This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch merge-svcs
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 61bf4ef52d add insertable=false and updateable=false to columns both a
@Column and a @JoinColumn for the same item.
add 36f17b4f5d * fix hibernate-jpa entity checking. * update column types
for mariadb. * reorganize database init scripts. * update to mariadb 10.11 and
use MariaDBDialect.
No new revisions were added by this update.
Summary of changes:
.../database_scripts/init/01-databases.sql | 106 ++---
.devcontainer/docker-compose-alt.yml | 4 +-
.devcontainer/docker-compose.yml | 2 +-
.run/APIServerStarter.run.xml | 6 +-
.run/AgentServiceApplication.run.xml | 6 -
.run/JobEngineStarter.run.xml | 9 -
.run/JobMonitorStarter.run.xml | 9 -
airavata-api/pom.xml | 18 +-
.../src/main/java/org/apache/airavata/Main.java | 134 ++++++
.../apache/airavata/MigrationSchemaGenerator.java | 4 +-
.../org/apache/airavata/api/AiravataAPIServer.java | 33 +-
.../airavata/api/handler/AiravataAPIHandler.java | 139 ------
.../catalog/sharing/db/entities/DomainEntity.java | 7 +-
.../catalog/sharing/db/entities/EntityEntity.java | 11 +-
.../catalog/sharing/db/entities/EntityPK.java | 2 +-
.../sharing/db/entities/EntityTypeEntity.java | 7 +-
.../catalog/sharing/db/entities/EntityTypePK.java | 2 +-
.../sharing/db/entities/GroupAdminEntity.java | 11 +-
.../catalog/sharing/db/entities/GroupAdminPK.java | 2 +-
.../sharing/db/entities/GroupMembershipEntity.java | 7 +-
.../sharing/db/entities/GroupMembershipPK.java | 2 +-
.../sharing/db/entities/PermissionTypeEntity.java | 9 +-
.../sharing/db/entities/PermissionTypePK.java | 4 +-
.../catalog/sharing/db/entities/SharingEntity.java | 9 +-
.../catalog/sharing/db/entities/SharingPK.java | 4 +-
.../catalog/sharing/db/entities/UserEntity.java | 10 +-
.../sharing/db/entities/UserGroupEntity.java | 7 +-
.../catalog/sharing/db/entities/UserGroupPK.java | 2 +-
.../catalog/sharing/db/entities/UserPK.java | 2 +-
...ository.java => AbstractSharingRepository.java} | 28 +-
.../sharing/db/repositories/DomainRepository.java | 5 +-
.../sharing/db/repositories/EntityRepository.java | 2 +-
.../db/repositories/EntityTypeRepository.java | 2 +-
.../db/repositories/GroupAdminRepository.java | 2 +-
.../db/repositories/GroupMembershipRepository.java | 2 +-
.../db/repositories/PermissionTypeRepository.java | 2 +-
.../sharing/db/repositories/SharingRepository.java | 2 +-
.../db/repositories/UserGroupRepository.java | 2 +-
.../sharing/db/repositories/UserRepository.java | 5 +-
.../{JPAUtils.java => SharingRegJPAUtils.java} | 16 +-
.../db/utils/SharingRegistryDBInitConfig.java | 3 +-
.../handler/SharingRegistryServerHandler.java | 11 -
.../apache/airavata/common/utils/DBInitConfig.java | 2 -
.../airavata/common/utils/DBInitializer.java | 38 +-
.../org/apache/airavata/common/utils/DBUtil.java | 9 +-
.../airavata/common/utils/DatabaseCreator.java | 39 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 36 +-
.../org/apache/airavata/common/utils/Version.java | 6 +-
.../impl/certificate/CertificateAuditInfo.java | 2 +-
.../handler/CredentialStoreServerHandler.java | 22 +-
.../store/notifier/NotifierBootstrap.java | 6 +-
.../AbstractCredentialStoreRepository.java | 201 +++++++++
.../store/repository/CommunityUserRepository.java | 259 +++++++++++
.../store/repository/CredentialsRepository.java | 312 +++++++++++++
.../store/store/CredentialReaderFactory.java | 4 +-
.../store/impl/CertificateCredentialWriter.java | 105 ++---
.../store/store/impl/CredentialReaderImpl.java | 209 +++++----
.../store/store/impl/SSHCredentialWriter.java | 75 ++--
.../store/store/impl/db/CommunityUserDAO.java | 250 -----------
.../store/store/impl/db/CommunityUserEntity.java | 154 +++++++
.../store/store/impl/db/CredentialsDAO.java | 495 ---------------------
.../store/store/impl/db/CredentialsEntity.java | 182 ++++++++
.../credential/store/store/impl/db/ParentDAO.java | 32 --
.../impl/util/CredentialStoreDBInitConfig.java | 2 +-
.../store/utils/CredentialSerializationUtils.java | 309 +++++++++++++
.../store/utils/CredentialStoreJPAUtils.java | 117 +++++
.../orchestrator/core/utils/OrchestratorUtils.java | 11 +-
.../commons/repositories/AbstractRepository.java | 16 +-
.../commons/tenant/entities/GatewayEntity.java | 6 +-
.../commons/user/entities/UserProfileEntity.java | 6 +-
.../{JPAUtils.java => ProfileSvcJPAUtils.java} | 17 +-
.../core/repositories/UserProfileRepository.java | 4 +-
.../core/utils/UserProfileCatalogDBInitConfig.java | 2 +-
.../AiravataWorkflowErrorEntity.java | 9 +-
.../ApplicationErrorEntity.java | 9 +-
.../HandlerErrorEntity.java | 9 +-
.../HandlerInputEntity.java | 3 +-
.../HandlerOutputEntity.java | 3 +-
.../appcatalog/ApplicationInputEntity.java | 3 +-
.../appcatalog/BatchQueueResourcePolicyEntity.java | 4 +-
.../appcatalog/ComputeResourcePolicyEntity.java | 4 +-
.../ComputeResourceReservationEntity.java | 4 +-
.../appcatalog/GroupComputeResourcePrefEntity.java | 4 +-
.../GroupSSHAccountProvisionerConfig.java | 6 +-
.../appcatalog/JobManagerCommandEntity.java | 4 +-
.../entities/appcatalog/LocalSubmissionEntity.java | 4 +-
.../appcatalog/ParallelismCommandEntity.java | 4 +-
.../entities/appcatalog/ParserConnectorEntity.java | 12 +-
.../appcatalog/ParserConnectorInputEntity.java | 12 +-
.../entities/appcatalog/ParserInputEntity.java | 4 +-
.../entities/appcatalog/ParserOutputEntity.java | 4 +-
.../appcatalog/ParsingTemplateInputEntity.java | 8 +-
.../SSHAccountProvisionerConfiguration.java | 4 +-
.../UserComputeResourcePreferenceEntity.java | 9 +-
.../appcatalog/UserStoragePreferenceEntity.java | 9 +-
.../ComputationalResourceSchedulingEntity.java | 2 +-
.../core/entities/expcatalog/ExperimentEntity.java | 3 +-
.../entities/expcatalog/ExperimentErrorEntity.java | 9 +-
.../entities/expcatalog/ExperimentInputEntity.java | 6 +-
.../expcatalog/ExperimentOutputEntity.java | 3 +-
.../expcatalog/ExperimentStatusEntity.java | 5 +-
.../core/entities/expcatalog/GatewayEntity.java | 1 +
.../GatewayUsageReportingCommandEntity.java | 3 +-
.../core/entities/expcatalog/JobEntity.java | 11 +-
.../core/entities/expcatalog/JobStatusEntity.java | 7 +-
.../core/entities/expcatalog/ProcessEntity.java | 13 +-
.../entities/expcatalog/ProcessErrorEntity.java | 9 +-
.../entities/expcatalog/ProcessInputEntity.java | 6 +-
.../entities/expcatalog/ProcessOutputEntity.java | 3 +-
.../entities/expcatalog/ProcessStatusEntity.java | 5 +-
.../entities/expcatalog/ProcessWorkflowEntity.java | 2 +-
.../entities/expcatalog/ProjectUserEntity.java | 19 +-
.../core/entities/expcatalog/TaskEntity.java | 10 +-
.../core/entities/expcatalog/TaskErrorEntity.java | 9 +-
.../core/entities/expcatalog/TaskStatusEntity.java | 5 +-
.../expcatalog/UserConfigurationDataEntity.java | 2 +-
.../core/entities/expcatalog/UserEntity.java | 8 +-
.../entities/replicacatalog/DataProductEntity.java | 5 +-
.../replicacatalog/DataReplicaLocationEntity.java | 5 +-
.../core/repositories/AbstractRepository.java | 4 +-
.../appcatalog/AppCatAbstractRepository.java | 2 +-
.../appcatalog/GwyResourceProfileRepository.java | 4 -
.../expcatalog/ExpCatAbstractRepository.java | 2 +-
.../replicacatalog/RepCatAbstractRepository.java | 2 +-
.../WorkflowCatAbstractRepository.java | 2 +-
.../core/utils/AppCatalogDBInitConfig.java | 22 +-
.../core/utils/ExpCatalogDBInitConfig.java | 40 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 11 +-
.../core/utils/JPAUtil/ExpCatalogJPAUtils.java | 11 +-
.../core/utils/JPAUtil/RepCatalogJPAUtils.java | 11 +-
.../utils/JPAUtil/WorkflowCatalogJPAUtils.java | 11 +-
.../core/utils/ReplicaCatalogDBInitConfig.java | 4 +-
.../core/utils/WorkflowCatalogDBInitConfig.java | 4 +-
.../src/main/resources/META-INF/persistence.xml | 72 ++-
.../src/main/resources/airavata-server.properties | 2 +-
...{appcatalog-mysql.sql => app-catalog-mysql.sql} | 135 +++---
.../{credstore-mysql.sql => cred-store-mysql.sql} | 11 +-
...{expcatalog-mysql.sql => exp-catalog-mysql.sql} | 115 +++--
...catalog-mysql.sql => replica-catalog-mysql.sql} | 19 +-
.../database_scripts/sharing-registry-mysql.sql | 30 +-
.../user-profile-catalog-mysql.sql | 29 +-
...atalog-derby.sql => workflow-catalog-mysql.sql} | 59 ++-
.../database_scripts/workflowcatalog-mysql.sql | 128 ------
.../main/resources/distribution/bin/airavata.sh | 2 +-
airavata-api/src/main/resources/dozer_mapping.xml | 8 +
airavata-api/src/main/resources/log4j2.xml | 2 +-
.../derby/airavata-server.properties | 2 +-
.../mysql/airavata-server.properties | 2 +-
.../store/cpi/SSHSummaryTest/SSHSummaryTest.java | 14 +-
.../store/store/impl/db/CommunityUserDAOTest.java | 105 +++--
.../store/store/impl/db/CredentialsDAOTest.java | 215 ++++-----
.../core/repositories/common/TestBase.java | 12 +-
.../src/test/resources/airavata-server.properties | 2 +-
airavata-api/src/test/resources/log4j2.xml | 1 +
.../templates/airavata-server.properties.j2 | 2 +-
.../ansible/roles/api-orch/templates/log4j2.xml.j2 | 1 +
.../helix_setup/templates/controller/log4j2.xml.j2 | 1 +
.../helix_setup/templates/parser-wm/log4j2.xml.j2 | 1 +
.../templates/participant/log4j2.xml.j2 | 1 +
.../helix_setup/templates/post-wm/log4j2.xml.j2 | 1 +
.../helix_setup/templates/pre-wm/log4j2.xml.j2 | 1 +
.../templates/email-monitor/log4j2.xml.j2 | 1 +
.../templates/realtime-monitor/log4j2.xml.j2 | 1 +
.../templates/airavata-server.properties.j2 | 2 +-
modules/agent-framework/agent-service/pom.xml | 1 +
.../resources/distribution/bin/agent-service.sh | 2 +-
.../agent-service/src/main/resources/log4j2.xml | 1 +
.../resources/distribution/bin/file-service.sh | 2 +-
modules/file-server/src/main/resources/log4j2.xml | 1 +
.../research-framework/research-service/pom.xml | 5 +-
.../resources/distribution/bin/research-service.sh | 2 +-
.../research-service/src/main/resources/log4j2.xml | 1 +
.../main/resources/distribution/bin/restproxy.sh | 2 +-
modules/restproxy/src/main/resources/log4j2.xml | 31 +-
pom.xml | 40 +-
175 files changed, 2742 insertions(+), 2314 deletions(-)
delete mode 100644 .run/JobEngineStarter.run.xml
delete mode 100644 .run/JobMonitorStarter.run.xml
rename
airavata-api/src/main/java/org/apache/airavata/catalog/sharing/db/repositories/{AbstractRepository.java
=> AbstractSharingRepository.java} (84%)
rename
airavata-api/src/main/java/org/apache/airavata/catalog/sharing/db/utils/{JPAUtils.java
=> SharingRegJPAUtils.java} (63%)
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/repository/AbstractCredentialStoreRepository.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/repository/CommunityUserRepository.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/repository/CredentialsRepository.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CommunityUserDAO.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CommunityUserEntity.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CredentialsDAO.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/CredentialsEntity.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/store/impl/db/ParentDAO.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/utils/CredentialSerializationUtils.java
create mode 100644
airavata-api/src/main/java/org/apache/airavata/credential/store/utils/CredentialStoreJPAUtils.java
rename
airavata-api/src/main/java/org/apache/airavata/profile/commons/utils/{JPAUtils.java
=> ProfileSvcJPAUtils.java} (74%)
rename airavata-api/src/main/resources/database_scripts/{appcatalog-mysql.sql
=> app-catalog-mysql.sql} (89%)
rename airavata-api/src/main/resources/database_scripts/{credstore-mysql.sql
=> cred-store-mysql.sql} (77%)
rename airavata-api/src/main/resources/database_scripts/{expcatalog-mysql.sql
=> exp-catalog-mysql.sql} (86%)
rename
airavata-api/src/main/resources/database_scripts/{replicacatalog-mysql.sql =>
replica-catalog-mysql.sql} (87%)
rename
airavata-api/src/main/resources/database_scripts/{airavataworkflowcatalog-derby.sql
=> workflow-catalog-mysql.sql} (83%)
delete mode 100644
airavata-api/src/main/resources/database_scripts/workflowcatalog-mysql.sql
