/dynamic/BasicTypeMapping.java | 4 +- .../model/graph/dynamic/DynamicNode.java | 4 +- .../model/graph/dynamic/DynamicPort.java | 4 +- .../model/graph/dynamic/PortAddable.java | 4 +- .../model/graph/dynamic/SchemaCompilerUtil.java | 4 +- .../workflow/model/graph/impl/EdgeImpl.java | 4 +- .../workflow/model/graph/impl/GraphImpl.java | 4 +- .../workflow/model/graph/impl/NodeImpl.java | 4 +- .../workflow/model/graph/impl/PortImpl.java | 4 +- .../graph/subworkflow/SubWorkflowNode.java | 4 +- .../workflow/model/graph/system/BlockNode.java | 4 +- .../model/graph/system/ConstantNode.java | 4 +- .../model/graph/system/DifferedInputNode.java | 7 +- .../model/graph/system/DoWhileNode.java | 4 +- .../model/graph/system/EndBlockNode.java | 4 +- .../model/graph/system/EndDoWhileNode.java | 4 +- .../model/graph/system/EndForEachNode.java | 4 +- .../workflow/model/graph/system/EndifNode.java | 4 +- .../workflow/model/graph/system/ExitNode.java | 4 +- .../model/graph/system/ForEachNode.java | 4 +- .../workflow/model/graph/system/IfNode.java | 4 +- .../workflow/model/graph/system/InputNode.java | 4 +- .../workflow/model/graph/system/MemoNode.java | 4 +- .../workflow/model/graph/system/OutputNode.java | 4 +- .../model/graph/system/ParameterNode.java | 4 +- .../model/graph/system/ReceiveNode.java | 4 +- .../model/graph/system/S3InputNode.java | 4 +- .../model/graph/system/StreamSourceNode.java | 4 +- .../model/graph/system/SystemDataPort.java | 4 +- .../workflow/model/graph/system/SystemNode.java | 4 +- .../workflow/model/graph/util/GraphUtil.java | 4 +- .../workflow/model/graph/ws/WSGraph.java | 4 +- .../workflow/model/graph/ws/WSGraphFactory.java | 4 +- .../workflow/model/graph/ws/WSNode.java | 4 +- .../workflow/model/graph/ws/WSPort.java | 4 +- .../workflow/model/graph/ws/WorkflowNode.java | 4 +- .../workflow/model/ode/ODEBPELTransformer.java | 19 +++ .../airavata/workflow/model/ode/ODEClient.java | 19 +++ .../model/ode/ODEDeploymentDescriptor.java | 19 +++ .../workflow/model/ode/ODEWSDLTransformer.java | 19 +++ .../workflow/model/ode/WSDLCleaner.java | 19 +++ .../model/utils/ApplicationVersion.java | 4 +- .../workflow/model/utils/FileConstants.java | 4 +- .../workflow/model/utils/MessageConstants.java | 4 +- .../workflow/model/utils/WorkflowConstants.java | 4 +- .../model/wf/InvalidDataFormatException.java | 4 +- .../workflow/model/wf/TridentTransformer.java | 4 +- .../airavata/workflow/model/wf/Workflow.java | 4 +- .../workflow/model/wf/WorkflowData.java | 4 +- .../model/wf/WorkflowExecutionState.java | 4 +- .../workflow/model/wf/WorkflowInput.java | 4 +- .../workflow/model/xsd/GFacSimpleTypesXSD.java | 4 +- .../model/xsd/LeadContextHeaderXSD.java | 4 +- .../workflow/model/xsd/LeadCrosscutXSD.java | 4 +- modules/workflow/pom.xml | 31 +++-- modules/workflow/workflow-core/pom.xml | 31 +++-- .../airavata/workflow/core/WorkflowBuilder.java | 4 +- .../workflow/core/WorkflowEnactmentService.java | 4 +- .../airavata/workflow/core/WorkflowFactory.java | 4 +- .../airavata/workflow/core/WorkflowInfo.java | 3 +- .../workflow/core/WorkflowInterpreter.java | 4 +- .../apache/airavata/workflow/core/XMLUtil.java | 4 +- .../airavata/workflow/core/XmlFormatter.java | 4 +- .../workflow/core/dag/edge/DirectedEdge.java | 4 +- .../airavata/workflow/core/dag/edge/Edge.java | 4 +- .../core/dag/nodes/ApplicationNode.java | 4 +- .../core/dag/nodes/ApplicationNodeImpl.java | 4 +- .../workflow/core/dag/nodes/InputNode.java | 4 +- .../workflow/core/dag/nodes/InputNodeImpl.java | 4 +- .../workflow/core/dag/nodes/NodeType.java | 4 +- .../workflow/core/dag/nodes/OutputNode.java | 4 +- .../workflow/core/dag/nodes/OutputNodeImpl.java | 4 +- .../workflow/core/dag/nodes/WorkflowNode.java | 4 +- .../airavata/workflow/core/dag/port/InPort.java | 4 +- .../workflow/core/dag/port/InputPortIml.java | 4 +- .../workflow/core/dag/port/OutPort.java | 4 +- .../workflow/core/dag/port/OutPortImpl.java | 4 +- .../airavata/workflow/core/dag/port/Port.java | 4 +- .../core/parser/JsonWorkflowParser.java | 4 +- .../workflow/core/parser/ParserException.java | 3 +- .../workflow/core/parser/WorkflowParser.java | 4 +- .../airavata/workflow/core/XMLUtilTest.java | 5 +- .../core/parser/JsonWorkflowParserTest.java | 4 +- modules/xbaya-gui/pom.xml | 26 +++- .../apache/airavata/xbaya/ThriftClientData.java | 4 +- .../airavata/xbaya/ThriftServiceType.java | 4 +- .../java/org/apache/airavata/xbaya/XBaya.java | 4 +- .../airavata/xbaya/XBayaConfiguration.java | 4 +- .../apache/airavata/xbaya/XBayaConstants.java | 4 +- .../org/apache/airavata/xbaya/XBayaEngine.java | 4 +- .../org/apache/airavata/xbaya/XBayaVersion.java | 4 +- .../component/registry/ComponentController.java | 4 +- .../registry/ComponentRegistryLoader.java | 4 +- .../xbaya/concurrent/PredicatedExecutable.java | 5 +- .../xbaya/concurrent/PredicatedTaskRunner.java | 5 +- .../xbaya/core/amazon/AmazonCredential.java | 4 +- .../xbaya/core/amazon/EC2InstanceResult.java | 4 +- .../xbaya/core/generators/BPELFiler.java | 4 +- .../xbaya/core/generators/ImageFiler.java | 4 +- .../xbaya/core/generators/JythonFiler.java | 4 +- .../xbaya/core/generators/ODEScriptFiler.java | 4 +- .../xbaya/core/generators/ScuflFiler.java | 4 +- .../xbaya/core/generators/WorkflowFiler.java | 4 +- .../xbaya/core/generators/XmlBeansFiler.java | 4 +- .../core/ide/XBayaExecutionModeListener.java | 4 +- .../xbaya/core/workflow/ParameterListModel.java | 4 +- .../xbaya/datadriven/WorkflowHarvester.java | 4 +- .../airavata/xbaya/file/XBayaPathConstants.java | 4 +- .../airavata/xbaya/gfac/GFacRegistryClient.java | 4 +- .../airavata/xbaya/gfac/SimpleWSClient.java | 4 +- .../xbaya/globus/FileTransferConstants.java | 4 +- .../xbaya/globus/GridFTPFileTransferClient.java | 19 +++ .../xbaya/graph/controller/NodeController.java | 4 +- .../xbaya/interpretor/ExperimentTemplate.java | 19 +++ .../GUIWorkflowInterpreterInteractorImpl.java | 19 +++ .../xbaya/interpretor/HeaderConstants.java | 4 +- .../SSWorkflowInterpreterInteractorImpl.java | 19 +++ .../StandaloneNotificationSender.java | 4 +- .../WorkFlowInterpreterException.java | 4 +- .../interpretor/WorkflowExecutionMessage.java | 4 +- .../interpretor/WorkflowExecutionTemplate.java | 19 +++ .../xbaya/interpretor/WorkflowInterpreter.java | 19 +++ .../WorkflowInterpreterConfiguration.java | 19 +++ .../WorkflowInterpreterInteractor.java | 19 +++ .../interpretor/WorkflowInterpreterInvoker.java | 4 +- .../WorkflowInterpretorEventListener.java | 19 +++ ...WorkflowInterpretorMessageReceiverInOut.java | 19 +++ .../WorkflowInterpretorSkeleton.java | 19 +++ .../xbaya/jython/lib/GFacServiceCreator.java | 4 +- .../xbaya/jython/lib/NotificationSender.java | 19 +++ .../xbaya/jython/lib/ServiceNotifiable.java | 4 +- .../jython/lib/ServiceNotificationSender.java | 19 +++ .../StandaloneServiceNotificationSender.java | 4 +- .../xbaya/jython/lib/WorkflowNotifiable.java | 4 +- .../xbaya/jython/runner/JythonClassLoader.java | 4 +- .../jython/runner/JythonOneTimeRunner.java | 4 +- .../jython/runner/JythonOneTimeRunnerImpl.java | 4 +- .../xbaya/jython/runner/JythonRunner.java | 4 +- .../xbaya/jython/script/JythonScript.java | 4 +- .../xbaya/menues/tools/ToolsMenuItem.java | 4 +- .../airavata/xbaya/messaging/EventData.java | 4 +- .../xbaya/messaging/EventDataListener.java | 4 +- .../xbaya/messaging/EventDataRepository.java | 4 +- .../airavata/xbaya/messaging/Monitor.java | 4 +- .../xbaya/messaging/MonitorException.java | 4 +- .../xbaya/messaging/NotificationHandler.java | 4 +- .../airavata/xbaya/messaging/event/Event.java | 4 +- .../xbaya/messaging/event/EventListener.java | 4 +- .../xbaya/messaging/event/EventProducer.java | 4 +- .../xbaya/modifier/WorkflowModifier.java | 4 +- .../xbaya/registry/PasswordCallbackImpl.java | 19 +++ .../xbaya/scufl/script/ScuflScript.java | 19 +++ .../xbaya/test/util/WorkflowCreator.java | 19 +++ .../org/apache/airavata/xbaya/ui/XBayaGUI.java | 4 +- .../ui/actions/AbstractBrowserActionItem.java | 4 +- .../ui/actions/registry/browser/AddAction.java | 4 +- .../actions/registry/browser/BrowserAction.java | 4 +- .../ui/actions/registry/browser/CopyAction.java | 4 +- .../actions/registry/browser/DeleteAction.java | 4 +- .../ui/actions/registry/browser/EditAction.java | 4 +- .../actions/registry/browser/ImportAction.java | 4 +- .../actions/registry/browser/RefreshAction.java | 4 +- .../ui/actions/registry/browser/ViewAction.java | 4 +- .../airavata/xbaya/ui/dialogs/AboutWindow.java | 4 +- .../airavata/xbaya/ui/dialogs/ErrorWindow.java | 4 +- .../ui/dialogs/GlobusFileTransferWindow.java | 19 +++ .../airavata/xbaya/ui/dialogs/TextWindow.java | 4 +- .../airavata/xbaya/ui/dialogs/WaitDialog.java | 4 +- .../airavata/xbaya/ui/dialogs/XBayaDialog.java | 4 +- .../dialogs/amazon/AmazonEC2InvokerWindow.java | 4 +- .../ui/dialogs/amazon/AmazonS3UtilsWindow.java | 4 +- .../xbaya/ui/dialogs/amazon/BucketsLoader.java | 4 +- .../dialogs/amazon/ChangeCredentialWindow.java | 4 +- .../amazon/EC2InstancesManagementWindow.java | 4 +- .../ui/dialogs/amazon/EC2LaunchWindow.java | 4 +- .../ui/dialogs/amazon/InstancesLoader.java | 4 +- .../xbaya/ui/dialogs/amazon/S3Downloader.java | 4 +- .../xbaya/ui/dialogs/amazon/S3Uploader.java | 4 +- .../ui/dialogs/component/URLRegistryWindow.java | 4 +- .../ui/dialogs/component/WebResigtryWindow.java | 4 +- .../amazon/InstanceConfigurationDialog.java | 4 +- .../system/ConstantConfigurationDialog.java | 4 +- .../DifferedInputConfigurationDialog.java | 4 +- .../graph/system/DoWhileConfigrationDialog.java | 4 +- .../system/EndBlockConfigurationDialog.java | 4 +- .../system/EndDoWhileConfigurationDialog.java | 4 +- .../system/EndForEachConfigurationDialog.java | 4 +- .../graph/system/EndifConfigurationDialog.java | 4 +- .../system/ForEachConfigurationDialog.java | 4 +- .../graph/system/IfConfigurationDialog.java | 4 +- .../graph/system/InputConfigurationDialog.java | 4 +- .../graph/system/MemoConfigurationDialog.java | 4 +- .../graph/system/OutputConfigurationDialog.java | 4 +- .../system/ReceiveConfigurationDialog.java | 4 +- .../ui/dialogs/graph/system/S3FileChooser.java | 4 +- .../system/StreamSourceConfigurationDialog.java | 4 +- .../graph/ws/ServiceInteractionWindow.java | 4 +- .../xbaya/ui/dialogs/graph/ws/WSNodeWindow.java | 4 +- .../monitor/MonitorConfigurationWindow.java | 4 +- .../xbaya/ui/dialogs/monitor/MonitorWindow.java | 4 +- .../dialogs/registry/NewRegistryUserDialog.java | 4 +- .../ui/dialogs/registry/RegistryWindow.java | 4 +- .../registry/browser/JCRBrowserDialog.java | 4 +- .../workflow/ParameterPropertyWindow.java | 4 +- .../dialogs/workflow/WorkflowImportWindow.java | 4 +- .../workflow/WorkflowPropertyWindow.java | 4 +- .../xbaya/ui/experiment/ExperimentMenu.java | 4 +- .../ui/experiment/LaunchApplicationWindow.java | 4 +- .../ui/experiment/RegistrySearchResult.java | 4 +- .../RegistryWorkflowPublisherWindow.java | 4 +- .../WorkflowInterpreterLaunchWindow.java | 4 +- .../apache/airavata/xbaya/ui/graph/EdgeGUI.java | 4 +- .../airavata/xbaya/ui/graph/GraphCanvas.java | 4 +- .../xbaya/ui/graph/GraphCanvasEvent.java | 4 +- .../xbaya/ui/graph/GraphCanvasListener.java | 4 +- .../airavata/xbaya/ui/graph/GraphGUI.java | 4 +- .../airavata/xbaya/ui/graph/GraphPieceGUI.java | 4 +- .../apache/airavata/xbaya/ui/graph/NodeGUI.java | 4 +- .../airavata/xbaya/ui/graph/Paintable.java | 4 +- .../apache/airavata/xbaya/ui/graph/PortGUI.java | 4 +- .../xbaya/ui/graph/amazon/InstanceNodeGUI.java | 4 +- .../graph/amazon/TerminateInstanceNodeGUI.java | 4 +- .../graph/subworkflow/SubWorkflowNodeGUI.java | 4 +- .../xbaya/ui/graph/system/BlockNodeGUI.java | 4 +- .../ui/graph/system/ConfigurableNodeGUI.java | 4 +- .../xbaya/ui/graph/system/ConstantNodeGUI.java | 4 +- .../ui/graph/system/DifferedInputHandler.java | 3 +- .../ui/graph/system/DifferedInputNodeGUI.java | 3 +- .../xbaya/ui/graph/system/DoWhileNodeGUI.java | 4 +- .../xbaya/ui/graph/system/EndBlockNodeGUI.java | 4 +- .../ui/graph/system/EndDoWhileNodeGUI.java | 4 +- .../ui/graph/system/EndForEachNodeGUI.java | 4 +- .../xbaya/ui/graph/system/EndifNodeGUI.java | 4 +- .../xbaya/ui/graph/system/ExitNodeGUI.java | 4 +- .../xbaya/ui/graph/system/ForEachNodeGUI.java | 4 +- .../xbaya/ui/graph/system/IfNodeGUI.java | 4 +- .../xbaya/ui/graph/system/InputNodeGUI.java | 4 +- .../xbaya/ui/graph/system/MemoNodeGUI.java | 4 +- .../xbaya/ui/graph/system/OutputNodeGUI.java | 4 +- .../xbaya/ui/graph/system/ReceiveNodeGUI.java | 4 +- .../xbaya/ui/graph/system/S3InputNodeGUI.java | 4 +- .../ui/graph/system/StreamSourceNodeGUI.java | 4 +- .../airavata/xbaya/ui/graph/ws/WSNodeGUI.java | 4 +- .../xbaya/ui/graph/ws/WorkflowNodeGUI.java | 4 +- .../xbaya/ui/menues/AmazonEC2MenuItem.java | 4 +- .../xbaya/ui/menues/ApplicationMenuItem.java | 4 +- .../airavata/xbaya/ui/menues/EditMenuItem.java | 4 +- .../airavata/xbaya/ui/menues/MenuIcons.java | 4 +- .../xbaya/ui/menues/RegistryMenuItem.java | 4 +- .../airavata/xbaya/ui/menues/RunMenuItem.java | 4 +- .../airavata/xbaya/ui/menues/ViewMenuItem.java | 4 +- .../airavata/xbaya/ui/menues/XBayaMenu.java | 4 +- .../airavata/xbaya/ui/menues/XBayaMenuItem.java | 4 +- .../xbaya/ui/monitor/MonitorEventHandler.java | 4 +- .../xbaya/ui/monitor/MonitorStarter.java | 4 +- .../xbaya/ui/monitor/ResourcePaintable.java | 4 +- .../airavata/xbaya/ui/utils/Cancelable.java | 4 +- .../airavata/xbaya/ui/utils/DrawUtils.java | 4 +- .../airavata/xbaya/ui/utils/ErrorMessages.java | 4 +- .../xbaya/ui/views/ComponentViewer.java | 4 +- .../xbaya/ui/views/JCRBrowserPanel.java | 19 +++ .../airavata/xbaya/ui/views/MonitorPanel.java | 4 +- .../xbaya/ui/views/ParameterPropertyPanel.java | 4 +- .../airavata/xbaya/ui/views/PortViewer.java | 4 +- .../airavata/xbaya/ui/widgets/GridPanel.java | 4 +- .../airavata/xbaya/ui/widgets/ScrollPanel.java | 4 +- .../xbaya/ui/widgets/TabLabelButton.java | 4 +- .../xbaya/ui/widgets/TableRenderable.java | 4 +- .../xbaya/ui/widgets/ToolbarButton.java | 4 +- .../xbaya/ui/widgets/XBayaComboBox.java | 4 +- .../xbaya/ui/widgets/XBayaComponent.java | 4 +- .../airavata/xbaya/ui/widgets/XBayaLabel.java | 3 +- .../xbaya/ui/widgets/XBayaLinkButton.java | 4 +- .../airavata/xbaya/ui/widgets/XBayaList.java | 4 +- .../xbaya/ui/widgets/XBayaTextArea.java | 4 +- .../xbaya/ui/widgets/XBayaTextComponent.java | 4 +- .../xbaya/ui/widgets/XBayaTextField.java | 4 +- .../airavata/xbaya/ui/widgets/XBayaToolBar.java | 4 +- .../xbaya/ui/widgets/XbayaEnhancedList.java | 4 +- .../xbaya/ui/widgets/amazon/S3Tree.java | 4 +- .../xbaya/ui/widgets/amazon/S3TreeModel.java | 4 +- .../ui/widgets/component/ComponentSelector.java | 4 +- .../component/ComponentSelectorEvent.java | 4 +- .../component/ComponentSelectorListener.java | 4 +- .../component/ComponentSourceTransferable.java | 4 +- .../widgets/component/ComponentTreeModel.java | 4 +- .../ui/widgets/component/ComponentTreeNode.java | 4 +- .../apache/airavata/xbaya/util/AmazonUtil.java | 4 +- .../org/apache/airavata/xbaya/util/Data.java | 4 +- .../apache/airavata/xbaya/util/GOConstants.java | 4 +- .../airavata/xbaya/util/GlobusOnlineUtils.java | 19 +++ .../airavata/xbaya/util/RegistryConstants.java | 4 +- .../airavata/xbaya/util/TransferFile.java | 4 +- .../apache/airavata/xbaya/util/XBayaUtil.java | 4 +- .../airavata/xbaya/workflow/WorkflowClient.java | 4 +- .../xbaya/workflow/WorkflowEngineException.java | 4 +- .../xbaya/workflow/proxy/ProxyWSDL.java | 4 +- .../xbaya/workflow/proxy/WorkflowClient.java | 4 +- .../xbaya/workflow/proxy/WorkflowContext.java | 4 +- .../workflow/proxy/WorkflowProxyException.java | 4 +- .../interpreter/ComplexForEachWorkflowTest.java | 19 +++ .../xbaya/interpreter/ComplexMathService.java | 4 +- .../interpreter/ComplexMathWorkflowTest.java | 19 +++ .../interpreter/CrossProductWorkflowTest.java | 19 +++ .../airavata/xbaya/interpreter/EchoService.java | 3 +- .../xbaya/interpreter/ForEachWorkflowTest.java | 19 +++ .../interpreter/LevenshteinDistanceService.java | 4 +- .../airavata/xbaya/interpreter/Listener.java | 19 +++ .../xbaya/interpreter/NotificationSender.java | 19 +++ .../xbaya/interpreter/RegistryServiceTest.java | 19 +++ .../interpreter/SimpleForEachWorkflowTest.java | 19 +++ .../interpreter/SimpleMathWorkflowTest.java | 19 +++ .../xbaya/interpreter/WorkflowTest.java | 19 +++ .../xbaya/interpreter/WorkflowTrackingTest.java | 19 +++ .../xbaya/interpreter/XBayaClientTest.java | 5 +- .../interpreter/XBayaConsolidatedTestSuite.java | 19 +++ .../xbaya/interpreter/utils/ConfigKeys.java | 5 +- .../xbaya/interpreter/utils/TestUtilServer.java | 19 +++ .../interpreter/utils/WorkflowTestUtils.java | 19 +++ pom.xml | 99 +++++++++++--- sandbox/amqpwstunnel/python/amqpwstunnel.py | 20 +++ sandbox/amqpwstunnel/wstest.html | 21 +++ sandbox/job-status-rest-server/api_test.py | 20 +++ sandbox/job-status-rest-server/app.py | 20 +++ .../example/logfile_checker/generate_logs.sh | 20 +++ .../example/logfile_checker/log_consumer.py | 20 +++ .../example/logfile_checker/log_streamer.py | 20 +++ .../simstream/example/logfile_checker/test.txt | 20 +++ .../example/mem_streamer/memory_consumption.py | 20 +++ .../example/mem_streamer/memory_streamer.py | 20 +++ .../application/alanine_dipeptide.py | 20 +++ .../example/openmm_example/openmm_consumer.py | 20 +++ .../openmm_example/openmm_log_consumer.py | 20 +++ .../openmm_example/openmm_rmsd_consumer.py | 20 +++ .../example/openmm_example/openmm_streamer.py | 20 +++ .../simstream/example/openmm_example/test.txt | 20 +++ sandbox/simstream/setup.py | 20 +++ sandbox/simstream/simstream/__init__.py | 20 +++ sandbox/simstream/simstream/datacollector.py | 20 +++ sandbox/simstream/simstream/datareporter.py | 20 +++ sandbox/simstream/simstream/eventhandler.py | 20 +++ sandbox/simstream/simstream/eventmonitor.py | 20 +++ .../simstream/simstream/pikaasyncconsumer.py | 20 +++ sandbox/simstream/simstream/pikaproducer.py | 20 +++ sandbox/simstream/simstream/simstream.py | 20 +++ .../component-cpis/generate-cpi-stubs.sh | 30 ++-- .../generate-thrift-stubs.sh | 30 ++-- tools/gsissh-cli-tools/README.txt | 20 +++ tools/gsissh-cli-tools/pom.xml | 29 ++-- .../ssh/cli/SSHApiClientWithMyProxyAuth.java | 4 +- tools/phoebus-integration/pom.xml | 26 +++- .../impl/PhoebusGridConfigurationHandler.java | 4 +- .../airavata/core/gfac/utils/PhoebusUtils.java | 4 +- tools/pom.xml | 26 +++- tools/rabbitmq-download-start.sh | 20 +++ 1679 files changed, 12712 insertions(+), 5992 deletions(-) ----------------------------------------------------------------------
