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Posted to commits@airavata.apache.org by di...@apache.org on 2019/04/18 17:50:56 UTC
[airavata] branch staging updated (ceeff05 -> ae059f7)
This is an automated email from the ASF dual-hosted git repository.
dimuthuupe pushed a change to branch staging
in repository https://gitbox.apache.org/repos/asf/airavata.git.
from ceeff05 Improving status monitor logic
new 6353b29 AIRAVATA-2960 Trigger dynamic enhancement of rep catalog entities
new d5b8e58 adding new amp gateway domain with ssl certificates
new 5ac9117 adding www redirect to ampgateway
new 4e3bf1b adding new Colorado Mines gateway
new 719f8ff adding new Colorado Mines gateway
new a5c836f Fixed a typo in Mines gateway notifications
new 057812f Adding new gateway Colorado Mines
new fdb37e7 added ssh key for the gateway storage resource
new 6305357 Adding new gateway, Distant Reader of Notredame university
new e67566a Adding new gateway, Distant Reader of Notredame university
new 99afa33 Fixed a tyop in notredame gateway id
new 7efc129 Added SSH key for the storage resource
new e388d05 Added new saver-x theme
new 9161ccd Updated file uploading maximum limits
new 3023838 Added CILogon for Distant Reader Gateway
new b838d9c Switching Maven repo URLs to https
new 958a42f Added CILogon for Colorado Mines Gateway
new f721057 Added new files sizes in to the SEAGrid
new 4b1a9e2 Adding --mem parameter to slurm template
new 88ca00b AIRAVATA-2997 Add experimentDataDir to Groovy script variables
new 1a0dd49 Fixing the suffix for --mem parameter in slurm script
new 8eb16e2 adding missing license headers
new ef64477 updated NOTICE file
new 68711b9 updating maven assembly plugin version
new 38e0b2a updating release notes for 0.17
new 871bfbd Updating mines gateway to a permanent domain
new e3edeec [maven-release-plugin] prepare branch master
new 305ccca [maven-release-plugin] prepare release airavata-0.17
new bcbfb67 [maven-release-plugin] prepare for next development iteration
new 391843a Fixing yml formatting issue
new eea0f0a SDSU Gateway details
new b7b52e2 Adding gateway super admin details to the vault
new 73eee99 Added gateway specific credentials
new 5df0432 Merge remote-tracking branch 'origin/master'
new b46c081 Added mines gateway theme repo details
new 91f02d6 Adding the new PfEC Hydro gateway
new f9cc11c Added few missing gateways to the list
new d00fb8b Adding SSH certificate and credential key for storage
new 348a383 Added CILogon details to PfEC-Hydro
new 7944596 Adding SSL certificates to SDState gateway
new 68c34b2 Added Sd state cilogon to the gateway
new 9c00bdb Changed uploading input files sizes in PfEC Hydro gateway
new 6583851 Added a new email to get new user account notification
new 191c7cb Added Distant Reader Gateway theme
new 0075857 Added new domain to the gateway
new ae059f7 Merge branch 'master' into staging
The 7640 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
.travis.yml | 20 ++
INSTALL | 5 +-
NOTICE | 233 ++++++++++++++++++++-
README | 2 +-
RELEASE_NOTES | 183 ++++++++++++++++
.../java/org/apache/airavata/api/Airavata.java | 28 +--
.../apache/airavata/api/airavata_apiConstants.java | 28 +--
.../org/apache/airavata/model/ComponentState.java | 28 +--
.../org/apache/airavata/model/ComponentStatus.java | 28 +--
.../java/org/apache/airavata/model/EdgeModel.java | 28 +--
.../java/org/apache/airavata/model/NodeModel.java | 28 +--
.../java/org/apache/airavata/model/PortModel.java | 28 +--
.../org/apache/airavata/model/WorkflowModel.java | 28 +--
.../org/apache/airavata/model/WorkflowState.java | 28 +--
.../org/apache/airavata/model/WorkflowStatus.java | 28 +--
.../accountprovisioning/SSHAccountProvisioner.java | 28 +--
.../SSHAccountProvisionerConfigParam.java | 28 +--
.../SSHAccountProvisionerConfigParamType.java | 28 +--
.../ApplicationDeploymentDescription.java | 28 +--
.../appdeployment/ApplicationModule.java | 28 +--
.../appcatalog/appdeployment/CommandObject.java | 28 +--
.../appcatalog/appdeployment/SetEnvPaths.java | 28 +--
.../ApplicationInterfaceDescription.java | 28 +--
.../appcatalog/computeresource/BatchQueue.java | 28 +--
.../computeresource/CloudJobSubmission.java | 28 +--
.../ComputeResourceDescription.java | 28 +--
.../model/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 +--
.../appcatalog/computeresource/ProviderName.java | 28 +--
.../computeresource/ResourceJobManager.java | 28 +--
.../computeresource/ResourceJobManagerType.java | 28 +--
.../computeresource/SSHJobSubmission.java | 28 +--
.../computeresource/UnicoreJobSubmission.java | 28 +--
.../gatewayprofile/ComputeResourcePreference.java | 28 +--
.../gatewayprofile/GatewayResourceProfile.java | 28 +--
.../gatewayprofile/StoragePreference.java | 28 +--
.../StorageResourceDescription.java | 28 +--
.../UserComputeResourcePreference.java | 28 +--
.../userresourceprofile/UserResourceProfile.java | 28 +--
.../userresourceprofile/UserStoragePreference.java | 28 +--
.../airavata/model/application/io/DataType.java | 28 +--
.../model/application/io/InputDataObjectType.java | 28 +--
.../model/application/io/OutputDataObjectType.java | 28 +--
.../apache/airavata/model/commons/ErrorModel.java | 28 +--
.../airavata/model/commons/ValidationResults.java | 28 +--
.../airavata/model/commons/ValidatorResult.java | 28 +--
.../model/commons/airavata_commonsConstants.java | 28 +--
.../credential/store/CertificateCredential.java | 28 +--
.../model/credential/store/CommunityUser.java | 28 +--
.../credential/store/CredentialOwnerType.java | 28 +--
.../model/credential/store/CredentialSummary.java | 28 +--
.../model/credential/store/PasswordCredential.java | 28 +--
.../model/credential/store/SSHCredential.java | 28 +--
.../model/credential/store/SummaryType.java | 28 +--
.../credential_store_data_modelsConstants.java | 28 +--
.../airavata/model/data/movement/DMType.java | 28 +--
.../model/data/movement/DataMovementInterface.java | 28 +--
.../model/data/movement/DataMovementProtocol.java | 28 +--
.../model/data/movement/GridFTPDataMovement.java | 28 +--
.../model/data/movement/LOCALDataMovement.java | 28 +--
.../model/data/movement/SCPDataMovement.java | 28 +--
.../model/data/movement/SecurityProtocol.java | 28 +--
.../model/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 +--
.../model/data/replica/ReplicaPersistentType.java | 28 +--
.../apache/airavata/model/dbevent/CrudType.java | 28 +--
.../airavata/model/dbevent/DBEventMessage.java | 28 +--
.../model/dbevent/DBEventMessageContext.java | 28 +--
.../airavata/model/dbevent/DBEventPublisher.java | 28 +--
.../model/dbevent/DBEventPublisherContext.java | 28 +--
.../airavata/model/dbevent/DBEventSubscriber.java | 28 +--
.../apache/airavata/model/dbevent/DBEventType.java | 28 +--
.../apache/airavata/model/dbevent/EntityType.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 +--
.../model/error/DuplicateEntryException.java | 28 +--
.../model/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 +--
.../airavata/model/experiment/ExperimentModel.java | 28 +--
.../model/experiment/ExperimentSearchFields.java | 28 +--
.../model/experiment/ExperimentStatistics.java | 28 +--
.../model/experiment/ExperimentSummaryModel.java | 28 +--
.../airavata/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 +--
.../apache/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 +--
.../model/messaging/event/ProcessIdentifier.java | 28 +--
.../messaging/event/ProcessStatusChangeEvent.java | 28 +--
.../event/ProcessStatusChangeRequestEvent.java | 28 +--
.../model/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 +--
.../parallelism/ApplicationParallelismType.java | 28 +--
.../airavata/model/process/ProcessModel.java | 28 +--
.../ComputationalResourceSchedulingModel.java | 28 +--
.../apache/airavata/model/security/AuthzToken.java | 28 +--
.../airavata/model/status/ExperimentState.java | 28 +--
.../airavata/model/status/ExperimentStatus.java | 28 +--
.../org/apache/airavata/model/status/JobState.java | 28 +--
.../apache/airavata/model/status/JobStatus.java | 28 +--
.../apache/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 +--
.../apache/airavata/model/status/TaskStatus.java | 28 +--
.../apache/airavata/model/task/DataStageType.java | 28 +--
.../airavata/model/task/DataStagingTaskModel.java | 28 +--
.../model/task/EnvironmentSetupTaskModel.java | 28 +--
.../model/task/JobSubmissionTaskModel.java | 28 +--
.../airavata/model/task/MonitorTaskModel.java | 28 +--
.../org/apache/airavata/model/task/TaskModel.java | 28 +--
.../org/apache/airavata/model/task/TaskTypes.java | 28 +--
.../org/apache/airavata/model/tenant/Tenant.java | 28 +--
.../model/tenant/TenantApprovalStatus.java | 28 +--
.../airavata/model/user/NSFDemographics.java | 28 +--
.../org/apache/airavata/model/user/Status.java | 28 +--
.../apache/airavata/model/user/USCitizenship.java | 28 +--
.../apache/airavata/model/user/UserProfile.java | 28 +--
.../org/apache/airavata/model/user/disability.java | 28 +--
.../org/apache/airavata/model/user/ethnicity.java | 28 +--
.../java/org/apache/airavata/model/user/race.java | 28 +--
.../model/user/user_profile_modelConstants.java | 28 +--
.../apache/airavata/model/workspace/Gateway.java | 28 +--
.../model/workspace/GatewayApprovalStatus.java | 28 +--
.../org/apache/airavata/model/workspace/Group.java | 28 +--
.../airavata/model/workspace/Notification.java | 28 +--
.../model/workspace/NotificationPriority.java | 28 +--
.../apache/airavata/model/workspace/Project.java | 28 +--
.../org/apache/airavata/model/workspace/User.java | 28 +--
airavata-services/pom.xml | 26 ++-
.../iam-admin-services-core/pom.xml | 21 ++
.../core/impl/TenantManagementKeycloakImpl.java | 4 +-
.../core/interfaces/TenantManagementInterface.java | 4 +-
.../admin/services/core/tests/SetupNewGateway.java | 19 ++
airavata-services/profile-service/pom.xml | 26 ++-
.../java-client-samples/pom.xml | 26 ++-
.../client/samples/TenantProfileSample.java | 19 ++
.../profile/client/samples/UserProfileSample.java | 19 ++
.../client/util/ProfileServiceClientUtil.java | 19 ++
.../profile-service-client-sdks/pom.xml | 28 ++-
.../profile-service-commons/pom.xml | 26 ++-
.../commons/repositories/AbstractRepository.java | 5 +-
.../commons/tenant/entities/GatewayEntity.java | 3 +-
.../user/entities/NSFDemographicsEntity.java | 5 +-
.../commons/user/entities/UserProfileEntity.java | 5 +-
.../service/profile/commons/utils/Committer.java | 5 +-
.../profile/commons/utils/JPAConstants.java | 3 +-
.../service/profile/commons/utils/JPAUtils.java | 5 +-
.../commons/utils/ObjectMapperSingleton.java | 3 +-
.../profile/commons/utils/QueryConstants.java | 19 ++
.../service/profile/commons/utils/Utils.java | 3 +-
.../profile-service/profile-service-server/pom.xml | 26 ++-
.../profile/handlers/IamAdminServicesHandler.java | 4 +-
.../handlers/TenantProfileServiceHandler.java | 5 +-
.../handlers/UserProfileServiceHandler.java | 5 +-
.../profile/server/ProfileServiceServer.java | 6 +-
.../service/profile/utils/ProfileServiceUtils.java | 19 ++
.../profile-service/profile-service-stubs/pom.xml | 26 ++-
.../client/ProfileServiceClientFactory.java | 3 +-
.../iam/admin/services/cpi/IamAdminServices.java | 19 ++
.../cpi/exception/IamAdminServicesException.java | 19 ++
.../cpi/iam_admin_services_cpiConstants.java | 19 ++
.../profile/tenant/cpi/TenantProfileService.java | 19 ++
.../exception/TenantProfileServiceException.java | 19 ++
.../tenant/cpi/profile_tenant_cpiConstants.java | 19 ++
.../profile/user/cpi/UserProfileService.java | 19 ++
.../cpi/exception/UserProfileServiceException.java | 19 ++
.../user/cpi/profile_user_cpiConstants.java | 19 ++
.../profile-service/profile-tenant-core/pom.xml | 26 ++-
.../core/repositories/TenantProfileRepository.java | 3 +-
.../profile-service/profile-user-core/pom.xml | 21 ++
.../exceptions/UserProfileRegistryException.java | 3 +-
.../core/repositories/UserProfileRepository.java | 5 +-
.../core/repositories/WorkspaceRepositoryTest.java | 5 +-
airavata-services/services-security/pom.xml | 21 ++
.../service/security/AiravataSecurityManager.java | 3 +-
.../security/DefaultAiravataSecurityManager.java | 3 +-
.../airavata/service/security/IdentityContext.java | 4 +-
.../service/security/KeyCloakSecurityManager.java | 5 +-
.../org/apache/airavata/service/security/Main.java | 5 +-
.../service/security/SecurityManagerFactory.java | 3 +-
.../service/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 +-
.../security/interceptor/SecurityInterceptor.java | 3 +-
.../security/interceptor/SecurityModule.java | 1 -
.../service/security/oauth/DefaultOAuthClient.java | 3 +-
.../service/security/xacml/DefaultPAPClient.java | 3 +-
.../service/security/xacml/DefaultXACMLPEP.java | 3 +-
dev-tools/ansible/NOTE | 20 ++
dev-tools/ansible/airavata-iam-setup.yml | 20 ++
dev-tools/ansible/ansible.cfg | 20 ++
dev-tools/ansible/database.yml | 20 ++
.../production/pga_config/ampgateway/vars.yml | 11 +-
.../pga_config/{saverx => distantreader}/vars.yml | 27 +--
.../production/pga_config/distantreader/vault.yml | 18 ++
.../pga_config/{hubzero => mines}/vars.yml | 25 +--
.../scigap/production/pga_config/mines/vault.yml | 18 ++
.../{iugeosurvey => pfec-hydro}/vars.yml | 28 +--
.../production/pga_config/pfec-hydro/vault.yml | 18 ++
.../scigap/production/pga_config/saverx/vars.yml | 4 +-
.../{newmexicostate => sdstate}/vars.yml | 31 +--
.../scigap/production/pga_config/sdstate/vault.yml | 18 ++
.../scigap/production/pga_config/seagrid/vars.yml | 4 +-
.../production/pga_config/searchingSRA/vars.yml | 3 +
dev-tools/ansible/keycloak.yml | 20 ++
dev-tools/ansible/pga-scigap-prod.yml | 7 +-
dev-tools/ansible/requirements.txt | 20 ++
.../roles/database/files/MariaDB_yum_CentOS_7.repo | 20 ++
.../ansible/roles/database/files/mysql-tmp.te | 20 ++
dev-tools/ansible/roles/keycloak/defaults/main.yml | 20 ++
dev-tools/ansible/roles/keycloak/tasks/main.yml | 20 ++
modules/airavata-helix/pom.xml | 1 +
.../common/utils/DBEventManagerConstants.java | 5 +-
.../airavata/common/utils/DBEventService.java | 5 +-
modules/compute-account-provisioning/pom.xml | 37 ++--
.../airavata/accountprovisioning/ConfigParam.java | 5 +-
.../accountprovisioning/InvalidSetupException.java | 5 +-
.../InvalidUsernameException.java | 5 +-
.../accountprovisioning/SSHAccountManager.java | 5 +-
.../accountprovisioning/SSHAccountProvisioner.java | 5 +-
.../SSHAccountProvisionerFactory.java | 5 +-
.../SSHAccountProvisionerProvider.java | 5 +-
.../airavata/accountprovisioning/SSHUtil.java | 5 +-
.../provisioner/IULdapSSHAccountProvisioner.java | 5 +-
.../IULdapSSHAccountProvisionerProvider.java | 5 +-
.../SSHAccountProvisionerFactoryTest.java | 5 +-
.../provisioner/TestSSHAccountProvisioner.java | 5 +-
.../TestSSHAccountProvisionerProvider.java | 5 +-
.../src/main/resources/SLURM_Groovy.template | 1 +
modules/db-event-manager/pom.xml | 26 ++-
.../db/event/manager/DBEventManagerRunner.java | 5 +-
.../manager/messaging/DBEventManagerException.java | 5 +-
.../messaging/DBEventManagerMessagingFactory.java | 5 +-
.../messaging/impl/DBEventMessageHandler.java | 5 +-
.../airavata/db/event/manager/utils/Constants.java | 3 +-
.../event/manager/utils/DbEventManagerZkUtils.java | 5 +-
modules/db-event-manager/src/test/java/Test.java | 5 +-
modules/distribution/pom.xml | 2 +-
.../messaging/core/impl/MessageConsumer.java | 3 +-
.../model/SSHAccountProvisionerConfiguration.java | 5 +-
.../SSHAccountProvisionerConfigurationPK.java | 5 +-
.../replica/catalog/ReplicaCatalogTest.java | 9 +-
.../messaging/RegistryServiceDBEventHandler.java | 5 +-
.../RegistryServiceDBEventMessagingFactory.java | 5 +-
...licaCatalog_lowercase_user_data_dir_example.sql | 20 ++
.../credentialStore_keycloak_migration.sql | 20 ++
.../expCatalog_keycloak_migration.sql | 20 ++
.../profileService_keycloak_migration.sql | 20 ++
.../sharingCatalog_keycloak_migration.sql | 20 ++
.../sharing-registry-distribution/pom.xml | 2 +-
.../messaging/SharingServiceDBEventHandler.java | 5 +-
.../SharingServiceDBEventMessagingFactory.java | 5 +-
.../airavata/sharing/registry/utils/Constants.java | 5 +-
.../registry/utils/ThriftDataModelConversion.java | 19 ++
.../airavata/sharing/registry/models/Domain.java | 19 ++
.../registry/models/DuplicateEntryException.java | 19 ++
.../sharing/registry/models/EntitySearchField.java | 19 ++
.../sharing/registry/models/EntityType.java | 19 ++
.../sharing/registry/models/GroupCardinality.java | 19 ++
.../sharing/registry/models/GroupChildType.java | 19 ++
.../sharing/registry/models/GroupMembership.java | 19 ++
.../sharing/registry/models/GroupType.java | 19 ++
.../sharing/registry/models/PermissionType.java | 19 ++
.../sharing/registry/models/SearchCondition.java | 19 ++
.../sharing/registry/models/SearchCriteria.java | 19 ++
.../airavata/sharing/registry/models/Sharing.java | 19 ++
.../registry/models/SharingRegistryException.java | 19 ++
.../sharing/registry/models/SharingType.java | 19 ++
.../airavata/sharing/registry/models/User.java | 19 ++
.../sharing/registry/models/UserGroup.java | 19 ++
.../registry/models/sharing_modelsConstants.java | 19 ++
.../sharing-service-docs/api-docs/index.html | 21 ++
.../sharing-service-docs/api-docs/sharing_cpi.html | 21 ++
.../api-docs/sharing_models.html | 21 ++
.../sharing-service-docs/api-docs/style.css | 22 +-
modules/user-profile-migration/pom.xml | 31 ++-
.../airavata/KeycloakIdentityServerClient.java | 19 ++
.../user-profile-migration.properties.template | 20 ++
pom.xml | 11 +-
.../service-cpis/generate-service-cpi-stubs.sh | 30 +--
317 files changed, 4376 insertions(+), 2383 deletions(-)
copy dev-tools/ansible/inventories/scigap/production/pga_config/{saverx => distantreader}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/distantreader/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{hubzero => mines}/vars.yml (67%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/mines/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{iugeosurvey => pfec-hydro}/vars.yml (66%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/pfec-hydro/vault.yml
copy dev-tools/ansible/inventories/scigap/production/pga_config/{newmexicostate => sdstate}/vars.yml (65%)
create mode 100644 dev-tools/ansible/inventories/scigap/production/pga_config/sdstate/vault.yml