From ebfc9031902c89b72f941a5cd221a60dfedd920a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Fri, 29 Sep 2023 21:32:33 +0200
Subject: [PATCH] rename
---
.gitignore | 2 +-
.gitlab-ci.yml | 7 +-
.gitlab/merge_request_templates/Default.md | 4 +-
CHANGELOG.md | 5 +-
CITATION.cff | 2 +-
DEPENDENCIES.md | 6 +-
Doxyfile | 2 +-
FEATURES.md | 12 +-
Makefile | 38 +--
README.md | 20 +-
README_CONFIGURATION.md | 2 +-
README_SETUP.md | 81 +++---
RELEASE_GUIDELINES.md | 10 +-
conf/core/authtoken.example.yaml | 2 +-
conf/core/jobs.csv | 2 +-
conf/core/log4j2-debug.properties | 4 +-
conf/core/server.conf | 40 +--
conf/core/usersources.ini.template | 6 +-
misc/bend_symlinks/README.md | 8 +-
misc/bend_symlinks/bend_symlinks.sh | 10 +-
misc/bend_symlinks/src/main.sh | 2 +-
misc/bend_symlinks/src/utils.sh | 2 +-
misc/check_symlinks/check_symlinks | 2 +-
misc/chown_script/README | 8 +-
misc/chown_script/chown_script_template | 2 +-
misc/chown_script/install | 10 +-
misc/chown_script/test_functions | 2 +-
misc/move_files/README.md | 10 +-
misc/move_files/move_files.py | 8 +-
misc/move_files/test_move_files.py | 4 +-
.../pam_authentication/ldap_authentication.sh | 2 +-
misc/pam_authentication/makefile | 2 +-
misc/pam_authentication/pam_authentication.c | 2 +-
misc/pam_authentication/pam_authentication.sh | 2 +-
.../pam_authentication/test_authentication.sh | 2 +-
mvn_install_jar.sh | 6 +-
pom.xml | 28 +-
scripting/bin/administration/diagnostics.py | 12 +-
scripting/bin/xls_from_csv.py | 2 +-
src/doc/CaosDB-Query-Language.md | 16 +-
src/doc/Data-Model.md | 4 +-
src/doc/FAQ.rst | 12 +-
src/doc/Makefile | 4 +-
src/doc/administration/configuration.rst | 16 +-
src/doc/administration/curl-access.rst | 20 +-
src/doc/administration/maintenance.rst | 32 +--
.../administration/server_side_scripting.rst | 6 +-
src/doc/concepts.rst | 4 +-
src/doc/conf.py | 22 +-
src/doc/development/api/xml/Makefile | 6 +-
.../development/api/xml/caosdb_openapi.yaml | 8 +-
.../development/api/xml/openapi_config.json | 8 +-
src/doc/development/benchmarking.rst | 20 +-
src/doc/development/devel.rst | 18 +-
src/doc/development/structure.rst | 24 +-
src/doc/development/testing.rst | 2 +-
src/doc/entity-permission-table.rst | 2 +-
src/doc/index.rst | 13 +-
src/doc/permissions.rst | 28 +-
src/doc/query-syntax.rst | 10 +-
src/doc/role-permission-table.rst | 2 +-
src/doc/roles.md | 4 +-
src/doc/specification/AbstractProperty.md | 16 +-
src/doc/specification/Authentication.rst | 4 +-
src/doc/specification/Datatype.md | 2 +-
src/doc/specification/Entity_Overview.md | 4 +-
src/doc/specification/Fileserver.md | 8 +-
src/doc/specification/RecordType.rst | 2 +-
.../specification/Server-side-scripting.md | 20 +-
src/doc/specification/entity_api.rst | 4 +-
src/doc/tutorials/data_model_tutorial.rst | 22 +-
src/doc/tutorials/setup_state_model.py | 6 +-
src/doc/tutorials/statemachine.rst | 2 +-
src/main/java/org/caosdb/datetime/Date.java | 6 +-
.../org/caosdb/datetime/DateTimeFactory2.java | 10 +-
.../datetime/DateTimeFactoryInterface.java | 4 +-
.../caosdb/datetime/DateTimeInterface.java | 6 +-
.../java/org/caosdb/datetime/DateTimeLexer.g4 | 2 +-
.../org/caosdb/datetime/DateTimeParser.g4 | 2 +-
.../datetime/DateTimeStringStrategy.java | 4 +-
.../org/caosdb/datetime/FragmentDateTime.java | 6 +-
...egorianCalendarDateTimeStringStrategy.java | 4 +-
.../java/org/caosdb/datetime/Interval.java | 4 +-
.../LeapSecondDateTimeStringStrategy.java | 4 +-
.../caosdb/datetime/SemiCompleteDateTime.java | 6 +-
.../java/org/caosdb/datetime/UTCDateTime.java | 8 +-
.../org/caosdb/datetime/UTCTimeZoneShift.java | 4 +-
.../org/caosdb/server/CaosAuthenticator.java | 21 +-
.../org/caosdb/server/CaosAuthorizer.java | 10 +-
.../org/caosdb/server/CaosDBException.java | 10 +-
.../java/org/caosdb/server/CaosDBServer.java | 148 +++++------
.../server/CaosDBServerConnectorHelper.java | 14 +-
.../java/org/caosdb/server/FileSystem.java | 40 +--
.../caosdb/server/HttpToHttpsRedirector.java | 4 +-
.../org/caosdb/server/ServerProperties.java | 33 ++-
.../server/ServerPropertiesSerializer.java | 4 +-
.../server/accessControl/ACMPermissions.java | 4 +-
.../AnonymousAuthenticationToken.java | 4 +-
.../server/accessControl/AnonymousRealm.java | 10 +-
.../accessControl/AuthenticationUtils.java | 28 +-
.../accessControl/CaosDBAuthorizingRealm.java | 12 +-
.../accessControl/CaosDBDefaultRealm.java | 8 +-
.../CaosDBRolePermissionResolver.java | 22 +-
.../caosdb/server/accessControl/Config.java | 2 +-
.../accessControl/ConsumedInfoCleanupJob.java | 6 +-
.../accessControl/CredentialsValidator.java | 4 +-
.../accessControl/HashPasswordValidator.java | 6 +-
.../accessControl/InternalUserSource.java | 12 +-
.../org/caosdb/server/accessControl/Mode.java | 4 +-
.../OneTimeAuthenticationToken.java | 15 +-
.../OneTimeTokenConsumedInfo.java | 2 +-
.../accessControl/OneTimeTokenToFile.java | 6 +-
.../org/caosdb/server/accessControl/Pam.java | 6 +-
.../server/accessControl/PamScriptCaller.java | 4 +-
.../server/accessControl/Principal.java | 6 +-
.../RealmUsernamePasswordToken.java | 4 +-
.../org/caosdb/server/accessControl/Role.java | 8 +-
.../SelfValidatingAuthenticationToken.java | 6 +-
.../server/accessControl/SessionToken.java | 11 +-
.../accessControl/SessionTokenRealm.java | 4 +-
.../SinglePermissionSubject.java | 2 +-
.../server/accessControl/UserSource.java | 10 +-
.../server/accessControl/UserSources.java | 33 ++-
.../server/accessControl/UserStatus.java | 4 +-
.../java/org/caosdb/server/caching/Cache.java | 6 +-
.../caosdb/server/caching/CacheHelper.java | 4 +-
.../caosdb/server/caching/JCSCacheHelper.java | 12 +-
.../server/database/BackendTransaction.java | 224 ++++++++--------
.../database/CacheableBackendTransaction.java | 6 +-
.../server/database/ChainTransaction.java | 6 +-
.../org/caosdb/server/database/Database.java | 4 +-
.../database/DatabaseAccessManager.java | 28 +-
.../database/access/AbstractAccess.java | 10 +-
.../caosdb/server/database/access/Access.java | 6 +-
.../database/access/AccessControlAccess.java | 6 +-
.../server/database/access/InfoAccess.java | 6 +-
.../server/database/access/InitAccess.java | 6 +-
.../database/access/TransactionAccess.java | 8 +-
.../MySQL/ConnectionException.java | 4 +-
.../MySQL/DatabaseConnectionPool.java | 30 +--
.../implementation/MySQL/DatabaseUtils.java | 30 +--
.../MySQL/MySQLDeleteEntityProperties.java | 14 +-
.../MySQL/MySQLDeletePassword.java | 12 +-
.../implementation/MySQL/MySQLDeleteRole.java | 12 +-
.../MySQL/MySQLDeleteSparseEntity.java | 14 +-
.../implementation/MySQL/MySQLDeleteUser.java | 10 +-
.../MySQL/MySQLGetAllNames.java | 10 +-
.../MySQL/MySQLGetChildren.java | 12 +-
.../MySQL/MySQLGetDependentEntities.java | 12 +-
.../MySQL/MySQLGetFileRecordByPath.java | 12 +-
.../MySQL/MySQLGetIDByName.java | 12 +-
.../implementation/MySQL/MySQLGetInfo.java | 12 +-
.../MySQL/MySQLGetUpdateableChecksums.java | 12 +-
.../implementation/MySQL/MySQLHelper.java | 14 +-
.../MySQL/MySQLInsertEntityDatatype.java | 12 +-
.../MySQL/MySQLInsertEntityProperties.java | 32 +--
.../MySQL/MySQLInsertLinCon.java | 12 +-
.../MySQL/MySQLInsertLogRecord.java | 10 +-
.../MySQL/MySQLInsertParents.java | 12 +-
.../implementation/MySQL/MySQLInsertRole.java | 12 +-
.../MySQL/MySQLInsertSparseEntity.java | 14 +-
.../MySQL/MySQLInsertTransactionHistory.java | 12 +-
.../implementation/MySQL/MySQLIsSubType.java | 12 +-
.../implementation/MySQL/MySQLListRoles.java | 12 +-
.../implementation/MySQL/MySQLListUsers.java | 14 +-
.../MySQL/MySQLLogUserVisit.java | 10 +-
.../MySQL/MySQLRetrieveAll.java | 18 +-
.../MySQL/MySQLRetrieveAllUncheckedFiles.java | 12 +-
.../MySQL/MySQLRetrieveDatatypes.java | 12 +-
.../MySQL/MySQLRetrieveEntityACL.java | 12 +-
.../MySQL/MySQLRetrieveLogRecord.java | 10 +-
.../MySQL/MySQLRetrieveParents.java | 14 +-
.../MySQL/MySQLRetrievePasswordValidator.java | 16 +-
.../MySQL/MySQLRetrievePermissionRules.java | 12 +-
.../MySQL/MySQLRetrieveProperties.java | 14 +-
.../MySQLRetrieveQueryTemplateDefinition.java | 12 +-
.../MySQL/MySQLRetrieveRole.java | 16 +-
.../MySQL/MySQLRetrieveSparseEntity.java | 14 +-
.../MySQL/MySQLRetrieveUser.java | 18 +-
.../MySQL/MySQLRetrieveVersionHistory.java | 14 +-
.../MySQLSetFileCheckedTimestampImpl.java | 12 +-
.../MySQL/MySQLSetFileChecksum.java | 10 +-
.../MySQL/MySQLSetPassword.java | 12 +-
.../MySQL/MySQLSetPermissionRules.java | 12 +-
.../MySQLSetQueryTemplateDefinition.java | 12 +-
.../implementation/MySQL/MySQLSyncStats.java | 12 +-
.../MySQL/MySQLTransaction.java | 12 +-
.../MySQL/MySQLUpdateSparseEntity.java | 14 +-
.../implementation/MySQL/MySQLUpdateUser.java | 12 +-
.../MySQL/MySQLUpdateUserRoles.java | 10 +-
.../implementation/MySQL/Replacement.java | 14 +-
.../UnixFileSystemCheckHash.java | 14 +-
.../UnixFileSystemCheckSize.java | 12 +-
.../UnixFileSystemFileExists.java | 12 +-
.../UnixFileSystemFileWasModifiedAfter.java | 12 +-
.../UnixFileSystemGetFileIterator.java | 14 +-
.../UnixFileSystem/UnixFileSystemHelper.java | 8 +-
.../UnixFileSystemTransaction.java | 16 +-
.../interfaces/BackendTransactionImpl.java | 6 +-
.../DeleteEntityPropertiesImpl.java | 10 +-
.../interfaces/DeletePasswordImpl.java | 6 +-
.../backend/interfaces/DeleteRoleImpl.java | 6 +-
.../interfaces/DeleteSparseEntityImpl.java | 10 +-
.../backend/interfaces/DeleteUserImpl.java | 6 +-
.../backend/interfaces/FileCheckHash.java | 8 +-
.../backend/interfaces/FileCheckSize.java | 6 +-
.../backend/interfaces/FileExists.java | 6 +-
.../interfaces/FileWasModifiedAfter.java | 6 +-
.../backend/interfaces/GetAllNamesImpl.java | 4 +-
.../backend/interfaces/GetChildrenImpl.java | 8 +-
.../interfaces/GetDependentEntitiesImpl.java | 8 +-
.../interfaces/GetFileIteratorImpl.java | 6 +-
.../interfaces/GetFileRecordByPathImpl.java | 8 +-
.../backend/interfaces/GetIDByNameImpl.java | 8 +-
.../backend/interfaces/GetInfoImpl.java | 8 +-
.../GetUpdateableChecksumsImpl.java | 8 +-
.../interfaces/InsertEntityDatatypeImpl.java | 6 +-
.../InsertEntityPropertiesImpl.java | 8 +-
.../backend/interfaces/InsertLinConImpl.java | 10 +-
.../interfaces/InsertLogRecordImpl.java | 6 +-
.../backend/interfaces/InsertParentsImpl.java | 10 +-
.../backend/interfaces/InsertRoleImpl.java | 8 +-
.../interfaces/InsertSparseEntityImpl.java | 8 +-
.../InsertTransactionHistoryImpl.java | 10 +-
.../backend/interfaces/IsSubTypeImpl.java | 8 +-
.../backend/interfaces/ListRolesImpl.java | 6 +-
.../backend/interfaces/ListUsersImpl.java | 6 +-
.../backend/interfaces/LogUserVisitImpl.java | 4 +-
.../backend/interfaces/RetrieveAllImpl.java | 8 +-
.../RetrieveAllUncheckedFilesImpl.java | 8 +-
.../interfaces/RetrieveDatatypesImpl.java | 8 +-
.../interfaces/RetrieveEntityACLImpl.java | 6 +-
.../interfaces/RetrieveLogRecordImpl.java | 6 +-
.../interfaces/RetrieveParentsImpl.java | 10 +-
.../RetrievePasswordValidatorImpl.java | 8 +-
.../RetrievePermissionRulesImpl.java | 8 +-
.../interfaces/RetrievePropertiesImpl.java | 10 +-
.../RetrieveQueryTemplateDefinitionImpl.java | 6 +-
.../backend/interfaces/RetrieveRoleImpl.java | 8 +-
.../interfaces/RetrieveSparseEntityImpl.java | 10 +-
.../backend/interfaces/RetrieveUserImpl.java | 10 +-
.../RetrieveVersionHistoryImpl.java | 6 +-
.../SetFileCheckedTimestampImpl.java | 8 +-
.../interfaces/SetFileChecksumImpl.java | 4 +-
.../backend/interfaces/SetPasswordImpl.java | 6 +-
.../interfaces/SetPermissionRulesImpl.java | 8 +-
.../SetQueryTemplateDefinitionImpl.java | 6 +-
.../backend/interfaces/SyncStatsImpl.java | 8 +-
.../interfaces/UpdateSparseEntityImpl.java | 10 +-
.../backend/interfaces/UpdateUserImpl.java | 8 +-
.../interfaces/UpdateUserRolesImpl.java | 6 +-
.../transaction/DeleteEntityProperties.java | 18 +-
.../transaction/DeleteEntityTransaction.java | 12 +-
.../backend/transaction/DeleteFile.java | 16 +-
.../backend/transaction/DeletePassword.java | 10 +-
.../backend/transaction/DeleteRole.java | 10 +-
.../transaction/DeleteSparseEntity.java | 16 +-
.../backend/transaction/DeleteUser.java | 12 +-
.../transaction/FileConsistencyCheck.java | 18 +-
.../backend/transaction/GetAllNames.java | 12 +-
.../backend/transaction/GetChildren.java | 12 +-
.../transaction/GetDependentEntities.java | 12 +-
.../backend/transaction/GetFileIterator.java | 10 +-
.../transaction/GetFileRecordByPath.java | 18 +-
.../backend/transaction/GetIDByName.java | 16 +-
.../database/backend/transaction/GetInfo.java | 12 +-
.../transaction/GetUpdateableChecksums.java | 12 +-
.../transaction/InsertEntityDatatype.java | 18 +-
.../transaction/InsertEntityProperties.java | 12 +-
.../transaction/InsertEntityTransaction.java | 12 +-
.../backend/transaction/InsertFile.java | 14 +-
.../backend/transaction/InsertLinCon.java | 12 +-
.../backend/transaction/InsertLogRecord.java | 10 +-
.../backend/transaction/InsertParents.java | 14 +-
.../backend/transaction/InsertRole.java | 12 +-
.../transaction/InsertSparseEntity.java | 24 +-
.../transaction/InsertTransactionHistory.java | 22 +-
.../backend/transaction/IsSubType.java | 12 +-
.../backend/transaction/ListRoles.java | 10 +-
.../backend/transaction/ListUsers.java | 10 +-
.../backend/transaction/LogUserVisit.java | 18 +-
.../backend/transaction/RetrieveAll.java | 16 +-
.../RetrieveAllUncheckedFiles.java | 12 +-
.../transaction/RetrieveDatatypes.java | 22 +-
.../RetrieveEntityACLTransaction.java | 16 +-
.../RetrieveFullEntityTransaction.java | 34 +--
.../transaction/RetrieveLogRecord.java | 10 +-
.../backend/transaction/RetrieveParents.java | 24 +-
.../RetrievePasswordValidator.java | 12 +-
.../transaction/RetrievePermissionRules.java | 14 +-
.../transaction/RetrieveProperties.java | 22 +-
.../RetrieveQueryTemplateDefinition.java | 12 +-
.../backend/transaction/RetrieveRole.java | 14 +-
.../transaction/RetrieveSparseEntity.java | 22 +-
.../backend/transaction/RetrieveUser.java | 16 +-
.../transaction/RetrieveVersionHistory.java | 14 +-
.../transaction/RetrieveVersionInfo.java | 12 +-
.../transaction/SetFileCheckedTimestamp.java | 12 +-
.../backend/transaction/SetFileChecksum.java | 8 +-
.../backend/transaction/SetPassword.java | 10 +-
.../transaction/SetPermissionRules.java | 12 +-
.../SetQueryTemplateDefinition.java | 12 +-
.../backend/transaction/SyncStats.java | 12 +-
.../transaction/UpdateEntityTransaction.java | 14 +-
.../transaction/UpdateSparseEntity.java | 18 +-
.../backend/transaction/UpdateUser.java | 14 +-
.../backend/transaction/UpdateUserRoles.java | 12 +-
.../transaction/VersionTransaction.java | 20 +-
.../EntityDoesNotExistException.java | 4 +-
.../EntityWasNotUniqueException.java | 4 +-
.../exceptions/IntegrityException.java | 4 +-
.../exceptions/RolledBackException.java | 4 +-
.../exceptions/TransactionException.java | 4 +-
.../caosdb/server/database/misc/DBHelper.java | 6 +-
.../server/database/misc/RollBackHandler.java | 8 +-
.../database/misc/TransactionBenchmark.java | 32 +--
.../server/database/proto/FlatProperty.java | 4 +-
.../caosdb/server/database/proto/LinCon.java | 4 +-
.../server/database/proto/ProtoGroup.java | 4 +-
.../server/database/proto/ProtoInfo.java | 4 +-
.../server/database/proto/ProtoProperty.java | 4 +-
.../server/database/proto/ProtoUser.java | 6 +-
.../server/database/proto/SparseEntity.java | 4 +-
.../database/proto/VersionHistoryItem.java | 2 +-
.../database/proto/VerySparseEntity.java | 4 +-
.../datatype/AbstractCollectionDatatype.java | 4 +-
.../server/datatype/AbstractDatatype.java | 14 +-
.../server/datatype/AbstractEnumValue.java | 6 +-
.../server/datatype/BooleanDatatype.java | 8 +-
.../caosdb/server/datatype/BooleanValue.java | 8 +-
.../org/caosdb/server/datatype/CaosEnum.java | 10 +-
.../datatype/CollectionDatatypeFactory.java | 4 +-
.../server/datatype/CollectionValue.java | 4 +-
.../server/datatype/DatatypeDefinition.java | 4 +-
.../server/datatype/DateTimeDatatype.java | 16 +-
.../server/datatype/DoubleDatatype.java | 8 +-
.../caosdb/server/datatype/FileDatatype.java | 4 +-
.../caosdb/server/datatype/GenericValue.java | 6 +-
.../server/datatype/IndexedSingleValue.java | 6 +-
.../server/datatype/IntegerDatatype.java | 8 +-
.../caosdb/server/datatype/ListDatatype.java | 6 +-
.../server/datatype/ListDatatypeFactory.java | 4 +-
.../server/datatype/ReferenceDatatype.java | 6 +-
.../server/datatype/ReferenceDatatype2.java | 10 +-
.../server/datatype/ReferenceValue.java | 14 +-
.../caosdb/server/datatype/SingleValue.java | 4 +-
.../caosdb/server/datatype/TextDatatype.java | 8 +-
.../org/caosdb/server/datatype/Value.java | 4 +-
.../org/caosdb/server/entity/Affiliation.java | 4 +-
.../caosdb/server/entity/ClientMessage.java | 4 +-
.../caosdb/server/entity/DeleteEntity.java | 4 +-
.../java/org/caosdb/server/entity/Entity.java | 60 ++---
.../org/caosdb/server/entity/EntityID.java | 2 +-
.../caosdb/server/entity/EntityInterface.java | 34 +--
.../caosdb/server/entity/FileProperties.java | 25 +-
.../caosdb/server/entity/InsertEntity.java | 4 +-
.../org/caosdb/server/entity/MagicTypes.java | 8 +-
.../org/caosdb/server/entity/Message.java | 10 +-
.../server/entity/NoSuchRoleException.java | 4 +-
.../caosdb/server/entity/RetrieveEntity.java | 4 +-
.../java/org/caosdb/server/entity/Role.java | 14 +-
.../caosdb/server/entity/StatementStatus.java | 4 +-
.../entity/StatementStatusInterface.java | 6 +-
.../server/entity/TransactionEntity.java | 14 +-
.../caosdb/server/entity/UpdateEntity.java | 8 +-
.../org/caosdb/server/entity/Version.java | 6 +-
.../caosdb/server/entity/WritableEntity.java | 4 +-
.../org/caosdb/server/entity/WriteEntity.java | 4 +-
.../server/entity/container/Container.java | 8 +-
.../entity/container/EntityByIdContainer.java | 6 +-
.../entity/container/ParentContainer.java | 24 +-
.../entity/container/PropertyContainer.java | 24 +-
.../entity/container/RetrieveContainer.java | 8 +-
.../container/TransactionContainer.java | 26 +-
.../entity/container/WritableContainer.java | 6 +-
.../server/entity/wrapper/EntityWrapper.java | 48 ++--
.../caosdb/server/entity/wrapper/Parent.java | 10 +-
.../server/entity/wrapper/Property.java | 20 +-
.../entity/xml/DomainToElementStrategy.java | 6 +-
.../entity/xml/EntityToElementStrategy.java | 18 +-
.../entity/xml/FileToElementStrategy.java | 6 +-
.../xml/IdAndServerMessagesOnlyStrategy.java | 2 +-
.../entity/xml/ParentToElementStrategy.java | 8 +-
.../entity/xml/PropertyToElementStrategy.java | 12 +-
.../entity/xml/SerializeFieldStrategy.java | 10 +-
.../server/entity/xml/ToElementStrategy.java | 6 +-
.../server/entity/xml/ToElementable.java | 4 +-
.../entity/xml/VersionXMLSerializer.java | 6 +-
.../AccessControlManagementServiceImpl.java | 137 +++++-----
.../caosdb/server/grpc/AuthInterceptor.java | 29 ++-
.../server/grpc/CaosDBToGrpcConverters.java | 239 +++++++++---------
.../caosdb/server/grpc/DownloadBuffer.java | 10 +-
.../grpc/EntityTransactionServiceImpl.java | 144 +++++------
.../org/caosdb/server/grpc/FileDownload.java | 10 +-
.../server/grpc/FileDownloadRegistration.java | 12 +-
.../caosdb/server/grpc/FileTransmission.java | 8 +-
.../grpc/FileTransmissionServiceImpl.java | 38 +--
.../org/caosdb/server/grpc/FileUpload.java | 14 +-
.../server/grpc/FileUploadRegistration.java | 8 +-
.../org/caosdb/server/grpc/GRPCServer.java | 14 +-
.../server/grpc/GeneralInfoServiceImpl.java | 34 +--
.../server/grpc/GrpcToCaosDBConverters.java | 112 ++++----
.../server/grpc/LoggingInterceptor.java | 9 +-
.../org/caosdb/server/grpc/UploadBuffer.java | 6 +-
.../org/caosdb/server/jobs/ContainerJob.java | 10 +-
.../org/caosdb/server/jobs/EntityJob.java | 6 +-
.../java/org/caosdb/server/jobs/FilesJob.java | 6 +-
.../java/org/caosdb/server/jobs/FlagJob.java | 4 +-
src/main/java/org/caosdb/server/jobs/Job.java | 54 ++--
.../org/caosdb/server/jobs/JobAnnotation.java | 8 +-
.../org/caosdb/server/jobs/JobConfig.java | 28 +-
.../org/caosdb/server/jobs/JobTarget.java | 6 +-
.../java/org/caosdb/server/jobs/Schedule.java | 6 +-
.../org/caosdb/server/jobs/ScheduledJob.java | 6 +-
.../caosdb/server/jobs/TransactionStage.java | 10 +-
.../server/jobs/core/AccessControl.java | 28 +-
.../org/caosdb/server/jobs/core/Atomic.java | 24 +-
.../core/CheckChildDependencyExistent.java | 16 +-
.../jobs/core/CheckDatatypePresent.java | 34 +--
.../server/jobs/core/CheckDescPresent.java | 10 +-
.../server/jobs/core/CheckEntityACLRoles.java | 26 +-
.../core/CheckFileStorageConsistency.java | 36 +--
.../server/jobs/core/CheckNamePresent.java | 10 +-
.../CheckNoAdditionalPropertiesPresent.java | 14 +-
.../jobs/core/CheckNoOverridesPresent.java | 12 +-
.../jobs/core/CheckParOblPropPresent.java | 22 +-
.../server/jobs/core/CheckParPresent.java | 10 +-
.../server/jobs/core/CheckParValid.java | 32 +--
.../server/jobs/core/CheckPropPresent.java | 10 +-
.../server/jobs/core/CheckPropValid.java | 28 +-
.../server/jobs/core/CheckQueryTemplate.java | 14 +-
.../CheckReferenceDependencyExistent.java | 16 +-
.../jobs/core/CheckRefidIsaParRefid.java | 38 +--
.../server/jobs/core/CheckRefidPresent.java | 6 +-
.../server/jobs/core/CheckRefidValid.java | 32 +--
.../jobs/core/CheckStateTransition.java | 22 +-
.../jobs/core/CheckTargetPathValid.java | 16 +-
.../server/jobs/core/CheckUnitPresent.java | 14 +-
.../server/jobs/core/CheckValueParsable.java | 18 +-
.../caosdb/server/jobs/core/DebugCalls.java | 14 +-
.../server/jobs/core/EntityStateJob.java | 54 ++--
.../caosdb/server/jobs/core/ExecuteQuery.java | 28 +-
.../org/caosdb/server/jobs/core/History.java | 20 +-
.../server/jobs/core/InheritInitialState.java | 16 +-
.../caosdb/server/jobs/core/Inheritance.java | 30 +--
.../server/jobs/core/InitEntityStateJobs.java | 42 +--
.../server/jobs/core/InsertFilesInDir.java | 58 ++---
.../server/jobs/core/JobFailureSeverity.java | 4 +-
.../jobs/core/LoadContainerFlagJobs.java | 14 +-
.../server/jobs/core/MakeStateMessage.java | 20 +-
.../server/jobs/core/MakeStateProperty.java | 12 +-
.../server/jobs/core/MatchFileProp.java | 14 +-
.../org/caosdb/server/jobs/core/NoCache.java | 10 +-
.../org/caosdb/server/jobs/core/Paging.java | 16 +-
.../caosdb/server/jobs/core/ParseUnit.java | 24 +-
.../org/caosdb/server/jobs/core/PickUp.java | 26 +-
.../jobs/core/ProcessNameProperties.java | 28 +-
.../server/jobs/core/RemoveDuplicates.java | 8 +-
.../caosdb/server/jobs/core/ResolveNames.java | 24 +-
.../caosdb/server/jobs/core/RetrieveACL.java | 20 +-
.../server/jobs/core/RetrieveAllJob.java | 18 +-
.../server/jobs/core/RetrieveOwner.java | 22 +-
.../server/jobs/core/RetriveAllNames.java | 16 +-
.../caosdb/server/jobs/core/SetImpToFix.java | 10 +-
.../jobs/core/SetImpToRecByDefault.java | 10 +-
.../org/caosdb/server/jobs/core/Strict.java | 20 +-
.../org/caosdb/server/jobs/core/TestMail.java | 26 +-
.../caosdb/server/jobs/core/UniqueName.java | 22 +-
.../jobs/core/UpdateUnitConverters.java | 18 +-
.../logging/RequestErrorLogMessage.java | 6 +-
.../log4j/CustomConfigurationFactory.java | 4 +-
.../permissions/AbstractEntityACLFactory.java | 4 +-
.../server/permissions/CaosPermission.java | 8 +-
.../caosdb/server/permissions/EntityACI.java | 4 +-
.../caosdb/server/permissions/EntityACL.java | 22 +-
.../server/permissions/EntityACLFactory.java | 2 +-
.../server/permissions/EntityPermission.java | 68 ++---
.../caosdb/server/permissions/Permission.java | 4 +-
.../server/permissions/PermissionRule.java | 6 +-
.../server/permissions/ResponsibleAgent.java | 4 +-
.../org/caosdb/server/permissions/Role.java | 4 +-
.../caosdb/server/query/Backreference.java | 14 +-
.../java/org/caosdb/server/query/CQLLexer.g4 | 2 +-
.../java/org/caosdb/server/query/CQLParser.g4 | 2 +-
.../server/query/CQLParsingErrorListener.java | 4 +-
.../org/caosdb/server/query/Conjunction.java | 10 +-
.../org/caosdb/server/query/Disjunction.java | 10 +-
.../server/query/EntityFilterContainer.java | 4 +-
.../server/query/EntityFilterInterface.java | 6 +-
.../org/caosdb/server/query/IDFilter.java | 6 +-
.../org/caosdb/server/query/Negation.java | 10 +-
.../java/org/caosdb/server/query/POV.java | 22 +-
.../java/org/caosdb/server/query/Query.java | 70 ++---
.../caosdb/server/query/QueryInterface.java | 6 +-
.../org/caosdb/server/query/RoleFilter.java | 8 +-
.../org/caosdb/server/query/StoredAt.java | 6 +-
.../org/caosdb/server/query/SubProperty.java | 10 +-
.../server/query/TransactionFilter.java | 18 +-
.../java/org/caosdb/server/query/Utils.java | 4 +-
.../caosdb/server/query/VersionFilter.java | 2 +-
.../AbstractCaosDBServerResource.java | 28 +-
.../resource/AuthenticationResource.java | 28 +-
.../server/resource/DefaultResource.java | 12 +-
.../server/resource/EntityOwnerResource.java | 12 +-
.../resource/EntityPermissionsResource.java | 10 +-
.../server/resource/FileSystemResource.java | 30 +--
.../caosdb/server/resource/InfoResource.java | 18 +-
.../server/resource/JdomRepresentation.java | 10 +-
.../server/resource/LogoutResource.java | 10 +-
.../resource/PermissionRulesResource.java | 24 +-
.../resource/ReReadableRepresentation.java | 4 +-
.../caosdb/server/resource/RolesResource.java | 30 +--
.../server/resource/ScriptingResource.java | 30 +--
.../server/resource/ServerLogsResource.java | 14 +-
.../resource/ServerPropertiesResource.java | 20 +-
.../server/resource/SharedFileResource.java | 14 +-
.../server/resource/ThumbnailsResource.java | 14 +-
.../caosdb/server/resource/UserResource.java | 39 +--
.../server/resource/UserRolesResource.java | 24 +-
.../caosdb/server/resource/Webinterface.java | 13 +-
.../resource/WebinterfaceBuildNumber.java | 6 +-
.../transaction/EntityNamesResource.java | 6 +-
.../resource/transaction/EntityResource.java | 32 +--
.../transaction/RetrieveEntityResource.java | 20 +-
.../server/scripting/CallerSerializer.java | 12 +-
.../scripting/ScriptingPermissions.java | 4 +-
.../server/scripting/ScriptingUtils.java | 23 +-
.../scripting/ServerSideScriptingCaller.java | 28 +-
.../server/scripting/TimeoutException.java | 4 +-
.../server/scripting/TimeoutProcess.java | 4 +-
.../transaction/AccessControlTransaction.java | 14 +-
.../server/transaction/ChecksumUpdater.java | 34 +--
.../transaction/DeleteRoleTransaction.java | 18 +-
.../transaction/DeleteUserTransaction.java | 22 +-
.../FileStorageConsistencyCheck.java | 34 +--
.../InsertLogRecordTransaction.java | 12 +-
.../transaction/InsertRoleTransaction.java | 18 +-
.../transaction/InsertUserTransaction.java | 36 +--
.../transaction/ListRolesTransaction.java | 12 +-
.../transaction/ListUsersTransaction.java | 10 +-
.../transaction/LogUserVisitTransaction.java | 6 +-
.../caosdb/server/transaction/Retrieve.java | 28 +-
.../server/transaction/RetrieveACL.java | 20 +-
.../RetrieveLogRecordTransaction.java | 14 +-
.../RetrievePasswordValidatorTransaction.java | 10 +-
.../RetrievePermissionRulesTransaction.java | 12 +-
.../transaction/RetrieveRoleTransaction.java | 14 +-
.../RetrieveSparseEntityByPath.java | 12 +-
.../RetrieveUserRolesTransaction.java | 12 +-
.../transaction/RetrieveUserTransaction.java | 16 +-
.../server/transaction/Transaction.java | 50 ++--
.../transaction/TransactionInterface.java | 14 +-
.../caosdb/server/transaction/UpdateACL.java | 30 +--
.../UpdatePermissionRulesTransaction.java | 14 +-
.../transaction/UpdateRoleTransaction.java | 24 +-
.../UpdateUserRolesTransaction.java | 16 +-
.../transaction/UpdateUserTransaction.java | 46 ++--
.../server/transaction/WriteTransaction.java | 64 ++---
.../WriteTransactionInterface.java | 4 +-
.../server/utils/AbstractObservable.java | 4 +-
.../server/utils/AsynchronousHasher.java | 6 +-
.../server/utils/ConfigurationException.java | 4 +-
.../java/org/caosdb/server/utils/CronJob.java | 8 +-
.../org/caosdb/server/utils/EntityStatus.java | 4 +-
.../org/caosdb/server/utils/FileUtils.java | 43 ++--
.../org/caosdb/server/utils/FlagInfo.java | 14 +-
.../caosdb/server/utils/HashAlgorithm.java | 4 +-
.../caosdb/server/utils/HashException.java | 8 +-
.../server/utils/HashNotReadyException.java | 4 +-
.../server/utils/HashTimeoutException.java | 4 +-
.../java/org/caosdb/server/utils/Hasher.java | 4 +-
.../java/org/caosdb/server/utils/Info.java | 30 +--
.../caosdb/server/utils/Initialization.java | 12 +-
.../caosdb/server/utils/NullPrintStream.java | 4 +-
.../org/caosdb/server/utils/Observable.java | 4 +-
.../server/utils/ObservableWrapper.java | 6 +-
.../org/caosdb/server/utils/Observer.java | 4 +-
.../org/caosdb/server/utils/Releasable.java | 4 +-
.../server/utils/ResultSetIterator.java | 8 +-
.../java/org/caosdb/server/utils/SHA512.java | 4 +-
.../org/caosdb/server/utils/Serializer.java | 4 +-
.../caosdb/server/utils/ServerMessages.java | 16 +-
.../org/caosdb/server/utils/ServerStat.java | 4 +-
.../server/utils/TransactionLogMessage.java | 8 +-
.../server/utils/UncloseableOutputStream.java | 4 +-
.../org/caosdb/server/utils/UndoHandler.java | 4 +-
.../org/caosdb/server/utils/Undoable.java | 4 +-
.../java/org/caosdb/server/utils/Utils.java | 14 +-
.../server/utils/WebinterfaceUtils.java | 20 +-
.../org/caosdb/server/utils/mail/Mail.java | 10 +-
.../server/utils/mail/MailFormatter.java | 4 +-
.../caosdb/server/utils/mail/MailHandler.java | 4 +-
.../caosdb/server/utils/mail/Mailable.java | 4 +-
.../server/utils/mail/SendMailHandler.java | 4 +-
.../utils/mail/SimpleMailFormatter.java | 4 +-
.../server/utils/mail/ToFileHandler.java | 10 +-
.../org/caosdb/unit/CaosDBSystemOfUnits.java | 8 +-
src/main/java/org/caosdb/unit/Converter.java | 4 +-
.../java/org/caosdb/unit/LinearConverter.java | 4 +-
src/main/java/org/caosdb/unit/Unit.java | 4 +-
.../java/org/caosdb/unit/UnknownUnit.java | 4 +-
.../org/caosdb/unit/WrappedConverter.java | 4 +-
.../caosdb/unit/WrappedLinearConverter.java | 4 +-
.../java/org/caosdb/unit/WrappedUnit.java | 4 +-
.../org/caosdb/datetime/DateTimeTest.java | 14 +-
.../caosdb/datetime/UTCTimeZoneShiftTest.java | 2 +-
src/test/java/org/caosdb/server/Misc.java | 14 +-
.../TestDefaultPamScriptCaller.java | 4 +-
.../server/authentication/AuthTokenTest.java | 54 ++--
.../caosdb/server/caching/TestCaching.java | 10 +-
.../caosdb/server/caching/TestNoCaching.java | 12 +-
.../database/DatabaseAccessManagerTest.java | 4 +-
.../implementation/MySQL/InsertTest.java | 30 +--
.../transaction/RetrieveFullEntityTest.java | 20 +-
.../backend/transactions/TestGetAllNames.java | 20 +-
.../caosdb/server/datatype/testBoolean.java | 18 +-
.../org/caosdb/server/entity/EntityTest.java | 6 +-
.../caosdb/server/entity/SelectionTest.java | 14 +-
.../container/PropertyContainerTest.java | 22 +-
.../xml/PropertyToElementStrategyTest.java | 22 +-
.../grpc/CaosDBToGrpcConvertersTest.java | 48 ++--
.../org/caosdb/server/jobs/JobConfigTest.java | 18 +-
.../org/caosdb/server/jobs/ScheduleTest.java | 8 +-
.../jobs/core/TestInsertFilesInDir.java | 6 +-
.../caosdb/server/logging/TestLogging.java | 12 +-
.../server/permissions/EntityACLTest.java | 103 ++++----
.../permissions/EntityPermissionTest.java | 50 ++--
.../java/org/caosdb/server/query/POVTest.java | 2 +-
.../org/caosdb/server/query/QueryTest.java | 20 +-
.../java/org/caosdb/server/query/TestCQL.java | 28 +-
.../resource/FileSystemResourceTest.java | 4 +-
.../TestAbstractCaosDBServerResource.java | 48 ++--
.../resource/TestScriptingResource.java | 56 ++--
.../resource/TestSharedFileResource.java | 22 +-
.../TestServerSideScriptingCaller.java | 62 ++---
.../server/transaction/RetrieveTest.java | 42 +--
.../caosdb/server/transaction/UpdateTest.java | 56 ++--
.../caosdb/server/utils/FileUtilsTest.java | 89 +++----
.../org/caosdb/server/utils/UtilsTest.java | 4 +-
.../server/utils/WebinterfaceUtilsTest.java | 10 +-
.../caosdb/server/utils/mail/TestMail.java | 12 +-
641 files changed, 4707 insertions(+), 4631 deletions(-)
diff --git a/.gitignore b/.gitignore
index c6fdfc4d..943855c5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,4 +47,4 @@ src/doc/development/api/xml/*.jar
# data directories
-CaosDBFileSystem
+LinkAheadFileSystem
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 885b7914..17beba26 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,5 +1,5 @@
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,7 +23,9 @@
#
variables:
- DEPLOY_REF: dev
+ # TODO Reset to "dev"
+ DEPLOY_REF: f-linkahead-rename
+ # TODO Rename to linkahead
CI_REGISTRY_IMAGE: $CI_REGISTRY/caosdb/src/caosdb-server/caosdb-server-testenv:latest
GIT_SUBMODULE_STRATEGY: normal
@@ -134,6 +136,7 @@ trigger_inttest:
CPPINT: $TMP_CPPINT
MYSQLBACKEND: $TMP_MYSQLBACKEND
trigger:
+ # TODO Rename to linkahead
project: caosdb/src/caosdb-deploy
branch: $DEPLOY_REF
strategy: depend
diff --git a/.gitlab/merge_request_templates/Default.md b/.gitlab/merge_request_templates/Default.md
index 3629e0ca..0d4d8e23 100644
--- a/.gitlab/merge_request_templates/Default.md
+++ b/.gitlab/merge_request_templates/Default.md
@@ -21,7 +21,7 @@ specs, finding more corner cases, concrete questions)?*
Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab
comments for the reviewer. They should guide the reviewer through the changes, explain your changes
and also point out open questions. For further good practices have a look at [our review
-guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
+guidelines](https://gitlab.com/linkahead/linkahead/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] All automated tests pass
- [ ] Reference related issues
@@ -49,7 +49,7 @@ guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
- [ ] In-code documentation and comments are up-to-date.
- [ ] Check: Are there specifications? Are they satisfied?
-For further good practices have a look at [our review guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md).
+For further good practices have a look at [our review guidelines](https://gitlab.com/linkahead/linkahead/-/blob/dev/REVIEW_GUIDELINES.md).
/assign me
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a4d71f73..943b0ef2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -36,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed ###
+* Renamed CaosDB to LinkAhead.
* The default behavior of the query `FIND SomeName [...]` (as well as COUNT and SELECT) is being
made configurable and changes:
* `FIND SomeName` will be interpreted as `FIND <FIND_QUERY_DEFAULT_ROLE>
@@ -246,7 +247,7 @@ process. It is identical to v0.7.1
### Added
-* Endpoint for CaosDB GRPC API 0.1 (see https://gitlab.com/caosdb-proto.git for
+* Endpoint for LinkAhead GRPC API 0.1 (see https://gitlab.com/caosdb-proto.git for
more).
Authentication is supported via a Basic scheme, using the well-known
"authentication" header.
@@ -369,7 +370,7 @@ process. It is identical to v0.7.1
* New query functionality: `ANY VERSION OF` modifier. E.g. `FIND ANY VERSION OF
RECORD WITH pname=val` returns all current and old versions of records where
`pname=val`. For further information, examples and limitations see the wiki
- page on [CQL](https://gitlab.com/caosdb/caosdb/-/wikis/manuals/CQL/CaosDB%20Query%20Language)
+ page on [CQL](https://gitlab.com/caosdb/caosdb/-/wikis/manuals/CQL/LinkAhead%20Query%20Language)
* New server property `SERVER_SIDE_SCRIPTING_BIN_DIRS` which accepts a comma or
space separated list as values. The server looks for scripts in all
directories in the order or the list and uses the first matching file.
diff --git a/CITATION.cff b/CITATION.cff
index a45e422c..1fdb5ba8 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -22,7 +22,7 @@ authors:
- family-names: Luther
given-names: Stefan
orcid: https://orcid.org/0000-0001-7214-8125
-title: "CaosDB - Server"
+title: "LinkAhead - Server"
version: 0.10.0
doi: 10.3390/data4020083
date-released: 2023-06-02
diff --git a/DEPENDENCIES.md b/DEPENDENCIES.md
index fbcb186e..7e062cb5 100644
--- a/DEPENDENCIES.md
+++ b/DEPENDENCIES.md
@@ -2,8 +2,8 @@
## For Building and Running the Server
-* `>=caosdb-proto 0.3.0`
-* `>=caosdb-mysqlbackend 5.0.0`
+* `>=linkahead-proto 0.3.0`
+* `>=linkahead-mysqlbackend 5.0.0`
* `>=Java 11`
* `>=Apache Maven 3.6.0`
* `>=Make 4.2`
@@ -13,7 +13,7 @@
## For Deploying a Web User Interface (optional)
-* `>=caosdb-webui 0.8.0`
+* `>=linkahead-webui 0.8.0`
## For Building the Documentation (optional)
diff --git a/Doxyfile b/Doxyfile
index 9d12b22c..83cafd69 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
-PROJECT_NAME = "CaosDB Server"
+PROJECT_NAME = "LinkAhead Server"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
diff --git a/FEATURES.md b/FEATURES.md
index 2c046dae..f4af2923 100644
--- a/FEATURES.md
+++ b/FEATURES.md
@@ -1,21 +1,21 @@
# Features
-* The CaosDB Server implements a CaosDB GRPC API Endpoint (v0.3.0)
+* The LinkAhead Server implements a LinkAhead GRPC API Endpoint (v0.3.0)
Authentication is supported via a Basic scheme, using the well-known
"authentication" header.
Notable limitations of the current implementation of the API:
* It is currently not possible to mix retrievals
- (caosdb.entity.v1.RetrieveRequest) with any other transaction type - so
+ (linkahead.entity.v1.RetrieveRequest) with any other transaction type - so
transaction are either read-only or write-only. The server throws an error
if it finds mixed read/write transactions.
* It is currently not possible to have more that one query
- (caosdb.entity.v1.Query) in a single transaction. The server throws an
+ (linkahead.entity.v1.Query) in a single transaction. The server throws an
error if it finds more than one query.
* Legacy XML/HTTP API (Deprecated)
-* Deployment of caosdb-webui (>=0.8.0)
+* Deployment of linkahead-webui (>=0.8.0)
* Server-side Scripting API (v0.1)
-* CaosDB Query Language Processor
-* CaosDB FileSystem
+* LinkAhead Query Language Processor
+* LinkAhead FileSystem
* User Management, Authentication and Authorization
* Internal authentication service
* Authentication via an external service (PAM, LDAP)
diff --git a/Makefile b/Makefile
index 29b7d5a5..9f629c33 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,8 +23,8 @@
# ** end header
#
-CAOSDB_SERVER_VERSION ?= $(shell mvn org.apache.maven.plugins:maven-help-plugin:3.1.0:evaluate -Dexpression=project.version -q -DforceStdout)
-CAOSDB_COMMAND_LINE_OPTIONS ?=
+LINKAHEAD_SERVER_VERSION ?= $(shell mvn org.apache.maven.plugins:maven-help-plugin:3.1.0:evaluate -Dexpression=project.version -q -DforceStdout)
+LINKAHEAD_COMMAND_LINE_OPTIONS ?=
SHELL:=/bin/bash
JPDA_PORT ?= 9000
JMX_PORT ?= 9090
@@ -33,7 +33,7 @@ compile: print-version easy-units
mvn compile
print-version:
- @echo "This is CaosDB $(CAOSDB_SERVER_VERSION)"
+ @echo "This is LinkAhead $(LINKAHEAD_SERVER_VERSION)"
runserver: print-version
mvn exec:java@run
@@ -42,14 +42,14 @@ run: compile
mvn exec:java@run
run-debug: jar
- java -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dcaosdb.debug=true -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dlinkahead.debug=true -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
run-debug-single:
- java -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=$(JMX_PORT) -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dcaosdb.debug=true -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -Dcom.sun.management.jmxremote -Dcom.sun.management.jmxremote.port=$(JMX_PORT) -Dcom.sun.management.jmxremote.ssl=false -Dcom.sun.management.jmxremote.authenticate=false -Xrunjdwp:transport=dt_socket,address=0.0.0.0:$(JPDA_PORT),server=y,suspend=n -Dlinkahead.debug=true -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
run-single:
- java -jar target/caosdb-server.jar $(CAOSDB_COMMAND_LINE_OPTIONS)
+ java -jar target/linkahead-server.jar $(LINKAHEAD_COMMAND_LINE_OPTIONS)
formatting:
mvn fmt:format
@@ -59,14 +59,14 @@ formatting:
jar: print-version easy-units
mvn -e package -DskipTests
@pushd target ; \
- ln -s caosdb-server-$(CAOSDB_SERVER_VERSION)-jar-with-dependencies.jar caosdb-server.jar; \
+ ln -s linkahead-server-$(LINKAHEAD_SERVER_VERSION)-jar-with-dependencies.jar linkahead-server.jar; \
popd
antlr:
mvn antlr4:antlr4
test: print-version easy-units
- MAVEN_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Dcaosdb.debug=true -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=0.0.0.0:$(JPDA_PORT)"
+ MAVEN_DEBUG_OPTS="-Xdebug -Xnoagent -Djava.compiler=NONE -Dlinkahead.debug=true -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=0.0.0.0:$(JPDA_PORT)"
mvn test -X
test_misc:
@@ -84,15 +84,15 @@ clean-antlr:
.PHONY: run-server-screen
run-server-screen:
- @if test "$$(screen -ls | grep -c 'caosdb-screen')" -eq "1"; then \
+ @if test "$$(screen -ls | grep -c 'linkahead-screen')" -eq "1"; then \
echo "server is probably running. try 'screen -ls'"; \
exit 1 ; \
fi
# start and wait for server
- @screen -L -S caosdb-screen -t server -d -m -A make run
+ @screen -L -S linkahead-screen -t server -d -m -A make run
@sleep 2
@while [ 1 -eq 1 ] ; do \
- screen -S caosdb-screen -X hardcopy .screen.log || break ; \
+ screen -S linkahead-screen -X hardcopy .screen.log || break ; \
[ $$(grep -c "org.restlet.ext.jetty.JettyServerHelper start" .screen.log) -eq 0 ] || break ; \
done; \
@@ -100,20 +100,20 @@ run-server-screen:
.PHONY: stop-server-screen
stop-server-screen:
# stop screen session with server
- @screen -S caosdb-screen -X hardcopy screen.log || true
- @screen -S caosdb-screen -p server -X stuff "^C"
+ @screen -S linkahead-screen -X hardcopy screen.log || true
+ @screen -S linkahead-screen -p server -X stuff "^C"
.PHONY: run-debug-screen
run-debug-screen:
- @if test "$$(screen -ls | grep -c 'caosdb-debug-screen')" -eq "1"; then \
+ @if test "$$(screen -ls | grep -c 'linkahead-debug-screen')" -eq "1"; then \
echo "server is probably running. try 'screen -ls'"; \
exit 1 ; \
fi
# start and wait for server
- @screen -L -S caosdb-debug-screen -t server -d -m -A make run-debug
+ @screen -L -S linkahead-debug-screen -t server -d -m -A make run-debug
@sleep 2
@while [ 1 -eq 1 ] ; do \
- screen -S caosdb-debug-screen -X hardcopy .screen.log || break ; \
+ screen -S linkahead-debug-screen -X hardcopy .screen.log || break ; \
[ $$(grep -c "org.restlet.ext.jetty.JettyServerHelper start" .screen.log) -eq 0 ] || break ; \
done; \
@@ -121,8 +121,8 @@ run-debug-screen:
.PHONY: stop-debug-screen
stop-debug-screen:
# stop screen session with debug server
- @screen -S caosdb-debug-screen -X hardcopy screen.log || true
- @screen -S caosdb-debug-screen -p server -X stuff "^C"
+ @screen -S linkahead-debug-screen -X hardcopy screen.log || true
+ @screen -S linkahead-debug-screen -p server -X stuff "^C"
.m2-local:
mkdir .m2-local
diff --git a/README.md b/README.md
index 3aac5df2..c98bdc63 100644
--- a/README.md
+++ b/README.md
@@ -3,8 +3,8 @@
## Welcome
-This is the **CaosDB Java Server** repository and a part of the
-CaosDB project.
+This is the **LinkAhead Java Server** repository and a part of the
+LinkAhead project.
## Setup
@@ -14,30 +14,30 @@ setup this code.
## Further Reading
-Please refer to the [official documentation](https://docs.indiscale.com/caosdb-server/) for more information.
+Please refer to the [official documentation](https://docs.linkahead.org/linkahead-server/) for more information.
## Contributing
-Thank you very much to all contributers—[past, present](https://gitlab.com/caosdb/caosdb/-/blob/dev/HUMANS.md), and prospective ones.
+Thank you very much to all contributers—[past, present](https://gitlab.com/linkahead/linkahead/-/blob/dev/HUMANS.md), and prospective ones.
### Code of Conduct
-By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/caosdb/caosdb/-/blob/dev/CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold our [Code of Conduct](https://gitlab.com/linkahead/linkahead/-/blob/dev/CODE_OF_CONDUCT.md).
### How to Contribute
* You found a bug, have a question, or want to request a feature? Please
-[create an issue](https://gitlab.com/caosdb/caosdb-server/-/issues).
+[create an issue](https://gitlab.com/linkahead/linkahead-server/-/issues).
* You want to contribute code? Please fork the repository and create a merge
request in GitLab and choose this repository as target. Make sure to select
"Allow commits from members who can merge the target branch" under Contribution
when creating the merge request. This allows our team to work with you on your request.
-- If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-server/),
+- If you have a suggestion for the [documentation](https://docs.linkahead.org/linkahead-server/),
the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
However, you can also create an issue for it.
-- You can also contact us at **info (AT) caosdb.org** and join the
- CaosDB community on
- [#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
+- You can also contact us at **info (AT) linkahead.org** and join the
+ LinkAhead community on
+ [#linkahead:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
## License
diff --git a/README_CONFIGURATION.md b/README_CONFIGURATION.md
index 27045eea..06b36ebd 100644
--- a/README_CONFIGURATION.md
+++ b/README_CONFIGURATION.md
@@ -9,7 +9,7 @@ The default configuration can be overriden by
1. the file ./conf/ext/server.conf
2. any file in ./conf/ext/server.conf.d/ in (approximately?) alphabetical order
-3. environment variables with the prefix `CAOSDB_CONFIG_`
+3. environment variables with the prefix `LINKAHEAD_CONFIG_`
in this order.
diff --git a/README_SETUP.md b/README_SETUP.md
index acb3a79a..b52c64ed 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -1,11 +1,11 @@
-# Getting Started with the CaosDB Server
+# Getting Started with the LinkAhead Server
Here, you find information on requirements, the installation, configuration and
-more. Note, that building the CaosDB Server from the sources and maintaining
+more. Note, that building the LinkAhead Server from the sources and maintaining
the server requires the knowledge/skill of an experienced Linux administrator.
**Note:** If you are looking for a quick and easy way to get startet, check
-out [the docker deployment](https://gitlab.indiscale.com/caosdb/src/caosdb-docker).
+out [the docker deployment](https://gitlab.com/linkahead/linkahead-docker).
## Requirements
@@ -37,9 +37,9 @@ On Fedora, the required packages can be installed with:
#### Web UI ###
- If the WebUI shall run, check out the respective submodule: `git submodule
- update --init caosdb-webui`
+ update --init linkahead-webui`
- Then configure and compile it according to its
- [documentation](https://docs.indiscale.com/caosdb-webui/getting_started.html).
+ [documentation](https://docs.linkahead.org/linkahead-webui/getting_started.html).
#### PAM ###
Authentication via PAM is possible, for this the PAM development library must be
@@ -50,11 +50,11 @@ installed and the pam user tool must be compiled:
- If you want, you can run a test now: `./pam_authentication.sh asdf` asks for a password for user
`asdf`. If no such user exists or the wrong passowrd is entered, it print `[FAILED]` and return
with a non-zero exit code.
-- If you want to run the CaosDB server without root privilege, you need to use
- the setuid bit for the binary. For example, if the user `caosdb` runs the
+- If you want to run the LinkAhead server without root privilege, you need to use
+ the setuid bit for the binary. For example, if the user `linkahead` runs the
server process the permissions of `bin/pam_authentication` should be the
following:
- `-rwsr-x--- 1 root caosdb pam_authentication`
+ `-rwsr-x--- 1 root linkahead pam_authentication`
##### Troubleshooting ####
If `make` fails with `pam_authentication.c:4:31: fatal error:
@@ -69,7 +69,7 @@ After a fresh clone of the repository, this is what you need to setup the
server:
1. Install the `proto` submodule (and submodules for those extensions you want, see above):
- `git submodule update --init caosdb-proto`
+ `git submodule update --init linkahead-proto`
2. Compile the server with `make compile`. This may take a while and there
needs to be an internet connection as packages are downloaded to be
integrated in the java file.
@@ -78,19 +78,19 @@ server:
3. Create an SSL certificate somewhere with a `Java Key Store` file. For
self-signed certificates (not recommended for production use) you can do:
- `mkdir certificates; cd certificates`
- - `keytool -genkey -keyalg RSA -alias selfsigned -keystore caosdb.jks -validity 375 -keysize 2048 -ext san=dns:localhost`
+ - `keytool -genkey -keyalg RSA -alias selfsigned -keystore linkahead.jks -validity 375 -keysize 2048 -ext san=dns:localhost`
Replace `localhost` by your host name, if you want.
- - `keytool -importkeystore -srckeystore caosdb.jks -destkeystore caosdb.p12 -deststoretype PKCS12 -srcalias selfsigned`
- - Export the public part only: `openssl pkcs12 -in caosdb.p12 -nokeys -out cert.pem`.
+ - `keytool -importkeystore -srckeystore linkahead.jks -destkeystore linkahead.p12 -deststoretype PKCS12 -srcalias selfsigned`
+ - Export the public part only: `openssl pkcs12 -in linkahead.p12 -nokeys -out cert.pem`.
The resulting `cert.pem` can safely be given to users to allow ssl
verification.
- You can check the content of the certificate with `openssl x509 -in cert.pem -text`
Alternatively, you can create a keystore from certificate files that you already have:
- `openssl pkcs12 -export -inkey privkey.pem -in fullchain.pem -out all-certs.pkcs12`
- - `keytool -importkeystore -srckeystore all-certs.pkcs12 -srcstoretype PKCS12 -deststoretype pkcs12 -destkeystore caosdb.jks`
+ - `keytool -importkeystore -srckeystore all-certs.pkcs12 -srcstoretype PKCS12 -deststoretype pkcs12 -destkeystore linkahead.jks`
4. Install/configure the MySQL back-end: see the `README_SETUP.md` of the
- `caosdb-mysqlbackend` repository
+ `linkahead-mysqlbackend` repository
5. Create an authtoken config (e.g. copy `conf/core/authtoken.example.yaml` to
`conf/ext/authtoken.yml` and change it)
6. If any of the settings in `conf/core/server.conf` do not fit your needs, create
@@ -98,7 +98,7 @@ server:
* Setup for MySQL back-end:
specify the fields `MYSQL_USER_NAME`, `MYSQL_USER_PASSWORD`,
`MYSQL_DATABASE_NAME`, and `MYSQL_HOST`.
- * Choose the host and ports under which CaosDB will be accessible. The host
+ * Choose the host and ports under which LinkAhead will be accessible. The host
is the IP address the server should listen on. Blank (the default) means
all interfaces, and `127.0.0.1` means only localhost.
* Setup the SSL certificate: Assuming that there is an appropriate `Java Key
@@ -108,8 +108,8 @@ server:
certificate passwords are stored in plaintext.
* Set the path to the authtoken config (see step 4)
* Set the file system paths:
- - `FILE_SYSTEM_ROOT`: The root for all the files managed by CaosDB.
- - `DROP_OFF_BOX`: Files can be put here for insertion into CaosDB.
+ - `FILE_SYSTEM_ROOT`: The root for all the files managed by LinkAhead.
+ - `DROP_OFF_BOX`: Files can be put here for insertion into LinkAhead.
- `TMP_FILES`: Temporary files go here, for example during script
execution or when uploading or moving files.
- `SHARED_FOLDER`: Folder for sharing files via cryptographic tokens,
@@ -118,23 +118,23 @@ server:
of directories (relative or absolute) where the server will be looking
for executables which are then callable as server-side scripts. By
default this list only contains `./scripting/bin`. If you want to
- include e.g. scripts which are maintained as part of the caosdb-webui
+ include e.g. scripts which are maintained as part of the linkahead-webui
repository (because they are intended for usage by the webui), you
- should add `./caosdb-webui/sss_bin/` as well.
+ should add `./linkahead-webui/sss_bin/` as well.
- `INSERT_FILES_IN_DIR_ALLOWED_DIRS`: add mounted filesystems here that
- shall be accessible by CaosDB
+ shall be accessible by LinkAhead
* Maybe set another `SESSION_TIMEOUT_MS`.
* See also [CONFIGURATION.rst](src/doc/administration/configuration.rst)
7. Copy `conf/core/usersources.ini.template` to `conf/ext/usersources.ini`.
* You can skip this if you do not want to use an external authentication.
- Local users (CaosDB realm) are always available.
+ Local users (`CaosDB` realm) are always available.
* Define the users/groups who you want to include/exclude.
* Assign at least one user the `administration` role.
- * For example, if the admin user is called `caosdb`, there should be the
+ * For example, if the admin user is called `linkahead`, there should be the
following lines:
```
- include.user = caosdb
- user.caosdb.roles = administration
+ include.user = linkahead
+ user.linkahead.roles = administration
```
* It is important that the file complies with the ini file specification.
Especially that there are no `properties` (aka `keys`) without a
@@ -149,7 +149,7 @@ Done!
`$ make run`
-This can take a while. Once you see `Starting org.caosdb.server.CaosDBServer
+This can take a while. Once you see `Starting org.linkahead.server.LinkAheadServer
application` the server is ready and you can try it out by connecting with a
client, e.g. the web client, if you installed it. Typically, you just need to
type `https://localhost:10443` in your Browser, assuming you used 10443 as port.
@@ -212,6 +212,21 @@ Done!
## Migration
+### From 0.9 to 0.10
+
+CaosDB is now LinkAhead! This name changes leads to a few necessary changes on the administrator
+side:
+
+* All configuration environment variables should change from `CAOSDB_CONFIG_...` to
+ `LINKAHEAD_CONFIG_...`. The old environment variables will remain deprecated but valid for some
+ time, but mixing old and new variables is forbidden: If you rename one, you have to rename all.
+* If you install LinkAhead from git, the submodules have changed their names, and most probably also
+ the remotes have different URLs now.
+* The default paths for the file system have changed. Make sure that your paths match your
+ configuration (see `server.conf` for the new default paths).
+* The Java class structure was renamed from `org.caosdb.server....` to `org.linkahead.server....`.
+ This may be relevant for you if you customized the `usersources.ini` or the logging configuration.
+
### From 0.1 to 0.2
A major change in the code is the renaming of the java packages (from
@@ -254,21 +269,21 @@ pip3 install .
### Installation without or with restricted internet connection on the host system
-It is of course possible to install CaosDB on servers which do not have an
+It is of course possible to install LinkAhead on servers which do not have an
internet connection or only have limited access to the internet.
-However, maven, which is used to build the CaosDB server, typically accesses
+However, maven, which is used to build the LinkAhead server, typically accesses
the internet very often, and some reconfiguration might be necessary to prevent
timeout issues and similar headache.
A recommendation to proceed is:
-- Clone the repositories (caosdb-server, caosdb-mysqlbackend and subrepository
- caosdb-webui) on a second machine that has internet connection.
-- Run `make install` and `make run` in the caosdb-server repository. This will
+- Clone the repositories (linkahead-server, linkahead-mysqlbackend and subrepository
+ linkahead-webui) on a second machine that has internet connection.
+- Run `make install` and `make run` in the linkahead-server repository. This will
download all required dependencies and setup all maven-related artifacts in
a folder called `.m2` typically located in the home directory.
- In addition to copying over the repositories for the server, mysqlbackend and
webui to the target host machine, also copy the complete `.m2` folder to the
- **home directory of the user that is running the CaosDB server**.
+ **home directory of the user that is running the LinkAhead server**.
- On the host machine, open the file `pom.xml` in the server repository.
- Look for the section `<repositories>`. There should be a `<respository>` with
`<id>local-maven-repo</id>`. It should be moved on top of the list of
@@ -285,7 +300,7 @@ Make sure that you:
- Installed the WebUI according to the section [Web UI]
- Run `make install` in the webui sub folder
-### How can I run the CaosDB server using ports 443 and 80?
+### How can I run the LinkAhead server using ports 443 and 80?
On standard linux setups, ports 443 and 80 cannot be opened by non-root processes.
@@ -303,6 +318,6 @@ Using authbind is a simple solution that is briefly described here:
- Install the package authbind
- Create (empty) files `/etc/authbind/byport/80` (and `.../443`), e.g. using `touch`
- Grant execution permissions for the user who runs the server to the new files.
-- Run the CaosDB server using authbind with the `--deep` option:
+- Run the LinkAhead server using authbind with the `--deep` option:
`authbind --deep make run`. The `--deep` option is necessary because the
server starts a subprocess which actually opens the ports.
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 1b5ae489..60a32fd8 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -1,8 +1,8 @@
-# Release Guidelines for the CaosDB Server
+# Release Guidelines for the LinkAhead Server
This document specifies release guidelines in addition to the general release
-guidelines of the CaosDB Project
-([RELEASE_GUIDELINES.md](https://gitlab.com/caosdb/caosdb/blob/dev/RELEASE_GUIDELINES.md))
+guidelines of the LinkAhead Project
+([RELEASE_GUIDELINES.md](https://gitlab.com/linkahead/linkahead/blob/dev/RELEASE_GUIDELINES.md))
## General Prerequisites
@@ -38,11 +38,11 @@ guidelines of the CaosDB Project
* `CHANGELOG.md`: Re-add the `[Unreleased]` section.
10. Add a gitlab release in the respective repository:
- https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/releases
+ https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/releases
Add a description, which can be a copy&paste from the CHANGELOG, possibly prepended by:
```md
# Changelog
-[See full changelog](https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/${TAG}/CHANGELOG.md)
+[See full changelog](https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/${TAG}/CHANGELOG.md)
```
diff --git a/conf/core/authtoken.example.yaml b/conf/core/authtoken.example.yaml
index 4d57c919..04211fa4 100644
--- a/conf/core/authtoken.example.yaml
+++ b/conf/core/authtoken.example.yaml
@@ -7,7 +7,7 @@
# Authentication Tokens.
#
# This yaml file contains an array of configuration objects which may have the
-# properties that are defined by the org.caosdb.server.accessControl.Config class.
+# properties that are defined by the org.linkahead.server.accessControl.Config class.
#
# These properties are:
#
diff --git a/conf/core/jobs.csv b/conf/core/jobs.csv
index 84795bee..72dd0423 100644
--- a/conf/core/jobs.csv
+++ b/conf/core/jobs.csv
@@ -1,5 +1,5 @@
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 Timm Fitsche <t.fitschen@indiscale.com>
# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
diff --git a/conf/core/log4j2-debug.properties b/conf/core/log4j2-debug.properties
index 3ae3ed26..cab0fc94 100644
--- a/conf/core/log4j2-debug.properties
+++ b/conf/core/log4j2-debug.properties
@@ -4,8 +4,8 @@
property.LOG_DIR = testlog
# for unit testing
-logger.caosdb_server_logging.name = org.caosdb.server.logging
-logger.caosdb_server_logging.level = TRACE
+logger.linkahead_server_logging.name = org.linkahead.server.logging
+logger.linkahead_server_logging.level = TRACE
# ${LOG_DIR}/debug.log
appender.debug.type = RandomAccessFile
diff --git a/conf/core/server.conf b/conf/core/server.conf
index 5df6c40c..ef5df36c 100644
--- a/conf/core/server.conf
+++ b/conf/core/server.conf
@@ -5,8 +5,8 @@ TIMEZONE=
# Set the name of the server owner
# e.g: SERVER_OWNER=XY Department
SERVER_OWNER=
-# Name of this CaosDB Server
-SERVER_NAME=CaosDB Server
+# Name of this LinkAhead Server
+SERVER_NAME=LinkAhead Server
# --------------------------------------------------
# The following paths are relative to the working directory of the server.
@@ -26,26 +26,26 @@ SERVER_SIDE_SCRIPTING_WORKING_DIR=./scripting/working/
# can go into a specific home directory for the respective script within this folder.
SERVER_SIDE_SCRIPTING_HOME_DIR=./scripting/home/
-# The CaosDB file system root.
-# The file hierarchy of CaosDB's internal file system starts at this folder.
-# An absolute file path of File objects within CaosDB is relative to this folder.
-FILE_SYSTEM_ROOT=./CaosDBFileSystem/FileSystemRoot/
+# The LinkAhead file system root.
+# The file hierarchy of LinkAhead's internal file system starts at this folder.
+# An absolute file path of File objects within LinkAhead is relative to this folder.
+FILE_SYSTEM_ROOT=./LinkAheadFileSystem/FileSystemRoot/
# Path to the drop off box.
-# This is were users can place files that should be picked up by the CaosDB drop off box program.
-DROP_OFF_BOX=./CaosDBFileSystem/DropOffBox/
+# This is were users can place files that should be picked up by the LinkAhead drop off box program.
+DROP_OFF_BOX=./LinkAheadFileSystem/DropOffBox/
# Location of temporary files
# All temporary files with the exception of files created by the scripting API will go into this folder.
-TMP_FILES=./CaosDBFileSystem/TMP/
+TMP_FILES=./LinkAheadFileSystem/TMP/
# Shared folder
# Additional folder for longer term storage of scripting API output.
# In contrast to the script's working directory, these subdirectories are publicly accessible.
-SHARED_FOLDER=./CaosDBFileSystem/Shared/
+SHARED_FOLDER=./LinkAheadFileSystem/Shared/
# Path to the chown script which is needed by the drop off box in order to change permissions of files.
-CHOWN_SCRIPT=./misc/chown_script/caosdb_chown_dropoffbox
+CHOWN_SCRIPT=./misc/chown_script/linkahead_chown_dropoffbox
# This file is responsible for setting individual user and group permissions.
USER_SOURCES_INI_FILE=./conf/ext/usersources.ini
@@ -58,7 +58,7 @@ AUTH_OPTIONAL=FALSE
# --------------------------------------------------
# MySQL settings
# --------------------------------------------------
-# Hostname of the mysql instance used by CaosDB
+# Hostname of the mysql instance used by LinkAhead
MYSQL_HOST=localhost
# Port of the mysql instance
MYSQL_PORT=3306
@@ -68,17 +68,17 @@ MYSQL_DATABASE_NAME=caosdb
MYSQL_USER_NAME=caosdb
# Password for the user
MYSQL_USER_PASSWORD=random1234
-# Schema of mysql procedures and tables which is required by this CaosDB instance
+# Schema of mysql procedures and tables which is required by this LinkAhead instance
MYSQL_SCHEMA_VERSION=v5.0
# --------------------------------------------------
# Server options
# --------------------------------------------------
-# The context root is a prefix which allows running multiple instances of CaosDB using the same
+# The context root is a prefix which allows running multiple instances of LinkAhead using the same
# hostname and port. Must start with "/".
CONTEXT_ROOT=
-#CONTEXT_ROOT=/caosdb
+#CONTEXT_ROOT=/linkahead
# Server bind/host address, which is the address to listen to. Set to blank, or
# 0.0.0.0 in IPv4, to listen to all. Set to 127.0.0.1 to make it available to
@@ -169,7 +169,7 @@ WEBUI_HTTP_HEADER_CACHE_MAX_AGE=28800
# --------------------------------------------------
# The handler that treats sent mails.
# The default handler pipes mails to a file.
-MAIL_HANDLER_CLASS=org.caosdb.server.utils.mail.ToFileHandler
+MAIL_HANDLER_CLASS=org.linkahead.server.utils.mail.ToFileHandler
# The file were the ToFileHanlder pipes messages to.
MAIL_TO_FILE_HANDLER_LOC=./
@@ -177,7 +177,7 @@ MAIL_TO_FILE_HANDLER_LOC=./
# Admin settings
# --------------------------------------------------
# Name of the administrator of this instance
-ADMIN_NAME=CaosDB Admin
+ADMIN_NAME=LinkAhead Admin
# Email of the administrator of this instance
ADMIN_EMAIL=
# An URL to the bugtracker for managing instance related bugs.
@@ -186,14 +186,14 @@ BUGTRACKER_URI=
# If set to true MySQL stores transaction benchmarks for all SQL queries. Used for benchmarking and debugging.
TRANSACTION_BENCHMARK_ENABLED=FALSE
#TRANSACTION_BENCHMARK_ENABLED=TRUE
-# Location of the configuration file for the CaosDB cache.
+# Location of the configuration file for the LinkAhead cache.
CACHE_CONF_LOC=./conf/core/cache.ccf
# Set this option to true to lobally disable caching. Used for debugging.
CACHE_DISABLE=false
# The server is allowed to create symlinks to files and folders within this whitelist of directories.
INSERT_FILES_IN_DIR_ALLOWED_DIRS=
-#INSERT_FILES_IN_DIR_ALLOWED_DIRS=/data/caosdb,/fileserver01/caosdb
+#INSERT_FILES_IN_DIR_ALLOWED_DIRS=/data/linkahead,/fileserver01/linkahead
# Sudo password of the system.
# Needed by the drop off box to set file permissions.
@@ -205,7 +205,7 @@ QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS=TRUE
# When checking the ACL of an entity roles which are unknown to the server
# raise an error (when set to MUST) or a warning (when set to SHOULD).
# Unknown roles occur when a user or group is removed or when entities are
-# loaded from other instances of the CaosDB Server where different users are
+# loaded from other instances of the LinkAhead Server where different users are
# present.
# CHECK_ENTITY_ACL_ROLES_MODE=[MUST,SHOULD]
CHECK_ENTITY_ACL_ROLES_MODE=MUST
diff --git a/conf/core/usersources.ini.template b/conf/core/usersources.ini.template
index fb328572..b0a72a2d 100644
--- a/conf/core/usersources.ini.template
+++ b/conf/core/usersources.ini.template
@@ -1,7 +1,7 @@
# -*- mode:conf; -*-
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -37,11 +37,11 @@ defaultRealm = PAM
# realm can be looked up in that realm's documentation.
#
# Hint: Realms are implemented by classes which are typically in the
-# org.caosdb.server.accessControl.Pam package and implement the UserSource interface.
+# org.linkahead.server.accessControl.Pam package and implement the UserSource interface.
# Options for authentication against Linux' PAM.
[PAM]
-class = org.caosdb.server.accessControl.Pam
+class = org.linkahead.server.accessControl.Pam
# The script which does the actual checking. It is possible to put custom
# scripts or the misc/pam_authentication/ldap_authentication.sh script here.
; pam_script = ./misc/pam_authentication/pam_authentication.sh
diff --git a/misc/bend_symlinks/README.md b/misc/bend_symlinks/README.md
index a1fa833e..f9eefec4 100644
--- a/misc/bend_symlinks/README.md
+++ b/misc/bend_symlinks/README.md
@@ -54,7 +54,7 @@
storage.
All symlinks below this directory are being process by
this script.
- E.g. '/mnt/caosdb_fs/ExperimentalData/'
+ E.g. '/mnt/linkahead_fs/ExperimentalData/'
TARGET_PATTERN A (extended sed-style) regular expression for matching
broken symlink targets.
TARGET_REPLACEMENT A (sed-style) replacement string for the new (fixed)
@@ -78,14 +78,14 @@
1. Files have been moved from '/mnt/data/current/experiments/' to
/mnt/data/archive/experiments/2019/'. Execute the script in the root
- directory of the caosdb server's internal file system:
+ directory of the LinkAhead server's internal file system:
$ ./bend_symlinks.sh -d ./ /mnt/data/current/experiments /mnt/data/archive/experiments/2019
2. A File was renamed from '/mnt/data/procotol.pdf' to
'/mnt/data/protocol.pdf'. The symlink is located at
- '/mnt/caosdb_fs/procotol.pdf'. Execute the script in the root directory
- of the caosdb server's internal file system:
+ '/mnt/linkahead_fs/procotol.pdf'. Execute the script in the root directory
+ of the linkahead server's internal file system:
$ ./bend_symlinks.sh ./ procotol\.pdf$ protocol.pdf
diff --git a/misc/bend_symlinks/bend_symlinks.sh b/misc/bend_symlinks/bend_symlinks.sh
index 5a296fcd..427d5c9f 100755
--- a/misc/bend_symlinks/bend_symlinks.sh
+++ b/misc/bend_symlinks/bend_symlinks.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019 IndiScale (info@indiscale.com)
@@ -74,7 +74,7 @@ USAGE="# Usage
storage.
All symlinks below this directory are being process by
this script.
- E.g. '/mnt/caosdb_fs/ExperimentalData/'
+ E.g. '/mnt/linkahead_fs/ExperimentalData/'
TARGET_PATTERN A (extended sed-style) regular expression for matching
broken symlink targets.
TARGET_REPLACEMENT A (sed-style) replacement string for the new (fixed)
@@ -98,14 +98,14 @@ USAGE="# Usage
1. Files have been moved from '/mnt/data/current/experiments/' to
/mnt/data/archive/experiments/2019/'. Execute the script in the root
- directory of the caosdb server's internal file system:
+ directory of the LinkAhead server's internal file system:
$ $0 -d ./ /mnt/data/current/experiments /mnt/data/archive/experiments/2019
2. A File was renamed from '/mnt/data/procotol.pdf' to
'/mnt/data/protocol.pdf'. The symlink is located at
- '/mnt/caosdb_fs/procotol.pdf'. Execute the script in the root directory
- of the caosdb server's internal file system:
+ '/mnt/linkahead_fs/procotol.pdf'. Execute the script in the root directory
+ of the LinkAhead server's internal file system:
$ $0 ./ procotol\\.pdf$ protocol.pdf
diff --git a/misc/bend_symlinks/src/main.sh b/misc/bend_symlinks/src/main.sh
index 1d148df3..98a9e29a 100644
--- a/misc/bend_symlinks/src/main.sh
+++ b/misc/bend_symlinks/src/main.sh
@@ -1,5 +1,5 @@
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019 IndiScale (info@indiscale.com)
diff --git a/misc/bend_symlinks/src/utils.sh b/misc/bend_symlinks/src/utils.sh
index 2ddda289..0d9b7d6f 100644
--- a/misc/bend_symlinks/src/utils.sh
+++ b/misc/bend_symlinks/src/utils.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019-2020 Timm Fitschen (t.fitschen@indiscale.com)
# Copyright (C) 2019-2020 IndiScale GmbH (info@indiscale.com)
diff --git a/misc/check_symlinks/check_symlinks b/misc/check_symlinks/check_symlinks
index 0f6eb0d1..a2a4f415 100755
--- a/misc/check_symlinks/check_symlinks
+++ b/misc/check_symlinks/check_symlinks
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/chown_script/README b/misc/chown_script/README
index 03f24071..421b877d 100644
--- a/misc/chown_script/README
+++ b/misc/chown_script/README
@@ -1,4 +1,4 @@
-* The chown_script for the caosdb DropOffBox.
+* The chown_script for the LinkAhead DropOffBox.
* @author: Timm Fitschen (timm.fitschen@ds.mpg.de)
* @date: 2015-10-12
@@ -21,8 +21,8 @@ COPY this into a file called "CONFIG" (upper case) and edit it to your own needs
--- copy below this line ---
#This config file defines the parameters needed for the installation as a KEY/VALUE list. A line beginning with `#` will be ignored.
-#DB_USER is the unix user who runs the caosdb server
-DB_USER=caosdb
+#DB_USER is the unix user who runs the LinkAhead server
+DB_USER=linkahead
#LOC_DROPOFFBOX is the directory of the DropOffBox. ATTENTION: The path must not end with `/`!
LOC_DROPOFFBOX=/path/to/dropOffBox
@@ -30,7 +30,7 @@ LOC_DROPOFFBOX=/path/to/dropOffBox
#LOC_SUDOERS is a directory which files are included by the sudoers file. ATTENTION: The path must not end with `/`!
LOC_SUDOERS=/etc/sudoers.d
-#LOC_PREFIX is the folder which the caosdb_chown_script is stored to. ATTENTION: The path must not end with `/`!
+#LOC_PREFIX is the folder which the linkahead_chown_script is stored to. ATTENTION: The path must not end with `/`!
LOC_PREFIX=/usr/local/sbin
--- copy above this line ---
diff --git a/misc/chown_script/chown_script_template b/misc/chown_script/chown_script_template
index bd006f7e..b4a6e8e2 100755
--- a/misc/chown_script/chown_script_template
+++ b/misc/chown_script/chown_script_template
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/chown_script/install b/misc/chown_script/install
index 55ab1fa2..01efaffb 100755
--- a/misc/chown_script/install
+++ b/misc/chown_script/install
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -137,7 +137,7 @@ fi
# promt for dbuser
# default: caosdb
-prompt "the unix user which who runs the caosdb server" DB_USER
+prompt "the unix user which who runs the LinkAhead server" DB_USER
# TODO
DB_GROUP=$DB_USER
@@ -146,13 +146,13 @@ DB_GROUP=$DB_USER
# default: /etc/sudoers.d/
prompt "the location of sudoers.d" LOC_SUDOERS -f
LOC_SUDOERS=$(get_abs_filename $LOC_SUDOERS)
-LOC_SUDO_SCRIPT="${LOC_SUDOERS}/caosdb_chown_script"
+LOC_SUDO_SCRIPT="${LOC_SUDOERS}/linkahead_chown_script"
# promt for prefix
# default: /usr/local/sbin/
prompt "the location of the script which is to be generated" LOC_PREFIX -f
LOC_PREFIX=$(get_abs_filename $LOC_PREFIX)
-LOC_SCRIPT="${LOC_PREFIX}/caosdb_chown_dropoffbox"
+LOC_SCRIPT="${LOC_PREFIX}/linkahead_chown_dropoffbox"
check_parameters
@@ -202,7 +202,7 @@ $CMD_CHOWN root:root $LOC_SCRIPT
chmod 500 $LOC_SCRIPT
## configure sudo
-echo -en "# Generated by caosdb install script. Do not edit!
+echo -en "# Generated by LinkAhead install script. Do not edit!
# CONTACT: Timm Fitschen (timm.fitschen@ds.mpg.de)
# DATE: 2015-10-09
$DB_USER ALL = (root) NOPASSWD: $LOC_SCRIPT
diff --git a/misc/chown_script/test_functions b/misc/chown_script/test_functions
index 303f612f..614cae74 100644
--- a/misc/chown_script/test_functions
+++ b/misc/chown_script/test_functions
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/move_files/README.md b/misc/move_files/README.md
index df67f202..8bd8ef33 100644
--- a/misc/move_files/README.md
+++ b/misc/move_files/README.md
@@ -4,9 +4,9 @@ Version: 0.1
Usage: `./move_files.py [-h] changes`
-This script moves files in the internal file system of the CaosDB server. It
+This script moves files in the internal file system of the LinkAhead server. It
reads file paths form a tsv file with columns from and to. For each line it
-creates an update of a caosdb file object where the path that equals "from" is
+creates an update of a LinkAhead file object where the path that equals "from" is
changed to "to".
positional arguments:
@@ -17,8 +17,10 @@ optional arguments:
# Tests
-The tests a integration tests which require a running test database and a sufficiently configured caosdb-pylib.
+The tests a integration tests which require a running test database and a sufficiently configured
+linkahead-pylib.
-Run `pytest test_move_files.py` to insert a bunch of test files, rename and subsequently delete them.
+Run `pytest test_move_files.py` to insert a bunch of test files, rename and subsequently delete
+them.
diff --git a/misc/move_files/move_files.py b/misc/move_files/move_files.py
index 7498feef..e2eb67d7 100755
--- a/misc/move_files/move_files.py
+++ b/misc/move_files/move_files.py
@@ -2,7 +2,7 @@
# encoding: utf-8
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Henrik tom Wörden
#
@@ -23,9 +23,9 @@
#
"""
-This script moves files in the internal file system of the CaosDB server. It
+This script moves files in the internal file system of the LinkAhead server. It
reads file paths form a tsv file with columns from and to. For each line it
-creates an update of a caosdb file object where the path that equals "from" is
+creates an update of a LinkAhead file object where the path that equals "from" is
changed to "to".
Version: 0.1
@@ -39,7 +39,7 @@ from argparse import ArgumentParser
import pandas as pd
from tqdm import tqdm
-import caosdb as db
+import linkahead as db
def rename(changes, chunksize=10):
diff --git a/misc/move_files/test_move_files.py b/misc/move_files/test_move_files.py
index 2edb7650..632f0a10 100644
--- a/misc/move_files/test_move_files.py
+++ b/misc/move_files/test_move_files.py
@@ -1,6 +1,6 @@
# encoding: utf-8
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 Henrik tom Wörden
#
@@ -24,7 +24,7 @@ import unittest
import pandas as pd
-import caosdb as db
+import linkahead as db
from move_files import rename
diff --git a/misc/pam_authentication/ldap_authentication.sh b/misc/pam_authentication/ldap_authentication.sh
index e58b5caa..cf15210d 100755
--- a/misc/pam_authentication/ldap_authentication.sh
+++ b/misc/pam_authentication/ldap_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (c) 2020 IndiScale GmbH
# Copyright (c) 2020 Daniel Hornung <d.hornung@indiscale.com>
diff --git a/misc/pam_authentication/makefile b/misc/pam_authentication/makefile
index 0cd1b7d2..4b786741 100644
--- a/misc/pam_authentication/makefile
+++ b/misc/pam_authentication/makefile
@@ -1,6 +1,6 @@
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/pam_authentication.c b/misc/pam_authentication/pam_authentication.c
index 4abef5bd..d2fd5d11 100644
--- a/misc/pam_authentication/pam_authentication.c
+++ b/misc/pam_authentication/pam_authentication.c
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/pam_authentication.sh b/misc/pam_authentication/pam_authentication.sh
index 972e48f1..d5214f5e 100755
--- a/misc/pam_authentication/pam_authentication.sh
+++ b/misc/pam_authentication/pam_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/misc/pam_authentication/test_authentication.sh b/misc/pam_authentication/test_authentication.sh
index ffaedd13..baebf02e 100755
--- a/misc/pam_authentication/test_authentication.sh
+++ b/misc/pam_authentication/test_authentication.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/mvn_install_jar.sh b/mvn_install_jar.sh
index b7bdb6cf..d1ea465c 100755
--- a/mvn_install_jar.sh
+++ b/mvn_install_jar.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -25,5 +25,5 @@
# Alexander Schlemmer, 01/2013
# Installiert die jar-Datei des Servers in das lokale mvn-Repository.
-mvn install:install-file -DgroupId=ds.mpg.de -DartifactId=caosdb-server \
- -Dversion=1.0 -Dpackaging=jar -Dfile=dist/CaosDBServer.jar
+mvn install:install-file -DgroupId=ds.mpg.de -DartifactId=linkahead-server \
+ -Dversion=1.0 -Dpackaging=jar -Dfile=dist/LinkAheadServer.jar
diff --git a/pom.xml b/pom.xml
index 76c2cd85..3cc7ee6e 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,10 +1,12 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+ * Copyright (C) 2023 Indiscale GmbH <info@indiscale.com>
+ * Copyright (C) 2023 Daniel Hornung <d.hornung@indiscale.com>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
@@ -23,13 +25,13 @@
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
- <groupId>org.caosdb</groupId>
- <artifactId>caosdb-server</artifactId>
+ <groupId>org.linkahead</groupId>
+ <artifactId>linkahead-server</artifactId>
<version>0.10.1-SNAPSHOT</version>
<packaging>jar</packaging>
- <name>CaosDB Server</name>
+ <name>LinkAhead Server</name>
<scm>
- <connection>scm:git:https://gitlab.indiscale.com/caosdb/src/caosdb-server.git</connection>
+ <connection>scm:git:https://gitlab.indiscale.com/caosdb/src/linkahead-server.git</connection>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -265,7 +267,7 @@
<transformers>
<transformer implementation="com.github.edwgiz.mavenShadePlugin.log4j2CacheTransformer.PluginsCacheFileTransformer"></transformer>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
</transformer>
</transformers>
</configuration>
@@ -312,7 +314,7 @@
<include>**/*.java</include>
</includes>
<systemPropertyVariables>
- <caosdb.debug>true</caosdb.debug>
+ <linkahead.debug>true</linkahead.debug>
<log4j2.debug>true</log4j2.debug>
</systemPropertyVariables>
<reuseForks>false</reuseForks>
@@ -339,7 +341,7 @@
<revisionPropertyName>project.revision</revisionPropertyName>
<versionPropertyName>project.version</versionPropertyName>
<timestampPropertyName>build.timestamp</timestampPropertyName>
- <outputDirectory>${basedir}/target/classes/org/caosdb/server/</outputDirectory>
+ <outputDirectory>${basedir}/target/classes/org/linkahead/server/</outputDirectory>
<outputName>build.properties</outputName>
</configuration>
</plugin>
@@ -354,7 +356,7 @@
<goal>java</goal>
</goals>
<configuration>
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
<arguments>
<argument>silent</argument>
</arguments>
@@ -366,13 +368,13 @@
<goal>java</goal>
</goals>
<configuration>
- <mainClass>org.caosdb.server.CaosDBServer</mainClass>
+ <mainClass>org.linkahead.server.LinkAheadServer</mainClass>
<arguments>
<argument>silent</argument>
</arguments>
<systemProperties>
<systemProperty>
- <key>caosdb.debug</key>
+ <key>linkahead.debug</key>
<value>true</value>
</systemProperty>
</systemProperties>
@@ -426,7 +428,7 @@
<artifactId>protobuf-maven-plugin</artifactId>
<version>0.6.1</version>
<configuration>
- <protoSourceRoot>${basedir}/caosdb-proto/proto/</protoSourceRoot>
+ <protoSourceRoot>${basedir}/linkahead-proto/proto/</protoSourceRoot>
<protocArtifact>com.google.protobuf:protoc:${protobuf.version}:exe:${os.detected.classifier}</protocArtifact>
<pluginId>grpc-java</pluginId>
<pluginArtifact>io.grpc:protoc-gen-grpc-java:${grpc.version}:exe:${os.detected.classifier}</pluginArtifact>
@@ -442,5 +444,5 @@
</plugin>
</plugins>
</build>
- <url>caosdb.org</url>
+ <url>linkahead.org</url>
</project>
diff --git a/scripting/bin/administration/diagnostics.py b/scripting/bin/administration/diagnostics.py
index ccecbd58..79a227fc 100755
--- a/scripting/bin/administration/diagnostics.py
+++ b/scripting/bin/administration/diagnostics.py
@@ -2,7 +2,7 @@
# -*- coding: utf-8 -*-
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -34,7 +34,7 @@ should not be executable for non-admin users.
import sys
TEST_MODULES = [
- "caosdb",
+ "linkahead",
"numpy",
"pandas",
"validate_email"
@@ -73,8 +73,8 @@ def get_query():
return get_option("query")
-def get_caosdb_info(auth_token):
- import caosdb as db
+def get_linkahead_info(auth_token):
+ import linkahead as db
result = dict()
result["version"] = db.version.version
@@ -136,8 +136,8 @@ def main():
auth_token = get_auth_token()
diagnostics["auth_token"] = auth_token
- if diagnostics["import"]["caosdb"][0] is True:
- diagnostics["caosdb"] = get_caosdb_info(auth_token)
+ if diagnostics["import"]["linkahead"][0] is True:
+ diagnostics["linkahead"] = get_linkahead_info(auth_token)
finally:
json.dump(diagnostics, sys.stdout)
diff --git a/scripting/bin/xls_from_csv.py b/scripting/bin/xls_from_csv.py
index 73bb6b0a..df05f7e5 100755
--- a/scripting/bin/xls_from_csv.py
+++ b/scripting/bin/xls_from_csv.py
@@ -1,6 +1,6 @@
#!/usr/bin/env python3
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2019 IndiScale GmbH
#
diff --git a/src/doc/CaosDB-Query-Language.md b/src/doc/CaosDB-Query-Language.md
index 6cbe64f1..0b8cd5a2 100644
--- a/src/doc/CaosDB-Query-Language.md
+++ b/src/doc/CaosDB-Query-Language.md
@@ -1,8 +1,8 @@
-# CaosDB Query Language Examples
+# LinkAhead Query Language Examples
-See syntax specification in [CaosDB Query Language Syntax](query-syntax).
+See syntax specification in [LinkAhead Query Language Syntax](query-syntax).
-In this chapter, the CaosDB Query Language (CQL) is presented as a means of
+In this chapter, the LinkAhead Query Language (CQL) is presented as a means of
formulating search commands, commonly referred to as queries. It is highly
recommended that you experiment with the examples provided, such as those found
on https://demo.indiscale.com. An interactive tour is also available on this
@@ -55,7 +55,7 @@ with some external tool.
`SELECT` queries offer to represent the query result in a tabular form.
If you replace the `FIND` keyword of a query with `SELECT x, y, z FROM`, then
-CaosDB will return the result as tabular data.
+LinkAhead will return the result as tabular data.
For example, instead of `FIND Guitar`, try out
`SELECT name, electric FROM Guitar`
@@ -75,7 +75,7 @@ like the creation time of a Record to restrict the query result set.
We already learned, that we can provide the name of a RecordType after the `FIND`
keyword. Let's call this part of the query "entity expression". In general, we
-need to identify with the entity expression one or more entities via their name, CaosDB ID
+need to identify with the entity expression one or more entities via their name, LinkAhead ID
or a pattern.
- `FIND Guitar`
- `FIND Guit*` ('*' represents none, one or more characters)
@@ -86,7 +86,7 @@ The result set will contain Entities that are either identified by the entity ex
directly (i.e. they have the name or the given ID) or the have such an Entity as
parent.
-As you know, CaosDB distincts among different Entity roles:
+As you know, LinkAhead distincts among different Entity roles:
- Entity
- Record
- RecordType
@@ -500,7 +500,7 @@ Note: When a property `responsible` with data type `Person` exists, the above `S
## Versioning
-Since Caosdb 0.2 entities are optionally version controlled. The query language will be extended to include versioning in the future. A current minimal implementation introduces the `ANY VERSION OF` modifier which can be used to return all matching versions in the results of `COUNT`, `FIND`, and `SELECT` queries.
+Since LinkAhead 0.2 entities are optionally version controlled. The query language will be extended to include versioning in the future. A current minimal implementation introduces the `ANY VERSION OF` modifier which can be used to return all matching versions in the results of `COUNT`, `FIND`, and `SELECT` queries.
### Example
@@ -513,7 +513,7 @@ Since Caosdb 0.2 entities are optionally version controlled. The query language
## Configuration
-In CaosDB Server implementations before version 0.9.0, the `FIND ename` query
+In LinkAhead Server implementations before version 0.9.0, the `FIND ename` query
would return any entity with that name and all children, regardless of the
entity's role. Basically, `FIND ename` *was* equivalent to `FIND ENTITY ename`.
Since 0.9.0 the default behavior has changed and now `FIND ename` is equivalent
diff --git a/src/doc/Data-Model.md b/src/doc/Data-Model.md
index b471b824..2c33e7da 100644
--- a/src/doc/Data-Model.md
+++ b/src/doc/Data-Model.md
@@ -1,5 +1,5 @@
-# CaosDB Data Model
+# LinkAhead Data Model
The data structure is built from some basic building blocks which are
shown in the following picture:
@@ -9,7 +9,7 @@ shown in the following picture:
It has a base object called **Entity**. Entities are either **Record
Types**, **Records**, or **Abstract Properties** (and Record like
objects for files). What *kind of data* is stored is defined by the
-Record Types. Actual data is then stored in CaosDB as Records which
+Record Types. Actual data is then stored in LinkAhead as Records which
are of some Record Type. Those Records can have Properties that
contain information about the Record. The following is a more detailed
explanation (also see this
diff --git a/src/doc/FAQ.rst b/src/doc/FAQ.rst
index 54bfb296..2caabbad 100644
--- a/src/doc/FAQ.rst
+++ b/src/doc/FAQ.rst
@@ -3,7 +3,7 @@ FAQs
====
These FAQs (frequently asked questions) can be extended, if *you* help us. Please `submit an issue
-<https://gitlab.com/caosdb/caosdb-server/issues/new>`__ if you have a question that should be
+<https://gitlab.com/linkahead/linkahead-server/issues/new>`__ if you have a question that should be
answered here.
.. contents:: Select your question:
@@ -18,12 +18,12 @@ with the ``add_property`` method and the ``LIST`` function.
.. code:: python
# with constructor
- p = caosdb.Property(name="ListOfDoubles", datatype=caosdb.LIST(caosdb.DOUBLE))
+ p = linkahead.Property(name="ListOfDoubles", datatype=linkahead.LIST(linkahead.DOUBLE))
# with add_property method
- my_entity.add_property(name="ListOfIntegers", datatype=caosdb.LIST(caosdb.INTEGER))
- my_entity.add_property(name="ListOfThings", datatype=caosdb.LIST("Thing"))
- my_entity.add_property(name="ListOfThings", datatype=caosdb.LIST(caosdb.RecordType('Thing'))
+ my_entity.add_property(name="ListOfIntegers", datatype=linkahead.LIST(linkahead.INTEGER))
+ my_entity.add_property(name="ListOfThings", datatype=linkahead.LIST("Thing"))
+ my_entity.add_property(name="ListOfThings", datatype=linkahead.LIST(linkahead.RecordType('Thing'))
Which data types are there?
===========================
@@ -49,7 +49,7 @@ And furthermore,…
.. code:: python
- p = caosdb.Property(name="Conductor", datatype="Person")
+ p = linkahead.Property(name="Conductor", datatype="Person")
will only accept those Entities as value which have a “Person”
RecordType as a direct or indirect parent.
diff --git a/src/doc/Makefile b/src/doc/Makefile
index 1f0af46e..73f5a4cf 100644
--- a/src/doc/Makefile
+++ b/src/doc/Makefile
@@ -1,4 +1,4 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2020 Daniel Hornung <d.hornung@indiscale.com>
@@ -47,7 +47,7 @@ doc-help:
# sphinx-build -M html . ../../build/doc
apidoc:
- $(SPHINXAPIDOC) -o _apidoc --update --title="CaosDB Server" ../main/
+ $(SPHINXAPIDOC) -o _apidoc --update --title="LinkAhead Server" ../main/
apixml:
$(MAKE) -C $(APIXMLDIR) doc
diff --git a/src/doc/administration/configuration.rst b/src/doc/administration/configuration.rst
index c91ac16b..778c9374 100644
--- a/src/doc/administration/configuration.rst
+++ b/src/doc/administration/configuration.rst
@@ -16,7 +16,7 @@ with a hash (`#`). Key-value lines must have the format `KEY_NAME=VALUE` or
The server default configuration is located at `./conf/core/server.conf`.
Upstream defaults are stored here. The possible configuration options are
documented inside the
-`default file <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/server.conf>`__.
+`default file <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/server.conf>`__.
User specific configuration should be in `./conf/ext/` and override settings
in `./conf/core/`.
@@ -27,7 +27,7 @@ The default configuration can be overriden by
2. any file in ./conf/ext/server.conf.d/ in (approximately?) alphabetical order
- 3. environment variables with the prefix `CAOSDB_CONFIG_`
+ 3. environment variables with the prefix `LINKAHEAD_CONFIG_`
in this order.
@@ -39,7 +39,7 @@ Further settings are to be set in files which are by default stored in `./conf/c
``global_entity_permissions.xml``
:doc:`Permissions<../permissions>` which are automatically set, based on user roles. See the
`default file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/global_entity_permissions.xml>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/global_entity_permissions.xml>`__.
``usersources.ini``
This file defines possible sources which are checked when a user tries to authenticate. Each
@@ -47,23 +47,23 @@ Further settings are to be set in files which are by default stored in `./conf/c
source. At the moment the best place to look for this specific documentation is at the API
documentation of :java:type:`UserSource` and its implementing classes. The provided `template
file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/usersources.ini.template>`__
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/usersources.ini.template>`__
also has some information. The general concept about authentication realms is described in
:java:type:`UserSources`.
``authtoken.yaml``
- Configuration for dispensed authentication tokens, which can be used to authenticate to CaosDB
+ Configuration for dispensed authentication tokens, which can be used to authenticate to LinkAhead
without the need of a user/password combination. One-time Authentication Tokens can be configure
to be issued for special purposes (e.g. a call of a server-side script or initial setup after the server start)
or to be written to a file on a regular basis. An example of a configuration is located at `./conf/core/authtoken.example.yaml`.
There is more documentation inside the `template file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
``cache.ccf``
Configuration for the Java Caching System (JCS) which can be used by the server. More
documentation is `upstream
<http://commons.apache.org/proper/commons-jcs/getting_started/intro.html>`_ and inside `the file
- <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/cache.ccf>`_.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/blob/dev/conf/core/cache.ccf>`_.
``log4j2-default.properties``, ``log4j2-debug.properties``
Configuration for logging, following the standard described by the `log4j library
@@ -82,4 +82,4 @@ Remark:
In the debug case, the server provides the ``_server_properties`` resource which allows the ``GET``
and ``POST`` methods to access the server's properties. The Python client library conveniently
-wraps this in the :any:`caosdb-pylib:caosdb.common.administration` module.
+wraps this in the :any:`linkahead-pylib:linkahead.common.administration` module.
diff --git a/src/doc/administration/curl-access.rst b/src/doc/administration/curl-access.rst
index 79b10a71..88d473a8 100644
--- a/src/doc/administration/curl-access.rst
+++ b/src/doc/administration/curl-access.rst
@@ -1,15 +1,15 @@
-Curl Access for CaosDB
+Curl Access for LinkAhead
======================
-As the API that is used to communicate with the CaosDB server is XML
+As the API that is used to communicate with the LinkAhead server is XML
over HTTP also simple HTTP clients, such as
`cURL <https://curl.haxx.se/>`__ can be used. cURL is an old and
established command line program for transferring files over networks
that implements various protocols including HTTP/HTTPS. It is installed
by default on many Linux distributions and can therefore be very useful
-for testing and debugging of CaosDB.
+for testing and debugging of LinkAhead.
-This small manual also gives some practical insights about the CaosDB
+This small manual also gives some practical insights about the LinkAhead
protocol itself.
Doing a simple retrieve
@@ -24,7 +24,7 @@ Let’s do a query on our demo instance:
curl "https://demo.indiscale.com/Entity/?query=FIND%20Experiment"
By default cURL sends an HTTP GET request which is needed for doing
-queries for CaosDB. CaosDB requires sending them to ``/Entity``. The
+queries for LinkAhead. LinkAhead requires sending them to ``/Entity``. The
query itself is specified after the HTTP query string ``?query=``.
``%20`` is specific to URL encoding and corresponds to a space (see
https://en.wikipedia.org/wiki/Percent-encoding for details). So the
@@ -36,7 +36,7 @@ The response should look like:
.. code:: xml
<?xml version="1.0" encoding="UTF-8"?>
- <?xml-stylesheet type="text/xsl" href="https://demo.indiscale.com/webinterface/webcaosdb.xsl" ?>
+ <?xml-stylesheet type="text/xsl" href="https://demo.indiscale.com/webinterface/weblinkahead.xsl" ?>
<Response srid="b56e3d1a442460c46dde924a54e8afba" timestamp="1561453363382" baseuri="https://demo.indiscale.com" count="3">
<UserInfo>
<Roles>
@@ -101,7 +101,7 @@ returned. Furthermore the response contains some additional information:
timestamp <https://en.wikipedia.org/wiki/Unix_time>`__ for this
request.
- ``baseuri="https://demo.indiscale.com"`` The base URI of the
- instance of CaosDB that performed the request.
+ instance of LinkAhead that performed the request.
- ``count="3"`` The number of results (2 ``RecordTypes`` and 1
``Record``)
@@ -155,7 +155,7 @@ Logging in
----------
You might have asked yourself, what we need the cookie for. The simple
-answer is: authentication. For many operations done on the CaosDB server
+answer is: authentication. For many operations done on the LinkAhead server
we have to log in first. The demo instance is configured to allow for
anonymous read access by default. But depending on the instance you are
accessing, even this might be disallowed.
@@ -192,7 +192,7 @@ password in the variable ``$PW``:
Custom Certificates
-------------------
-If you are running your own CaosDB instance it might be necessary to use
+If you are running your own LinkAhead instance it might be necessary to use
a custom SSL certificate.
You can specify this using the option ``--cacert``, e.g.:
@@ -238,7 +238,7 @@ The attributes have the following meaning: - ``upload=testfile.bla`` The
filename given here is actually no filename, but an identifier to find
the multipart data chunk that contains the file. I called it
``testfile.bla`` for simplicity here. -
-``destination="/test/testfile.bla"`` The destination path on the CaosDB
+``destination="/test/testfile.bla"`` The destination path on the LinkAhead
server file system.
Before looking at the other attributes let’s have a look at the file
diff --git a/src/doc/administration/maintenance.rst b/src/doc/administration/maintenance.rst
index 5b9faeb1..245a8b1b 100644
--- a/src/doc/administration/maintenance.rst
+++ b/src/doc/administration/maintenance.rst
@@ -1,42 +1,42 @@
-Maintenance of the CaosDB Server
+Maintenance of the LinkAhead Server
================================
Creating a Backup
-----------------
-In order to create a full backup of CaosDB, the state of the SQL-Backend (MySQL, MariaDB)
-has to be saved and the internal file system of CaosDB (symbolic links to
+In order to create a full backup of LinkAhead, the state of the SQL-Backend (MySQL, MariaDB)
+has to be saved and the internal file system of LinkAhead (symbolic links to
file systems that are mounted and uploaded files) has to be saved.
-You find the documentation on how to backup the SQL-Backend :any:`caosdb-mysqlbackend:Maintenance`
+You find the documentation on how to backup the SQL-Backend :any:`linkahead-mysqlbackend:Maintenance`
In order to save the file backend we recommend to tar the file system. However,
you could use other backup methods that allow to restore the file system.
-The CaosDB internal file system is located at the path defined by the
+The LinkAhead internal file system is located at the path defined by the
``FILE_SYSTEM_ROOT`` configuration variable (see :any:`configuration`).
The command could look like::
- tar czvf /path/to/new/backup /path/to/caosdb/filesystem.tar.gz
+ tar czvf /path/to/new/backup /path/to/linkahead/filesystem.tar.gz
-You can also save the content of CaosDB using XML. This is **not recommended** since it produces
+You can also save the content of LinkAhead using XML. This is **not recommended** since it produces
less reproducible results than a plain SQL backup. However there may be cases in which an XML backup
-is necessary, e.g., when transferring entities between two different CaosDB instances.
+is necessary, e.g., when transferring entities between two different LinkAhead instances.
Collect the entities that you want to export in a
-:any:`Container<caosdb-pylib:caosdb.common.models.Container>`, named ``cont`` here. Then you can
+:any:`Container<linkahead-pylib:linkahead.common.models.Container>`, named ``cont`` here. Then you can
export the XML with::
- from caosadvancedtools.export_related import invert_ids
+ from linkaheadadvancedtools.export_related import invert_ids
from lxml import etree
invert_ids(cont)
xml = etree.tounicode(cont.to_xml(
local_serialization=True), pretty_print=True)
- with open("caosdb_data.xml"), "w") as fi:
+ with open("linkahead_data.xml"), "w") as fi:
fi.write(xml)
@@ -44,21 +44,21 @@ Restoring a Backup
------------------
.. warning::
- CaosDB should be offline before restoring data.
+ LinkAhead should be offline before restoring data.
If you want to restore the internal file system, simply replace it. E.g. if your
backup is a tarball::
- tar xvf /path/to/caosroot.tar.gz
+ tar xvf /path/to/linkaheadroot.tar.gz
-You find the documentation on how to restore the data in the SQL-Backend :any:`caosdb-mysqlbackend:Maintenance`
+You find the documentation on how to restore the data in the SQL-Backend :any:`linkahead-mysqlbackend:Maintenance`
If you want to restore the entities exported to XML, you can do::
cont = db.Container()
- with open("caosdb_data.xml") as fi:
+ with open("linkahead_data.xml") as fi:
cont = cont.from_xml(fi.read())
cont.insert()
@@ -68,6 +68,6 @@ User Management
The configuration of authentication mechanisms is done via the ``usersources.ini`` file (see
:any:`configuration`).
-We recommend the Python tools (:any:`caosdb-pylib:administration`) for further administrative tasks
+We recommend the Python tools (:any:`linkahead-pylib:administration`) for further administrative tasks
(e.g. setting user passwords).
diff --git a/src/doc/administration/server_side_scripting.rst b/src/doc/administration/server_side_scripting.rst
index 6dc08999..f23e2ba8 100644
--- a/src/doc/administration/server_side_scripting.rst
+++ b/src/doc/administration/server_side_scripting.rst
@@ -4,7 +4,7 @@ Server-Side Scripting
Introduction
------------
-Small computation task, like some visualization, might be easily implemented in Python or some other language, but cumbersome to integrate into the server. Furthermore, the CaosDB server should stay a general tool without burden from specific projects. Also, one might want to trigger some standardized processing task from the web interface for convenience. For these situations the "server side scripting" is intended.
+Small computation task, like some visualization, might be easily implemented in Python or some other language, but cumbersome to integrate into the server. Furthermore, the LinkAhead server should stay a general tool without burden from specific projects. Also, one might want to trigger some standardized processing task from the web interface for convenience. For these situations the "server side scripting" is intended.
Concepts
------------
@@ -49,8 +49,8 @@ script invocation from a skeleton directory, located in the server directory, in
- `readme.md` :: A small text file describing the purpose of the directory.
-Users of CaosDB are invited to populate the directory with whatever their
-scripts need (for example a `.pycaosdb.ini` file).
+Users of LinkAhead are invited to populate the directory with whatever their
+scripts need (for example a `.pylinkahead.ini` file).
Invocation
------------
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
index 4403c958..0eef6b6a 100644
--- a/src/doc/concepts.rst
+++ b/src/doc/concepts.rst
@@ -1,5 +1,5 @@
-Basic concepts of the CaosDB server
+Basic concepts of the LinkAhead server
===================================
.. toctree::
@@ -10,6 +10,6 @@ Basic concepts of the CaosDB server
permissions
roles
-The CaosDB server provides the HTTP API resources to users and client libraries. It uses a plain
+The LinkAhead server provides the HTTP API resources to users and client libraries. It uses a plain
MariaDB/MySQL database as backend for data storage, raw files are stored separately on the file
system.
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 6b9b1f56..cd202080 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -14,14 +14,14 @@
#
# import os
# import sys
-# sys.path.insert(0, os.path.abspath('../caosdb'))
+# sys.path.insert(0, os.path.abspath('../linkahead'))
import sphinx_rtd_theme
from os.path import dirname, abspath
# -- Project information -----------------------------------------------------
-project = 'caosdb-server'
+project = 'linkahead-server'
copyright = '2023, IndiScale GmbH'
author = 'Daniel Hornung, Timm Fitschen'
@@ -69,7 +69,7 @@ master_doc = 'index'
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
@@ -118,7 +118,7 @@ html_css_files = [
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
-htmlhelp_basename = 'caosdb-serverdoc'
+htmlhelp_basename = 'linkahead-serverdoc'
# -- Options for LaTeX output ------------------------------------------------
@@ -145,7 +145,7 @@ latex_elements = {
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
- (master_doc, 'caosdb-server.tex', 'caosdb-server Documentation',
+ (master_doc, 'linkahead-server.tex', 'linkahead-server Documentation',
'IndiScale GmbH', 'manual'),
]
@@ -155,7 +155,7 @@ latex_documents = [
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- (master_doc, 'caosdb-server', 'caosdb-server Documentation',
+ (master_doc, 'linkahead-server', 'linkahead-server Documentation',
[author], 1)
]
@@ -166,8 +166,8 @@ man_pages = [
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- (master_doc, 'caosdb-server', 'caosdb-server Documentation',
- author, 'caosdb-server', 'One line description of project.',
+ (master_doc, 'linkahead-server', 'linkahead-server Documentation',
+ author, 'linkahead-server', 'One line description of project.',
'Miscellaneous'),
]
@@ -209,8 +209,8 @@ javadoc_url_map = {
# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
intersphinx_mapping = {
"python": ("https://docs.python.org/", None),
- "caosdb-pylib": ("https://docs.indiscale.com/caosdb-pylib/", None),
- "caosdb-mysqlbackend": ("https://docs.indiscale.com/caosdb-mysqlbackend/", None),
+ "linkahead-pylib": ("https://docs.linkahead.org/linkahead-pylib/", None),
+ "linkahead-mysqlbackend": ("https://docs.linkahead.org/linkahead-mysqlbackend/", None),
}
@@ -228,4 +228,4 @@ autosectionlabel_prefix_document = True
# -- Options for sphinx_a4doc ------------------------------------------------
-a4_base_path = abspath(dirname(__file__) + '/../main/java/org/caosdb/server/query')
+a4_base_path = abspath(dirname(__file__) + '/../main/java/org/linkahead/server/query')
diff --git a/src/doc/development/api/xml/Makefile b/src/doc/development/api/xml/Makefile
index b2314adb..1eaf731e 100644
--- a/src/doc/development/api/xml/Makefile
+++ b/src/doc/development/api/xml/Makefile
@@ -1,4 +1,4 @@
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2021 Daniel Hornung <d.hornung@indiscale.com>
@@ -25,11 +25,11 @@ BUILDDIR ?= ../../../_static/api/xml/
doc:
mkdir -p $(BUILDDIR)
[ -e openapi-generator-cli.jar ] || wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.2.0/openapi-generator-cli-5.2.0.jar -O openapi-generator-cli.jar
- java -jar openapi-generator-cli.jar generate -i caosdb_openapi.yaml --config openapi_config.json -g html2 -o $(BUILDDIR)
+ java -jar openapi-generator-cli.jar generate -i linkahead_openapi.yaml --config openapi_config.json -g html2 -o $(BUILDDIR)
## Not needed (the same code anyway?)
# [ -e swagger-codegen-cli.jar ] || wget https://repo1.maven.org/maven2/io/swagger/codegen/v3/swagger-codegen-cli/3.0.27/swagger-codegen-cli-3.0.27.jar -O swagger-codegen-cli.jar
-# java -jar swagger-codegen-cli.jar generate -i caosdb_openapi.yaml -l html2 -o $(BUILDDIR)
+# java -jar swagger-codegen-cli.jar generate -i linkahead_openapi.yaml -l html2 -o $(BUILDDIR)
diff --git a/src/doc/development/api/xml/caosdb_openapi.yaml b/src/doc/development/api/xml/caosdb_openapi.yaml
index b2e0b744..f60a0a72 100644
--- a/src/doc/development/api/xml/caosdb_openapi.yaml
+++ b/src/doc/development/api/xml/caosdb_openapi.yaml
@@ -1,7 +1,7 @@
openapi: "3.0.3"
info:
- title: CaosDB XML REST API
- description: The XML API of CaosDB, see also https://docs.indiscale.com/caosdb-server
+ title: LinkAhead XML REST API
+ description: The XML API of LinkAhead, see also https://docs.linkahead.org/linkahead-server
version: 0.0-poc.1
servers:
- url: https://demo.indiscale.com
@@ -83,7 +83,7 @@ paths:
get:
operationId: executeQuery
summary: Return the entities matching the given query
- description: Use arbitrary CaosDB queries to retrieve all matching entities
+ description: Use arbitrary LinkAhead queries to retrieve all matching entities
parameters:
- name: query
in: query
@@ -400,7 +400,7 @@ components:
properties:
datatype:
type: string
- description: The CaosDB datatype of this property
+ description: The LinkAhead datatype of this property
example: BOOLEAN
xml:
attribute: true
diff --git a/src/doc/development/api/xml/openapi_config.json b/src/doc/development/api/xml/openapi_config.json
index f27abea7..3f861b15 100644
--- a/src/doc/development/api/xml/openapi_config.json
+++ b/src/doc/development/api/xml/openapi_config.json
@@ -1,8 +1,8 @@
{
- "appName": "CaosDB",
- "appDescription": "CaosDB, the open data management toolkit",
- "infoUrl": "https://docs.indiscale.com/caosdb-server",
+ "appName": "LinkAhead",
+ "appDescription": "LinkAhead, the open data management toolkit",
+ "infoUrl": "https://docs.linkahead.org/linkahead-server",
"infoEmail": "info@indiscale.com",
"licenseInfo": "License: AGPLv3",
- "licenseUrl": "https://gitlab.com/caosdb/caosdb-server/-/blob/dev/LICENSE.md"
+ "licenseUrl": "https://gitlab.com/linkahead/linkahead-server/-/blob/dev/LICENSE.md"
}
diff --git a/src/doc/development/benchmarking.rst b/src/doc/development/benchmarking.rst
index 60d36d12..577bb522 100644
--- a/src/doc/development/benchmarking.rst
+++ b/src/doc/development/benchmarking.rst
@@ -1,7 +1,7 @@
-Benchmarking CaosDB
+Benchmarking LinkAhead
===================
-Benchmarking CaosDB may encompass several distinct areas: How much time
+Benchmarking LinkAhead may encompass several distinct areas: How much time
is spent in the server’s Java code, how much time is spent inside the
SQL backend, are the same costly methods called more than once? This
documentation tries to answer some questions connected with these
@@ -32,8 +32,8 @@ Tools for the benchmarking
For averaging over many runs of comparable requests and for putting the
database into a representative state, Python scripts are used. The
-scripts can be found in the ``caosdb-dev-tools`` repository, located at
-https://gitlab.indiscale.com/caosdb/src/caosdb-dev-tools in the folder
+scripts can be found in the ``linkahead-dev-tools`` repository, located at
+https://gitlab.indiscale.com/caosdb/src/linkahead-dev-tools in the folder
``benchmarking``:
Python Script ``fill_database.py``
@@ -47,7 +47,7 @@ The script inserts predefined amounts of randomized Entities into the
database, RecordTypes, Properties and Records. Each Record has a random
(but with defined average) number of Properties, some of which may be
references to other Records which have been inserted before. Actual
-insertion of the Entities into CaosDB is done in chunks of a defined
+insertion of the Entities into LinkAhead is done in chunks of a defined
size.
Users can tell the script to store times needed for the insertion of
@@ -70,7 +70,7 @@ An sql file is automatically executed which enables the correct
mariadb needs to be enabled. Add ``performance_schema=ON`` to the
configuration file of mariadb as it needs to be enabled on start up.
This script expects the MariaDB server to be accessible on 127.0.0.1
-with the default caosdb user and password (caosdb;random1234).
+with the default linkahead user and password (caosdb; random1234).
You might consider to increase
``performance_schema_events_transactions_history_long_size``.
@@ -194,7 +194,7 @@ following for the mariadb service:
networks:
# available on port 3306, host name 'sqldb'
- - caosnet
+ - linkaheadnet
ports:
- 3306:3306
@@ -207,7 +207,7 @@ Manual Java-side benchmarking
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Benchmarking can be done using the ``TransactionBenchmark`` class (in
-package ``org.caosdb.server.database.misc``).
+package ``org.linkahead.server.database.misc``).
- Single timings can be added to instances of that class via the
``addBenchmark(object, time)`` method. Multiple benchmarks for the
@@ -288,7 +288,7 @@ In the sampler settings, you may want to add these expressions to the
blocked packages: ``org.restlet.**, com.mysql.**``. Branches on the call
tree which are entirely inside the blacklist, will become leaves.
Alternatively, specify a whitelist, for example with
-``org.caosdb.server.database.backend.implementation.**``, if you only
+``org.linkahead.server.database.backend.implementation.**``, if you only
want to see the time spent for certain MySQL calls.
How to set up a representative database
@@ -318,7 +318,7 @@ requests to the server are started.
When doing performance tests which are used for detailed analysis, it is
important that
-1. CaosDB is in a reproducible state, which should be documented
+1. LinkAhead is in a reproducible state, which should be documented
2. all measurements are repeated several times to account for inevitable
variance in access (for example file system caching, network
variablity etc.)
diff --git a/src/doc/development/devel.rst b/src/doc/development/devel.rst
index cf0ba37e..8c552a31 100644
--- a/src/doc/development/devel.rst
+++ b/src/doc/development/devel.rst
@@ -1,5 +1,5 @@
-Developing CaosDB
-=================
+Developing LinkAhead
+====================
.. toctree::
:glob:
@@ -8,20 +8,20 @@ Developing CaosDB
Structure of the Java code <structure>
Testing the server code <testing>
Logging server output <logging>
- Benchmarking CaosDB <benchmarking>
+ Benchmarking LinkAhead <benchmarking>
-CaosDB is an Open-Source project, so anyone may modify the source as they like. These pages aim to
-provide some help for all CaosDB developers.
+LinkAhead is an Open-Source project, so anyone may modify the source as they like. These pages aim
+to provide some help for all LinkAhead developers.
-More generally, these are the most common ways to contribute to CaosDB:
+More generally, these are the most common ways to contribute to LinkAhead:
- You found a bug, have a question, or want to request a feature? Please `create an issue
- <https://gitlab.com/caosdb/caosdb-server/-/issues>`_.
+ <https://gitlab.com/linkahead/linkahead-server/-/issues>`_.
- You want to contribute code? Please fork the repository and create a merge request in GitLab and
choose this repository as target. Make sure to select "Allow commits from members who can merge
the target branch" under Contribution when creating the merge request. This allows our team to
work with you on your request.
-- If you have a suggestion for this `documentation <https://docs.indiscale.com/caosdb-server/>`_,
+- If you have a suggestion for this `documentation <https://docs.linkahead.org/linkahead-server/>`_,
the preferred way is also a merge request as describe above (the documentation resides in
``src/doc``). However, you can also create an issue for it.
-- You can also contact the developers at *info (AT) caosdb.de*.
+- You can also contact the developers at *info (AT) linkahead.org*.
diff --git a/src/doc/development/structure.rst b/src/doc/development/structure.rst
index 3848e983..8c2d0334 100644
--- a/src/doc/development/structure.rst
+++ b/src/doc/development/structure.rst
@@ -1,7 +1,7 @@
-CaosDB's Internal Structure
+LinkAhead's Internal Structure
===========================
-The CaosDB server
+The LinkAhead server
- builds upon the `Restlet <https://restlet.talend.com/>`_ framework to provide a REST interface to
the network. See the :ref:`HTTP Resources` section for more information.
@@ -16,28 +16,28 @@ The CaosDB server
HTTP Resources
--------------
-HTTP resources are implemented in the :java:ref:`resource<org.caosdb.server.resource>` package, in
-classes inheriting from :java:ref:`AbstractCaosDBServerResource` (which inherits Restlet's
-:java:ref:`Resource<org.restlet.resource.Resource>` class). The main :java:ref:`CaosDBServer` class
+HTTP resources are implemented in the :java:ref:`resource<org.linkahead.server.resource>` package, in
+classes inheriting from :java:ref:`AbstractLinkAheadServerResource` (which inherits Restlet's
+:java:ref:`Resource<org.restlet.resource.Resource>` class). The main :java:ref:`LinkAheadServer` class
defines which HTTP resource (for example ``/Entity/{specifier}``) will be handled by which class
(:java:ref:`EntityResource` in this case).
Implementing classes need to overwrite for example the ``httpGetInChildClass()`` method (or methods
corresponding to other HTTP request methods such as POST, PUT, ...). Typically, they might call the
-``execute()`` method of a :java:ref:`Transaction<org.caosdb.server.transaction.Transaction>` object.
+``execute()`` method of a :java:ref:`Transaction<org.linkahead.server.transaction.Transaction>` object.
Transactions are explained in detail in the :ref:`Transactions and Schedules<transactions>` section.
.. uml::
@startuml
- abstract AbstractCaosDBServerResource {
+ abstract AbstractLinkAheadServerResource {
{abstract} httpGetInChildClass()
{abstract} httpPostInChildClass()
{abstract} ...InChildClass()
}
abstract RetrieveEntityResource
class EntityResource
- AbstractCaosDBServerResource <|-- RetrieveEntityResource
+ AbstractLinkAheadServerResource <|-- RetrieveEntityResource
RetrieveEntityResource <|-- EntityResource
@enduml
@@ -46,7 +46,7 @@ Transactions are explained in detail in the :ref:`Transactions and Schedules<tra
MySQL Backend
-------------
-The MySQL backend in CaosDB may be substituted by other backends, but at the time of writing this
+The MySQL backend in LinkAhead may be substituted by other backends, but at the time of writing this
documentation, only MySQL (MariaDB is used for testing) is implemented. There are the following
main packages which handle the backend:
@@ -108,7 +108,7 @@ For example, the structure when getting an Entity ID by name looks like this:
Transactions and Schedules
--------------------------
-In CaosDB, several client requests may be handled concurrently. This poses no problem as long as
+In LinkAhead, several client requests may be handled concurrently. This poses no problem as long as
only read-only requests are processed, but writing transactions need to block other requests.
Therefore all transactions (between their first and last access) block write transactions other than
themselves from writing to the backend, while read transactions may happen at any time, except when
@@ -116,13 +116,13 @@ a write transaction actually writes to the backend.
.. note::
- There is a fine distinction between write transactions on the CaosDB server and actually writing
+ There is a fine distinction between write transactions on the LinkAhead server and actually writing
to the backend, since even transactions which need only very short write access to the backend may
require extensive read access before, for example to check for permissions or to check if the
intended write action makes sense (linked entities must exist, they may need to be of the correct
RecordType, etc.).
-The request handling in CaosDB is organized in the following way:
+The request handling in LinkAhead is organized in the following way:
- HTTP resources usually create a :java:ref:`Transaction` object and call its
:java:ref:`Transaction.execute()` method. Entities are passed to and from the transaction via
diff --git a/src/doc/development/testing.rst b/src/doc/development/testing.rst
index 2587695d..aa8cfd41 100644
--- a/src/doc/development/testing.rst
+++ b/src/doc/development/testing.rst
@@ -8,7 +8,7 @@ and incorrect input.
Writing tests
~~~~~~~~~~~~~
-Tests go into ``src/test/java/caosdb/``, the files there can serve as examples for
+Tests go into ``src/test/java/linkahead/``, the files there can serve as examples for
writing tests.
Running tests with Maven
diff --git a/src/doc/entity-permission-table.rst b/src/doc/entity-permission-table.rst
index 1ff75f21..efcb1c4f 100644
--- a/src/doc/entity-permission-table.rst
+++ b/src/doc/entity-permission-table.rst
@@ -3,7 +3,7 @@
Entity Permissions
==================
-Permission to the following actions can be granted or denied in CaosDB:
+Permission to the following actions can be granted or denied in LinkAhead:
.. list-table:: Entity permission actions
:header-rows: 1
diff --git a/src/doc/index.rst b/src/doc/index.rst
index e34afd38..ed19ceb2 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -1,6 +1,6 @@
-Welcome to caosdb-server's documentation!
-=========================================
+Welcome to the documentation of the LinkAhead server!
+=====================================================
.. toctree::
:maxdepth: 2
@@ -12,7 +12,7 @@ Welcome to caosdb-server's documentation!
Concepts <concepts>
tutorials
FAQ
- Query Language <CaosDB-Query-Language>
+ Query Language <LinkAhead-Query-Language>
administration
Development <development/devel>
Dependencies <DEPENDENCIES>
@@ -21,11 +21,14 @@ Welcome to caosdb-server's documentation!
Glossary
Server Internals<_apidoc/packages>
-Welcome to the CaosDB, the flexible semantic data management toolkit!
+Welcome to the LinkAhead, the flexible semantic data management toolkit!
+
+.. note::
+ LinkAhead was formerly known as CaosDB, the name was changed in 2023.
This documentation helps you to :doc:`get started<README_SETUP>`,
explains the most important :doc:`concepts<concepts>` and has
-information if you want to :doc:`develop<development/devel>` CaosDB
+information if you want to :doc:`develop<development/devel>` LinkAhead
yourself.
diff --git a/src/doc/permissions.rst b/src/doc/permissions.rst
index 3d9c5ed7..109b26e8 100644
--- a/src/doc/permissions.rst
+++ b/src/doc/permissions.rst
@@ -1,7 +1,7 @@
Permissions
===========
-CaosDB has a fine grained role-based permission system. Each interaction with
+LinkAhead has a fine grained role-based permission system. Each interaction with
the server is governed by the current role(s) of the user, by default this is
the ``anonymous`` role. The permissions for an action which involves one or more
objects are set either manually or via default permissions which can be
@@ -126,15 +126,15 @@ How to set permissions
There are multiple ways to set role and entity permissions. The most
common and best tested way currently is to set global default *entity* permissions
in the ``global_entity_permissions.xml`` config file, and role-based *role*
-permissions with the ``caosdb_admin.py`` `utility script
-<https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/src/caosdb/utils/caosdb_admin.py>`__
-of CaosDB's Python library which is also used to `manage users and
-roles <https://docs.indiscale.com/caosdb-pylib/administration.html>`__. Below you
+permissions with the ``linkahead_admin.py`` `utility script
+<https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/src/linkahead/utils/linkahead_admin.py>`__
+of LinkAhead's Python library which is also used to `manage users and
+roles <https://docs.linkahead.org/linkahead-pylib/administration.html>`__. Below you
find a more detailed description of the possible ways of setting permissions.
- **Config file:** Some default permissions are typically set in the
``global_entity_permissions.xml`` file, see also the `default file
- <https://gitlab.com/caosdb/caosdb-server/-/blob/main/conf/core/global_entity_permissions.xml>`__. Here,
+ <https://gitlab.com/linkahead/linkahead-server/-/blob/main/conf/core/global_entity_permissions.xml>`__. Here,
you can set the default permissions that every entity on the server has. The
global default permissions can **only** be set in this file; all other ways
below can only change the permissions of individual entities. Note that you
@@ -147,22 +147,22 @@ find a more detailed description of the possible ways of setting permissions.
set with one of the other ways explained below.
- **API:** Both REST and GRPC API allow to set the permissions. This hasn't been
documented properly yet, but for the GRPC API, `the specification
- <https://gitlab.com/caosdb/caosdb-proto/-/blob/main/proto/caosdb/acm/v1alpha1/main.proto>`__
+ <https://gitlab.com/linkahead/linkahead-proto/-/blob/main/proto/linkahead/acm/v1alpha1/main.proto>`__
may give some insight.
- **The Python library:** The permissions can also conveniently be set via the
Python library. Currently the best documentation is inside various files
which use the permission API:
- The `example file
- <https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/examples/set_permissions.py>`__
- - The ``caosdb_admin.py`` `utility script
- <https://gitlab.com/caosdb/caosdb-pylib/-/blob/main/src/caosdb/utils/caosdb_admin.py>`__
- - There is a comprehensive `example <https://docs.indiscale.com/caosdb-pylib/gallery/curator-permissions.html>`_
- in PyCaosDB's gode gallery.
+ <https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/examples/set_permissions.py>`__
+ - The ``linkahead_admin.py`` `utility script
+ <https://gitlab.com/linkahead/linkahead-pylib/-/blob/main/src/linkahead/utils/linkahead_admin.py>`__
+ - There is a comprehensive `example <https://docs.linkahead.org/linkahead-pylib/gallery/curator-permissions.html>`_
+ in PyLinkAhead's gode gallery.
- The `integration tests
- <https://gitlab.com/caosdb/caosdb-pyinttest/-/blob/main/tests/test_permissions.py>`__
+ <https://gitlab.com/linkahead/linkahead-pyinttest/-/blob/main/tests/test_permissions.py>`__
also cover quite a bit of the permission API.
- **WebUI:** This is currently work in progress. A WebUI ACM module which uses the
GRPC interface is under `active development
- <https://gitlab.indiscale.com/caosdb/src/caosdb-webui2>`__.
+ <https://gitlab.indiscale.com/caosdb/src/linkahead-webui2>`__.
diff --git a/src/doc/query-syntax.rst b/src/doc/query-syntax.rst
index 00df440f..3e15427c 100644
--- a/src/doc/query-syntax.rst
+++ b/src/doc/query-syntax.rst
@@ -1,14 +1,14 @@
-CaosDB Query Language Syntax
+LinkAhead Query Language Syntax
============================
-This is the documentation of the CaosDB Query Language Syntax. The
+This is the documentation of the LinkAhead Query Language Syntax. The
authoritative specification of the syntax is the ANTLR4 grammar you can find in
the source code:
-`CQLParser.g4 <https://gitlab.com/caosdb/caosdb-server/-/blob/main/src/main/java/org/caosdb/server/query/CQLParser.g4>`__
+`CQLParser.g4 <https://gitlab.com/linkahead/linkahead-server/-/blob/main/src/main/java/org/linkahead/server/query/CQLParser.g4>`__
and
-`CQLLexer.g4 <https://https://gitlab.com/caosdb/caosdb-server/-/blob/main/src/main/java/org/caosdb/server/query/CQLLexer.g4>`__
+`CQLLexer.g4 <https://https://gitlab.com/linkahead/linkahead-server/-/blob/main/src/main/java/org/linkahead/server/query/CQLLexer.g4>`__
-See examples in :doc:`Query Language<CaosDB-Query-Language>`.
+See examples in :doc:`Query Language<LinkAhead-Query-Language>`.
.. a4:autogrammar:: CQLParser.g4
diff --git a/src/doc/role-permission-table.rst b/src/doc/role-permission-table.rst
index 2860407f..ce46dc53 100644
--- a/src/doc/role-permission-table.rst
+++ b/src/doc/role-permission-table.rst
@@ -3,7 +3,7 @@
Role Permissions
================
-Roles in CaosDB can have the following permissions
+Roles in LinkAhead can have the following permissions
.. list-table:: Role permissions
:header-rows: 1
diff --git a/src/doc/roles.md b/src/doc/roles.md
index 838b3d9e..b83cb200 100644
--- a/src/doc/roles.md
+++ b/src/doc/roles.md
@@ -2,8 +2,8 @@
## Users and roles ##
-Interaction with CaosDB happens either as an authenticated *user* or without
-authentication. In CaosDB, users can have zero, one or more *roles*, several
+Interaction with LinkAhead happens either as an authenticated *user* or without
+authentication. In LinkAhead, users can have zero, one or more *roles*, several
users may have the same role, and there may be roles without any users.
## What are users and roles good for? ##
diff --git a/src/doc/specification/AbstractProperty.md b/src/doc/specification/AbstractProperty.md
index 062ef205..fd65d9b2 100644
--- a/src/doc/specification/AbstractProperty.md
+++ b/src/doc/specification/AbstractProperty.md
@@ -6,10 +6,10 @@ up-to-date description of the `Property` entity.
## Note ##
> This document has not been updated for a long time. Although it is concerned with the mostly
-> stable API, its content may no longer reflect the actual CaosDB behavior.
+> stable API, its content may no longer reflect the actual LinkAhead behavior.
## Introduction
-An `AbstractProperty` is one of the basal objects of CaosDB.
+An `AbstractProperty` is one of the basal objects of LinkAhead.
An `AbstractProperty` MUST have the following _qualities_ (shortcut in brackets):
* a persistent id (`id`)
* an unique name (`name`)
@@ -42,7 +42,7 @@ An `AbstractProperty` is represented in xml by a `<Property/>` tag. It's _qualit
Depending on the purpose of the xml document (shall it represent an object in the database or an object _to be posted _to the database?) the `<Property/>` tag may actually have just a few of the mentioned "quality-attributes".
### GET AbstractProperty
-Any xml representation of an `AbstractProperty` that is retrieved from the CaosDB Server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
+Any xml representation of an `AbstractProperty` that is retrieved from the LinkAhead Server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
#### text
<Property id="$id" name="$name" description="$description" generator="$generator" creator="$creator" created="$created" type="text" />
@@ -62,10 +62,10 @@ Any xml representation of an `AbstractProperty` that is retrieved from the CaosD
<Property id="$id" name="$name" description="$description" generator="$generator" creator="$creator" created="$created" type="file" />
'''General Notes:
-* If the called Property does not exist or if the Property called without permission, the CaosDB Server will return an Error.
+* If the called Property does not exist or if the Property called without permission, the LinkAhead Server will return an Error.
### POST AbstractProperty
-Any xml representation of an `AbstractProperty` that is to be posted to the CaosDB server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
+Any xml representation of an `AbstractProperty` that is to be posted to the LinkAhead server MUST have exactly ONE of the following forms, depending on the `AbstractProperty's` type:
#### text
<Property name="$name" description="$description" generator="$generator" type="text" />
@@ -85,10 +85,10 @@ Any xml representation of an `AbstractProperty` that is to be posted to the Caos
<Property name="$name" description="$description" generator="$generator" type="file" />
*General Notes:*
-* The `AbstractProperty's` `id` and timestamp (`created`) will be generated by the CaosDB Server.
-* The `AbstractProperty's` creator will be determined by the CaosDB Server depending on it's policy configuration.
+* The `AbstractProperty's` `id` and timestamp (`created`) will be generated by the LinkAhead Server.
+* The `AbstractProperty's` creator will be determined by the LinkAhead Server depending on it's policy configuration.
* Any given attribute beyond these will be *ignored*.
-* If the `<Property/>` tag isn't compliant with these the CaosDB Server will return an Error.
+* If the `<Property/>` tag isn't compliant with these the LinkAhead Server will return an Error.
----
## Examples
diff --git a/src/doc/specification/Authentication.rst b/src/doc/specification/Authentication.rst
index 3fcd25da..a8d4d33a 100644
--- a/src/doc/specification/Authentication.rst
+++ b/src/doc/specification/Authentication.rst
@@ -2,7 +2,7 @@
Authentication
==============
-Some features of CaosDB are available to registered users only. Making any changes to the data stock
+Some features of LinkAhead are available to registered users only. Making any changes to the data stock
via HTTP requires authentication.
Sessions
@@ -18,7 +18,7 @@ username:
The user name, for example ``admin`` (on demo.indiscale.com).
password:
- The password, for example ``caosdb`` (on demo.indiscale.com).
+ The password, for example ``linkahead`` (on demo.indiscale.com).
Logout
------
diff --git a/src/doc/specification/Datatype.md b/src/doc/specification/Datatype.md
index 6354d6f2..795e2408 100644
--- a/src/doc/specification/Datatype.md
+++ b/src/doc/specification/Datatype.md
@@ -55,7 +55,7 @@ The DateTime data type exists in (currently) three flavors which are dynamically
* It is allowed to ommit the nanosecond part of a UTCDateTime (`2016-01-01T13:23:00CEST`). This indicates a precision of seconds for a UTCDateTime value.
### Date
- Description:: This DATETIME flavor stores values which represent a single date, month or year according to the [gregorian calendar](https://en.wikipedia.org/wiki/Gregorian_Calendar). A month/year is conceived as a single date with the presion of a month/year. This concept is useful if you try to understand the query semantics which are explained [elsewhere](../CaosDB-Query-Language.html#pov-property-operator-value).
+ Description:: This DATETIME flavor stores values which represent a single date, month or year according to the [gregorian calendar](https://en.wikipedia.org/wiki/Gregorian_Calendar). A month/year is conceived as a single date with the presion of a month/year. This concept is useful if you try to understand the query semantics which are explained [elsewhere](../LinkAhead-Query-Language.html#pov-property-operator-value).
Format:: `Y[YYY][-MM[-dd]]` (where square brackets mean that the expression is optional).
Range:: Any valid date according to the gregorian calendar from `-9999-01-01` to `9999-12-31` (and respective dates with lower precision. E.g. the year `-9999`). There is no year `0`.
* Note: Date is a specialization of [#SemiCompleteDateTime].
diff --git a/src/doc/specification/Entity_Overview.md b/src/doc/specification/Entity_Overview.md
index ca197e50..7c60b8b4 100644
--- a/src/doc/specification/Entity_Overview.md
+++ b/src/doc/specification/Entity_Overview.md
@@ -1,4 +1,4 @@
-# Overview of the CaosDB Entities' structure
+# Overview of the LinkAhead Entities' structure
**Warning:** This overview may be outdated.
@@ -12,7 +12,7 @@ Date: 2017-12-17
## Introduction
-CaosDB is a database management system that stores it's data into `Entities`. An `Entity` can be thought of as the equivalent to tables, rows, columns and the tuples that fill the tables of a traditional RDBMS. Entities are not only used to store the data they also define the structure of the data.
+LinkAhead is a database management system that stores it's data into `Entities`. An `Entity` can be thought of as the equivalent to tables, rows, columns and the tuples that fill the tables of a traditional RDBMS. Entities are not only used to store the data they also define the structure of the data.
## Formal Definition
diff --git a/src/doc/specification/Fileserver.md b/src/doc/specification/Fileserver.md
index dd3e0f37..4701ea6f 100644
--- a/src/doc/specification/Fileserver.md
+++ b/src/doc/specification/Fileserver.md
@@ -1,12 +1,12 @@
# Fileserver
## Info
-There are several ways to utilize the file server component of CaosDB. It is possible to upload a file or a whole folder including subfolders via HTTP and the _drop off box_. It is possible to download a file via HTTP identified by its ID or by its path in the internal file system. Furthermore, it is possible to get the files metadata via HTTP as an xml.
+There are several ways to utilize the file server component of LinkAhead. It is possible to upload a file or a whole folder including subfolders via HTTP and the _drop off box_. It is possible to download a file via HTTP identified by its ID or by its path in the internal file system. Furthermore, it is possible to get the files metadata via HTTP as an xml.
## File upload
### Drop off box
-The drop off box is a directory on the CaosDB server's local file system, specified in the `server.conf` file in the server's basepath (something like `~/CaosDB/server/server.conf`). The key in the `server.conf` is called `dropoffbox`. Since the drop off box directory is writable for all, users can push their files or complete folders via a `mv` or a `cp` (recommended!) in that folder. The server deletes files older than their maximum lifetime (24 hours by default, specified `in server.conf`). But within their lifetime a user can prompt the server to pick up the file (or folder) from the drop off box in order to transfer it to the internal file system.
+The drop off box is a directory on the LinkAhead server's local file system, specified in the `server.conf` file in the server's basepath (something like `~/LinkAhead/server/server.conf`). The key in the `server.conf` is called `dropoffbox`. Since the drop off box directory is writable for all, users can push their files or complete folders via a `mv` or a `cp` (recommended!) in that folder. The server deletes files older than their maximum lifetime (24 hours by default, specified `in server.conf`). But within their lifetime a user can prompt the server to pick up the file (or folder) from the drop off box in order to transfer it to the internal file system.
Now, the user may send a pick up request to `POST http://host:port/mpidsserver/FilesDropOff` with a similar body:
@@ -38,9 +38,9 @@ where
There is an example on file upload using cURL described in detail in [the curl section of this
documentation](../administration/curl-access.md).
-File upload via HTTP is implemented in a [rfc1867](http://www.ietf.org/rfc/rfc1867.txt) consistent way. This is a de-facto standard that defines a file upload as a part of an HTML form submission. This concept shall not be amplified here. But it has to be noticed that this protocol is not designed for uploads of complete structured folders. Therefore the CaosDB file components have to impose that structure on the upload protocol.
+File upload via HTTP is implemented in a [rfc1867](http://www.ietf.org/rfc/rfc1867.txt) consistent way. This is a de-facto standard that defines a file upload as a part of an HTML form submission. This concept shall not be amplified here. But it has to be noticed that this protocol is not designed for uploads of complete structured folders. Therefore the LinkAhead file components have to impose that structure on the upload protocol.
-CaosDB's file upload resource does exclusively accept POST requests of MIME media type `multipart/form-data`. The first part of each POST body is expected to be a form-data text field, containing information about the files to be uploaded. It has to meet the following requirements:
+LinkAhead's file upload resource does exclusively accept POST requests of MIME media type `multipart/form-data`. The first part of each POST body is expected to be a form-data text field, containing information about the files to be uploaded. It has to meet the following requirements:
* `Content-type: text/plain; charset=UTF-8`
* `Content-disposition: form-data; name="FileRepresentation"`
diff --git a/src/doc/specification/RecordType.rst b/src/doc/specification/RecordType.rst
index 53e8e161..16a9d4a5 100644
--- a/src/doc/specification/RecordType.rst
+++ b/src/doc/specification/RecordType.rst
@@ -103,7 +103,7 @@ Examples
The following examples have not been updated in a while and may
serve as a starting point, but are not guaranteed to be fully
- applicable to the most recent versions of CaosDB.
+ applicable to the most recent versions of LinkAhead.
GET Requests
~~~~~~~~~~~~
diff --git a/src/doc/specification/Server-side-scripting.md b/src/doc/specification/Server-side-scripting.md
index 18dfe9ea..5da939fe 100644
--- a/src/doc/specification/Server-side-scripting.md
+++ b/src/doc/specification/Server-side-scripting.md
@@ -1,13 +1,13 @@
# Server-Side Scripting API (v0.1)
-The CaosDB Server can execute scripts (bash/python/perl) and
+The LinkAhead Server can execute scripts (bash/python/perl) and
compiled executables. The scripts can be invoked by a remote-procedure-call
(RPC) protocol. Both, the requirements for the scripts and the
RPC are described in this document.
## Configuration of the Server
-The CaosDB Server has two relevant properties:
+The LinkAhead Server has two relevant properties:
### `SERVER_SIDE_SCRIPTING_BIN_DIR`
is the directory where executable scripts are to be placed. The server will not execute scripts which are out side of this directory. This directory must be readable and executable for the server. But it should not be readable or executable for anyone else.
@@ -50,7 +50,7 @@ is the directory under which the server creates temporary working directories. T
3. Zero or more parameter form fields with a unique name which starts with the string `-p` (positional command line arguments).
4. Zero or more file form fields which have a unique field name and a unique file name (upload files). If the field names or file names are not unique, the behavior is not defined.
5. A parameter form field with name="timeout" (the request timeout)
- 6. A parameter form field with name="auth-token" and a valid CaosDB AuthToken string or "generate" as value.
+ 6. A parameter form field with name="auth-token" and a valid LinkAhead AuthToken string or "generate" as value.
## How Does the Server Call the Script?
* The server executes the script in a temporary working directory, called *PWD* (which will be deleted afterwards).
@@ -81,9 +81,9 @@ where the user uploads `my.conf` as `-Oconfig-file` and `my.input.tsv` as `-p1`,
$SERVER_SIDE_SCRIPTING_BIN_DIR/my/script.py --config-file=.upload_files/my.conf --algorithm=fast analyze .upload_files/my.input.tsv
```
-## CaosDB Server Response
+## LinkAhead Server Response
-The CaosDB Server responds with an xml document. The root element is the usual `/Response`. If no errors occurred (which would be represented with `/Response/Error` elements) the result of the script execution is represented as a `/Response/script/` element.
+The LinkAhead Server responds with an xml document. The root element is the usual `/Response`. If no errors occurred (which would be represented with `/Response/Error` elements) the result of the script execution is represented as a `/Response/script/` element.
* It has a `code` attribute which contains the exit code value of the execution.
* It has `stdout` and `stderr` children which contain the dump of the stdout and stderr file of the execution environment.
@@ -100,13 +100,13 @@ The CaosDB Server responds with an xml document. The root element is the usual `
</Response>
```
-## CaosDB Clients and Authentication Token
+## LinkAhead Clients and Authentication Token
-A special use case for server side scripting is the automated execution of CaosDB clients. These clients need to connect to the CaosDB Server and thus need a way to authenticate themselves.
+A special use case for server side scripting is the automated execution of LinkAhead clients. These clients need to connect to the LinkAhead Server and thus need a way to authenticate themselves.
For this special case the server can pass an Authentication Token which can be used by the script to authenticate itself. If the invocation request send a particulare AuthToken in the form, this AuthToken will be passed to the script with the `--auth-token` option. Otherwise, if the `auth-token` field has "generate" as value, a fresh AuthToken is generated which belongs to the user who requested the script execution.
Thus the script is executed (and connects back to the server) as the user who called the script in the first place.
-A CaosDB client might use the python client library to connect to the server with that AuthToken.
+A LinkAhead client might use the python client library to connect to the server with that AuthToken.
### Example Script
@@ -115,7 +115,7 @@ A CaosDB client might use the python client library to connect to the server wit
# -*- coding: utf-8 -*-
#
# ** header v3.0
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -150,7 +150,7 @@ specified with the commandline option --exit
import sys
from os import listdir
-from caosdb import configure_connection, execute_query
+from linkahead import configure_connection, execute_query
# parse --auth-token option and configure connection
diff --git a/src/doc/specification/entity_api.rst b/src/doc/specification/entity_api.rst
index 3f6bdbcf..99710537 100644
--- a/src/doc/specification/entity_api.rst
+++ b/src/doc/specification/entity_api.rst
@@ -6,7 +6,7 @@ The Entity API
:caption: Contents:
:hidden:
- Overview of the CaosDB Entities' structure<Entity_Overview>
+ Overview of the LinkAhead Entities' structure<Entity_Overview>
.. note::
@@ -16,7 +16,7 @@ The Entity API
The details of the specification, including interactive examples, can
be found `here
-<https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/tree/dev/src/doc/development/api/xml/caosdb_openapi.yaml>`_.
+<https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/tree/dev/src/doc/development/api/xml/linkahead_openapi.yaml>`_.
Note that some commands may require authentication, which can be done with
an authentication cookie as described in the :doc:`api
documentation<Authentication>`. Specialities of the :doc:`scripting
diff --git a/src/doc/tutorials/data_model_tutorial.rst b/src/doc/tutorials/data_model_tutorial.rst
index c1de9b08..f510266c 100644
--- a/src/doc/tutorials/data_model_tutorial.rst
+++ b/src/doc/tutorials/data_model_tutorial.rst
@@ -3,7 +3,7 @@ Data model tutorial
Data models are a central concept of research data management. The
open-source framework LinkAhead makes it easy to create an `agile
-data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+data model <https://docs.linkahead.org/linkahead-server/Data-Model.html>`__
which suits your needs, so you can profit from your collected data fast.
.. contents::
@@ -15,7 +15,7 @@ Frequently asked questions about data models
What is a data model?
~~~~~~~~~~~~~~~~~~~~~
-In LinkAhead, the `data model <https://docs.indiscale.com/caosdb-server/Data-Model.html>`__
+In LinkAhead, the `data model <https://docs.linkahead.org/linkahead-server/Data-Model.html>`__
describes in a generic way how the data is structured. This document will help you understand this
concept and how you can adjust the data model to your needs.
@@ -44,9 +44,9 @@ will be available to all cell culture experiments.
A simple data model, with four RecordTypes
In LinkAhead, the data model consists of *RecordTypes* and *Properties*. Each `*RecordType*
-<https://docs.indiscale.com/caosdb-server/Data-Model.html#record-types>`__ corresponds to one type
+<https://docs.linkahead.org/linkahead-server/Data-Model.html#record-types>`__ corresponds to one type
of data set, for example an experiment, a cell culture experiment or a cell line. And each data set
-can have `*Properties* <https://docs.indiscale.com/caosdb-server/Data-Model.html#properties>`__
+can have `*Properties* <https://docs.linkahead.org/linkahead-server/Data-Model.html#properties>`__
which define it further: for example
the number of dishes in a cell culture experiment, a publication
describing a cell line or the cell line which was used for an
@@ -102,17 +102,17 @@ Modifying the data model in LinkAhead
The easiest way to change the data model is to `use the LinkAhead
web
-application <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__.
+application <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html>`__.
But the first step is to look at the current data model (*RecordTypes*
and *Properties*) and your current situation, to find out what you need
changed. It may help to ask yourself these questions:
- Do you want to describe data of existing types in more detail? -> :ref:`Create
*Properties*<new_property>` if necessary, then `add
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#add-properties-to-an-existing-recordtype>`__
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#add-properties-to-an-existing-recordtype>`__
these *Properties* to the existing *RecordTypes*.
- Do you need to add a property more than once? -> Make that property `a list property
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#make-a-property-into-a-list>`__\
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#make-a-property-into-a-list>`__\
.
- Are there completely new types of data? -> :ref:`Create a new
*RecordType* <new_recordtype>` .
@@ -127,11 +127,11 @@ changed. It may help to ask yourself these questions:
*RecordType* <new_recordtype>` .
- Are there *Properties* or *RecordTypes* which were created in the past, but will never be used? ->
`Delete them
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#delete-an-entity>`__.
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#delete-an-entity>`__.
Once you know what you want to do, open the LinkAhead web application, log in and click on the “Edit
Mode” button in the menu. Then follow one of the instructions in the next sections or the general `Edit
-Mode documentation <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html>`__..
+Mode documentation <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html>`__..
.. figure:: img/edit_mode_button.png
:alt: The Edit Mode button appears when a user is logged in.
@@ -162,7 +162,7 @@ the data model.
3. Click on the “Create Property” button in the toolbox. A dialog for
the new Property shows up.
4. Follow the `WebUI documentation
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-property>`__ for Property
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#new-property>`__ for Property
creation.
.. _new_recordtype:
@@ -187,7 +187,7 @@ Create a new RecordType
the new Property shows up.
4. Follow the `WebUI documentation
- <https://docs.indiscale.com/caosdb-webui/tutorials/edit_mode.html#new-recordtype>`__ for
+ <https://docs.linkahead.org/linkahead-webui/tutorials/edit_mode.html#new-recordtype>`__ for
RecordType creation.
What about letting users only choose from a fixed set of values (a.k.a. enums)?
diff --git a/src/doc/tutorials/setup_state_model.py b/src/doc/tutorials/setup_state_model.py
index 0a1a7daa..27cc528c 100755
--- a/src/doc/tutorials/setup_state_model.py
+++ b/src/doc/tutorials/setup_state_model.py
@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# encoding: utf-8
#
-# This file is a part of the CaosDB Project.
+# This file is a part of the LinkAhead Project.
#
# Copyright (C) 2021 Indiscale GmbH <info@indiscale.com>
# Copyright (C) 2021 Henrik tom Wörden <h.tomwoerden@indiscale.com>
@@ -33,8 +33,8 @@ order:
"""
from argparse import ArgumentParser, RawDescriptionHelpFormatter
-import caosdb as db
-from caosdb.common.administration import generate_password
+import linkahead as db
+from linkahead.common.administration import generate_password
def teardown(args):
diff --git a/src/doc/tutorials/statemachine.rst b/src/doc/tutorials/statemachine.rst
index dc46885a..693d95bd 100644
--- a/src/doc/tutorials/statemachine.rst
+++ b/src/doc/tutorials/statemachine.rst
@@ -9,7 +9,7 @@ In order to use the state machine functionality you have to set the
corresponding server setting: ``EXT_ENTITY_STATE=ENABLED``.
Also, a few RecordTypes and Properties are required. You can use the
-script `setup_state_model.py <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/src/doc/tutorials/setup_state_model.py>`_
+script `setup_state_model.py <https://gitlab.com/linkahead/linkahead-server/-/blob/dev/src/doc/tutorials/setup_state_model.py>`_
to create those or you may have a look at it to see what is needed (``setup_state_data_model`` function).
Defining the State Machine
diff --git a/src/main/java/org/caosdb/datetime/Date.java b/src/main/java/org/caosdb/datetime/Date.java
index 2b7aa522..e6e40d13 100644
--- a/src/main/java/org/caosdb/datetime/Date.java
+++ b/src/main/java/org/caosdb/datetime/Date.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Calendar;
import java.util.GregorianCalendar;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class Date extends SemiCompleteDateTime {
diff --git a/src/main/java/org/caosdb/datetime/DateTimeFactory2.java b/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
index 14088ea5..93773a28 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeFactory2.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Arrays;
import java.util.Calendar;
import java.util.TimeZone;
import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
-import org.caosdb.server.query.CQLParsingErrorListener;
-import org.caosdb.server.query.CQLParsingErrorListener.ParsingError;
+import org.linkahead.server.query.CQLParsingErrorListener;
+import org.linkahead.server.query.CQLParsingErrorListener.ParsingError;
/**
- * Factory which parses string into CaosDB's DATETIME values.
+ * Factory which parses string into LinkAhead's DATETIME values.
*
* @author tf
*/
diff --git a/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java b/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
index c81018f9..08065bbc 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeFactoryInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Date;
diff --git a/src/main/java/org/caosdb/datetime/DateTimeInterface.java b/src/main/java/org/caosdb/datetime/DateTimeInterface.java
index e6f1b933..acd5ef69 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeInterface.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
-import org.caosdb.server.datatype.SingleValue;
+import org.linkahead.server.datatype.SingleValue;
public interface DateTimeInterface extends SingleValue {
diff --git a/src/main/java/org/caosdb/datetime/DateTimeLexer.g4 b/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
index 1be8e285..9e814d97 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
+++ b/src/main/java/org/caosdb/datetime/DateTimeLexer.g4
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/datetime/DateTimeParser.g4 b/src/main/java/org/caosdb/datetime/DateTimeParser.g4
index 3923e9c3..2dd15720 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeParser.g4
+++ b/src/main/java/org/caosdb/datetime/DateTimeParser.g4
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
index 635b2cfa..a95b9e26 100644
--- a/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/DateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
diff --git a/src/main/java/org/caosdb/datetime/FragmentDateTime.java b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
index 38c16a98..6f5f23b1 100644
--- a/src/main/java/org/caosdb/datetime/FragmentDateTime.java
+++ b/src/main/java/org/caosdb/datetime/FragmentDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.server.datatype.Value;
+import org.linkahead.server.datatype.Value;
public abstract class FragmentDateTime implements DateTimeInterface {
diff --git a/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
index 459f1d59..8983694e 100644
--- a/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/GregorianCalendarDateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.text.SimpleDateFormat;
import java.util.Calendar;
diff --git a/src/main/java/org/caosdb/datetime/Interval.java b/src/main/java/org/caosdb/datetime/Interval.java
index 9890fb4c..f4e6f1c2 100644
--- a/src/main/java/org/caosdb/datetime/Interval.java
+++ b/src/main/java/org/caosdb/datetime/Interval.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
public interface Interval extends DateTimeInterface {
diff --git a/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java b/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
index 5aff2dce..b2ef6edd 100644
--- a/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
+++ b/src/main/java/org/caosdb/datetime/LeapSecondDateTimeStringStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.text.SimpleDateFormat;
import java.util.Calendar;
diff --git a/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java b/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
index 5bd4daca..71786ca6 100644
--- a/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
+++ b/src/main/java/org/caosdb/datetime/SemiCompleteDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class SemiCompleteDateTime extends FragmentDateTime implements Interval {
diff --git a/src/main/java/org/caosdb/datetime/UTCDateTime.java b/src/main/java/org/caosdb/datetime/UTCDateTime.java
index 1dd86cc9..af1aec2f 100644
--- a/src/main/java/org/caosdb/datetime/UTCDateTime.java
+++ b/src/main/java/org/caosdb/datetime/UTCDateTime.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,16 +22,16 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.GregorianCalendar;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.datatype.Value;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.datatype.Value;
public class UTCDateTime implements Interval {
diff --git a/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java b/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
index 5cd9de48..16505f24 100644
--- a/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
+++ b/src/main/java/org/caosdb/datetime/UTCTimeZoneShift.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import java.util.Date;
import java.util.TimeZone;
diff --git a/src/main/java/org/caosdb/server/CaosAuthenticator.java b/src/main/java/org/caosdb/server/CaosAuthenticator.java
index b26e5000..c7a727ae 100644
--- a/src/main/java/org/caosdb/server/CaosAuthenticator.java
+++ b/src/main/java/org/caosdb/server/CaosAuthenticator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.AuthenticationToken;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.Context;
import org.restlet.Request;
import org.restlet.Response;
@@ -37,11 +37,12 @@ import org.restlet.security.Authenticator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class CaosAuthenticator extends Authenticator {
+public class LinkAheadAuthenticator extends Authenticator {
- private static final Logger logger = LoggerFactory.getLogger(CaosAuthenticator.class.getName());
+ private static final Logger logger =
+ LoggerFactory.getLogger(LinkAheadAuthenticator.class.getName());
- public CaosAuthenticator(final Context context) {
+ public LinkAheadAuthenticator(final Context context) {
super(context);
}
@@ -64,7 +65,7 @@ public class CaosAuthenticator extends Authenticator {
// anonymous users
if (!subject.isAuthenticated()
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("TRUE")) {
subject.login(AnonymousAuthenticationToken.getInstance());
}
diff --git a/src/main/java/org/caosdb/server/CaosAuthorizer.java b/src/main/java/org/caosdb/server/CaosAuthorizer.java
index 58e814a3..f73bf1ea 100644
--- a/src/main/java/org/caosdb/server/CaosAuthorizer.java
+++ b/src/main/java/org/caosdb/server/CaosAuthorizer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.security.Authorizer;
-public class CaosAuthorizer extends Authorizer {
+public class LinkAheadAuthorizer extends Authorizer {
@Override
protected boolean authorize(final Request request, final Response response) {
diff --git a/src/main/java/org/caosdb/server/CaosDBException.java b/src/main/java/org/caosdb/server/CaosDBException.java
index 617dfdff..da51b02d 100644
--- a/src/main/java/org/caosdb/server/CaosDBException.java
+++ b/src/main/java/org/caosdb/server/CaosDBException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
-public class CaosDBException extends RuntimeException {
+public class LinkAheadException extends RuntimeException {
private static final long serialVersionUID = -6679522664294087311L;
- public CaosDBException(final String string) {
+ public LinkAheadException(final String string) {
super(string);
}
- public CaosDBException(final Throwable t) {
+ public LinkAheadException(final Throwable t) {
super(t);
}
}
diff --git a/src/main/java/org/caosdb/server/CaosDBServer.java b/src/main/java/org/caosdb/server/CaosDBServer.java
index 2a115c5c..c22581e0 100644
--- a/src/main/java/org/caosdb/server/CaosDBServer.java
+++ b/src/main/java/org/caosdb/server/CaosDBServer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
@@ -42,53 +42,53 @@ import org.apache.shiro.env.BasicIniEnvironment;
import org.apache.shiro.mgt.SecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.CaosDBAuthorizingRealm;
-import org.caosdb.server.accessControl.CaosDBDefaultRealm;
-import org.caosdb.server.accessControl.ConsumedInfoCleanupJob;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.SessionTokenRealm;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveDatatypes;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.container.Container;
-import org.caosdb.server.grpc.GRPCServer;
-import org.caosdb.server.jobs.core.AccessControl;
-import org.caosdb.server.jobs.core.CheckStateTransition;
-import org.caosdb.server.logging.RequestErrorLogMessage;
-import org.caosdb.server.resource.AuthenticationResource;
-import org.caosdb.server.resource.DefaultResource;
-import org.caosdb.server.resource.EntityOwnerResource;
-import org.caosdb.server.resource.EntityPermissionsResource;
-import org.caosdb.server.resource.FileSystemResource;
-import org.caosdb.server.resource.InfoResource;
-import org.caosdb.server.resource.LogoutResource;
-import org.caosdb.server.resource.PermissionRulesResource;
-import org.caosdb.server.resource.RolesResource;
-import org.caosdb.server.resource.ScriptingResource;
-import org.caosdb.server.resource.ServerLogsResource;
-import org.caosdb.server.resource.ServerPropertiesResource;
-import org.caosdb.server.resource.SharedFileResource;
-import org.caosdb.server.resource.ThumbnailsResource;
-import org.caosdb.server.resource.UserResource;
-import org.caosdb.server.resource.UserRolesResource;
-import org.caosdb.server.resource.Webinterface;
-import org.caosdb.server.resource.WebinterfaceBuildNumber;
-import org.caosdb.server.resource.transaction.EntityNamesResource;
-import org.caosdb.server.resource.transaction.EntityResource;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.transaction.ChecksumUpdater;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Initialization;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.ConsumedInfoCleanupJob;
+import org.linkahead.server.accessControl.LinkAheadAuthorizingRealm;
+import org.linkahead.server.accessControl.LinkAheadDefaultRealm;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.SessionTokenRealm;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveDatatypes;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.container.Container;
+import org.linkahead.server.grpc.GRPCServer;
+import org.linkahead.server.jobs.core.AccessControl;
+import org.linkahead.server.jobs.core.CheckStateTransition;
+import org.linkahead.server.logging.RequestErrorLogMessage;
+import org.linkahead.server.resource.AuthenticationResource;
+import org.linkahead.server.resource.DefaultResource;
+import org.linkahead.server.resource.EntityOwnerResource;
+import org.linkahead.server.resource.EntityPermissionsResource;
+import org.linkahead.server.resource.FileSystemResource;
+import org.linkahead.server.resource.InfoResource;
+import org.linkahead.server.resource.LogoutResource;
+import org.linkahead.server.resource.PermissionRulesResource;
+import org.linkahead.server.resource.RolesResource;
+import org.linkahead.server.resource.ScriptingResource;
+import org.linkahead.server.resource.ServerLogsResource;
+import org.linkahead.server.resource.ServerPropertiesResource;
+import org.linkahead.server.resource.SharedFileResource;
+import org.linkahead.server.resource.ThumbnailsResource;
+import org.linkahead.server.resource.UserResource;
+import org.linkahead.server.resource.UserRolesResource;
+import org.linkahead.server.resource.Webinterface;
+import org.linkahead.server.resource.WebinterfaceBuildNumber;
+import org.linkahead.server.resource.transaction.EntityNamesResource;
+import org.linkahead.server.resource.transaction.EntityResource;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.transaction.ChecksumUpdater;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Initialization;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
import org.quartz.JobDetail;
import org.quartz.Scheduler;
import org.quartz.SchedulerException;
@@ -118,9 +118,9 @@ import org.restlet.util.Series;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-public class CaosDBServer extends Application {
+public class LinkAheadServer extends Application {
- private static Logger logger = LoggerFactory.getLogger(CaosDBServer.class);
+ private static Logger logger = LoggerFactory.getLogger(LinkAheadServer.class);
private static ServerProperties SERVER_PROPERTIES = null;
private static Component component = null;
private static ArrayList<Runnable> postShutdownHooks = new ArrayList<Runnable>();
@@ -169,12 +169,12 @@ public class CaosDBServer extends Application {
* Parse the command line arguments.
*
* <ul>
- * <li>"--no-backend": flag to run caosdb without any backend (for testing purposes)
+ * <li>"--no-backend": flag to run linkahead without any backend (for testing purposes)
* <li>"--no-tls": flag to start only a http server (no https server)
* </ul>
*
* <p>The --no-backend flag is only available in the debug mode which is controlled by the
- * `caosdb.debug` JVM Property.
+ * `linkahead.debug` JVM Property.
*
* @param args
*/
@@ -321,13 +321,13 @@ public class CaosDBServer extends Application {
public static Ini getShiroConfig() {
final Ini config = new Ini();
final Section mainSec = config.addSection("main");
- mainSec.put("CaosDB", CaosDBDefaultRealm.class.getCanonicalName());
+ mainSec.put("CaosDB", LinkAheadDefaultRealm.class.getCanonicalName());
mainSec.put("SessionTokenValidator", SessionTokenRealm.class.getCanonicalName());
- mainSec.put("CaosDBAuthorizingRealm", CaosDBAuthorizingRealm.class.getCanonicalName());
+ mainSec.put("LinkAheadAuthorizingRealm", LinkAheadAuthorizingRealm.class.getCanonicalName());
mainSec.put("AnonymousRealm", AnonymousRealm.class.getCanonicalName());
mainSec.put(
"securityManager.realms",
- "$CaosDB, $SessionTokenValidator, $CaosDBAuthorizingRealm, $AnonymousRealm");
+ "$CaosDB, $SessionTokenValidator, $LinkAheadAuthorizingRealm, $AnonymousRealm");
// disable shiro's default session management. We have quasi-stateless
// sessions
@@ -432,7 +432,7 @@ public class CaosDBServer extends Application {
.add(new org.restlet.ext.jetty.HttpServerHelper(null));
// Create a component.
- component = new CaosDBComponent();
+ component = new LinkAheadComponent();
final Server httpServer =
new Server(
@@ -450,7 +450,7 @@ public class CaosDBServer extends Application {
parameters.add("maxTotalConnections", Integer.toString(maxTotalConnections));
// Create an application (this class).
- final Application application = new CaosDBServer();
+ final Application application = new LinkAheadServer();
application
.getStatusService()
.setContactEmail(getServerProperty(ServerProperties.KEY_ADMIN_EMAIL));
@@ -491,10 +491,10 @@ public class CaosDBServer extends Application {
final int maxTotalConnections)
throws Exception {
- Engine.getInstance().getRegisteredServers().add(new CaosDBServerConnectorHelper(null));
+ Engine.getInstance().getRegisteredServers().add(new LinkAheadServerConnectorHelper(null));
// Create a component.
- component = new CaosDBComponent();
+ component = new LinkAheadComponent();
final Server httpsServer =
new Server(
@@ -503,7 +503,7 @@ public class CaosDBServer extends Application {
server_bind_address,
port_https,
(Restlet) null,
- "org.caosdb.server.CaosDBServerConnectorHelper");
+ "org.linkahead.server.LinkAheadServerConnectorHelper");
component.getServers().add(httpsServer);
// redirector http to https
@@ -540,7 +540,7 @@ public class CaosDBServer extends Application {
parameters.add("certAlias", "1");
// Create an application (this class).
- final Application application = new CaosDBServer();
+ final Application application = new LinkAheadServer();
application
.getStatusService()
.setContactEmail(
@@ -572,7 +572,7 @@ public class CaosDBServer extends Application {
@Override
public Restlet createInboundRoot() {
/** Authenticator. Protects the protectedRouter. */
- final CaosAuthenticator authenticator = new CaosAuthenticator(getContext());
+ final LinkAheadAuthenticator authenticator = new LinkAheadAuthenticator(getContext());
/** ProtectedRouter. Is protected by the authenticator. */
final Router protectedRouter =
@@ -676,7 +676,7 @@ public class CaosDBServer extends Application {
});
// baseRouter.attachDefault(authenticator);
- final CaosAuthorizer authorizer = new CaosAuthorizer();
+ final LinkAheadAuthorizer authorizer = new LinkAheadAuthorizer();
// The protectedRouter handles the request if the authorization
// succeeds.
@@ -800,7 +800,7 @@ public class CaosDBServer extends Application {
public static ServerInfo getServerInfo() {
if (serverInfo == null) {
serverInfo = new ServerInfo();
- serverInfo.setAgent("CaosDB Server");
+ serverInfo.setAgent("LinkAhead Server");
}
return serverInfo;
}
@@ -864,7 +864,7 @@ public class CaosDBServer extends Application {
}
public static boolean isDebugMode() {
- return Boolean.getBoolean("caosdb.debug");
+ return Boolean.getBoolean("linkahead.debug");
}
/**
@@ -888,24 +888,24 @@ public class CaosDBServer extends Application {
}
}
-class CaosDBComponent extends Component {
+class LinkAheadComponent extends Component {
private static Logger request_error_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_ERRORS_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_ERRORS_LOGGER);
private static Logger request_time_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_TIME_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_TIME_LOGGER);
- public CaosDBComponent() {
+ public LinkAheadComponent() {
super();
String responseLogFormat =
- CaosDBServer.getServerProperty(ServerProperties.KEY_REST_RESPONSE_LOG_FORMAT);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_REST_RESPONSE_LOG_FORMAT);
if ("OFF".equalsIgnoreCase(responseLogFormat)) {
getLogService().setEnabled(false);
} else if (responseLogFormat != null && !responseLogFormat.isEmpty()) {
getLogService().setResponseLogFormat(responseLogFormat);
}
- setName(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_NAME));
- setOwner(CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_OWNER));
+ setName(LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_NAME));
+ setOwner(LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_OWNER));
}
/**
@@ -923,7 +923,7 @@ class CaosDBComponent extends Component {
final long t1 = System.currentTimeMillis();
// The server request ID is just a long random number
request.getAttributes().put("SRID", UUID.randomUUID().toString());
- response.setServerInfo(CaosDBServer.getServerInfo());
+ response.setServerInfo(LinkAheadServer.getServerInfo());
super.handle(request, response);
log(request, response, t1);
}
diff --git a/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java b/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
index 8a9749bc..4a7ea3f0 100644
--- a/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
+++ b/src/main/java/org/caosdb/server/CaosDBServerConnectorHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.util.LinkedList;
import org.restlet.Server;
-public class CaosDBServerConnectorHelper extends org.restlet.ext.jetty.HttpsServerHelper {
+public class LinkAheadServerConnectorHelper extends org.restlet.ext.jetty.HttpsServerHelper {
- private static LinkedList<CaosDBServerConnectorHelper> instances =
- new LinkedList<CaosDBServerConnectorHelper>();
+ private static LinkedList<LinkAheadServerConnectorHelper> instances =
+ new LinkedList<LinkAheadServerConnectorHelper>();
- public CaosDBServerConnectorHelper(final Server server) {
+ public LinkAheadServerConnectorHelper(final Server server) {
super(server);
}
- public static LinkedList<CaosDBServerConnectorHelper> getInstances() {
+ public static LinkedList<LinkAheadServerConnectorHelper> getInstances() {
return instances;
}
diff --git a/src/main/java/org/caosdb/server/FileSystem.java b/src/main/java/org/caosdb/server/FileSystem.java
index c0531465..d53e0ddb 100644
--- a/src/main/java/org/caosdb/server/FileSystem.java
+++ b/src/main/java/org/caosdb/server/FileSystem.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import com.google.common.io.Files;
import java.io.File;
@@ -35,17 +35,17 @@ import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.regex.Pattern;
import org.apache.commons.fileupload.FileItemStream;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class FileSystem {
private static String filesystem = null;
@@ -108,10 +108,10 @@ public class FileSystem {
}
public static void init() {
- filesystem = CaosDBServer.getServerProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT);
- dropOffBox = CaosDBServer.getServerProperty(ServerProperties.KEY_DROP_OFF_BOX);
- tmpdir = CaosDBServer.getServerProperty(ServerProperties.KEY_TMP_FILES);
- sharedDir = CaosDBServer.getServerProperty(ServerProperties.KEY_SHARED_FOLDER);
+ filesystem = LinkAheadServer.getServerProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT);
+ dropOffBox = LinkAheadServer.getServerProperty(ServerProperties.KEY_DROP_OFF_BOX);
+ tmpdir = LinkAheadServer.getServerProperty(ServerProperties.KEY_TMP_FILES);
+ sharedDir = LinkAheadServer.getServerProperty(ServerProperties.KEY_SHARED_FOLDER);
check();
}
@@ -152,10 +152,10 @@ public class FileSystem {
* @return FileProperties of the uploaded File.
* @throws NoSuchAlgorithmException
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
public static final FileProperties upload(final FileItemStream item, final String session)
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
String checksum = null;
// Name of the temporary FILE object.
@@ -209,7 +209,7 @@ public class FileSystem {
* @throws NoSuchAlgorithmException
* @throws IOException
* @throws Message
- * @throws CaosDBException
+ * @throws LinkAheadException
* @throws InterruptedException
*/
public static final FileProperties pickUp(final String path, final String session)
diff --git a/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java b/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
index 5f15406f..ffe2fd74 100644
--- a/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
+++ b/src/main/java/org/caosdb/server/HttpToHttpsRedirector.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import org.restlet.Request;
import org.restlet.Response;
diff --git a/src/main/java/org/caosdb/server/ServerProperties.java b/src/main/java/org/caosdb/server/ServerProperties.java
index 93a0c747..acffb8a2 100644
--- a/src/main/java/org/caosdb/server/ServerProperties.java
+++ b/src/main/java/org/caosdb/server/ServerProperties.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server;
+package org.linkahead.server;
import java.io.BufferedInputStream;
import java.io.File;
@@ -31,10 +31,10 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.Properties;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -44,6 +44,9 @@ public class ServerProperties extends Properties implements Observable {
private static final long serialVersionUID = -6178774548807398071L;
private static Logger logger = LoggerFactory.getLogger(ServerProperties.class.getName());
+ public static final String prefix = "LINKAHEAD_CONFIG_";
+ public static final String prefix_old = "CAOSDB_CONFIG_";
+
public static final String KEY_FILE_SYSTEM_ROOT = "FILE_SYSTEM_ROOT";
public static final String KEY_DROP_OFF_BOX = "DROP_OFF_BOX";
public static final String KEY_TMP_FILES = "TMP_FILES";
@@ -162,7 +165,7 @@ public class ServerProperties extends Properties implements Observable {
final ServerProperties serverProperties = new ServerProperties();
final String basepath = System.getProperty("user.dir");
- final URL url = CaosDBServer.class.getResource("/build.properties");
+ final URL url = LinkAheadServer.class.getResource("/build.properties");
serverProperties.load(url.openStream());
// load standard config
@@ -185,9 +188,21 @@ public class ServerProperties extends Properties implements Observable {
}
// load env vars
+ final ArrayList<String> vars_set = new ArrayList<>();
for (final java.util.Map.Entry<String, String> envvar : System.getenv().entrySet()) {
- if (envvar.getKey().startsWith("CAOSDB_CONFIG_") && envvar.getKey().length() > 14) {
- serverProperties.setProperty(envvar.getKey().substring(14), envvar.getValue());
+ if (envvar.getKey().startsWith(prefix) && envvar.getKey().length() > prefix.length()) {
+ serverProperties.setProperty(envvar.getKey().substring(prefix.length()), envvar.getValue());
+ vars_set.append(envvar.getKey().substring(prefix.length()));
+ }
+ }
+ for (final java.util.Map.Entry<String, String> envvar : System.getenv().entrySet()) {
+ if (envvar.getKey().startsWith(prefix_old) && envvar.getKey().length() > prefix.length()) {
+ serverProperties.setProperty(envvar.getKey().substring(prefix.length()), envvar.getValue());
+ if (vars_set.contains(envvar.getKey().substring(prefix.length()))){
+ throw new IOException("You must not set server variables using environment variables"
+ +" with keys with both prefixes: the old, deprecated 'CAOSDB_' and the new"
+ +"'LINKAHEAD' one.");
+ }
}
}
diff --git a/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java b/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
index f68538a3..5e478c83 100644
--- a/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
+++ b/src/main/java/org/caosdb/server/ServerPropertiesSerializer.java
@@ -1,11 +1,11 @@
-package org.caosdb.server;
+package org.linkahead.server;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Properties;
-import org.caosdb.server.utils.Serializer;
import org.jdom2.Element;
+import org.linkahead.server.utils.Serializer;
public class ServerPropertiesSerializer implements Serializer<Properties, Element> {
diff --git a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
index 07503692..5495f933 100644
--- a/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
+++ b/src/main/java/org/caosdb/server/accessControl/ACMPermissions.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collections;
import java.util.HashSet;
diff --git a/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
index 97b6f9ee..1302d18c 100644
--- a/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/AnonymousAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java b/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
index 92b37c0e..bf52611e 100644
--- a/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/AnonymousRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
import org.apache.shiro.authc.SimpleAuthenticationInfo;
import org.apache.shiro.authc.credential.AllowAllCredentialsMatcher;
import org.apache.shiro.realm.AuthenticatingRealm;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class AnonymousRealm extends AuthenticatingRealm {
@Override
protected AuthenticationInfo doGetAuthenticationInfo(AuthenticationToken token) {
- if (CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ if (LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return new SimpleAuthenticationInfo(token.getPrincipal(), null, getName());
}
diff --git a/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java b/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
index dc40e72e..b2af88a2 100644
--- a/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
+++ b/src/main/java/org/caosdb/server/accessControl/AuthenticationUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
-import static org.caosdb.server.utils.Utils.URLDecodeWithUTF8;
+import static org.linkahead.server.utils.Utils.URLDecodeWithUTF8;
import java.sql.Timestamp;
import java.util.Collection;
import java.util.LinkedList;
import org.apache.shiro.authz.AuthorizationInfo;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.permissions.ResponsibleAgent;
-import org.caosdb.server.permissions.Role;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.permissions.ResponsibleAgent;
+import org.linkahead.server.permissions.Role;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.Cookie;
import org.restlet.data.CookieSetting;
@@ -76,7 +76,7 @@ public class AuthenticationUtils {
0,
cookieName,
Utils.URLEncodeWithUTF8(token.toString()),
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
exp_in_sec,
@@ -132,7 +132,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TIMEOUT_COOKIE,
Utils.URLEncodeWithUTF8(t),
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
exp_in_sec,
@@ -163,7 +163,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TOKEN_COOKIE,
"invalid",
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
0,
@@ -183,7 +183,7 @@ public class AuthenticationUtils {
0,
AuthenticationUtils.SESSION_TIMEOUT_COOKIE,
"invalid",
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT) + "/",
null,
null,
0,
@@ -192,7 +192,7 @@ public class AuthenticationUtils {
}
public static Collection<String> getRoles(Subject user) {
- return new CaosDBAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals()).getRoles();
+ return new LinkAheadAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals()).getRoles();
}
public static boolean isFromOneTimeTokenRealm(Subject subject) {
@@ -202,6 +202,6 @@ public class AuthenticationUtils {
}
public static AuthorizationInfo getAuthorizationInfo(Subject user) {
- return new CaosDBAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals());
+ return new LinkAheadAuthorizingRealm().doGetAuthorizationInfo(user.getPrincipals());
}
}
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java b/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
index 52f8d3db..a8c803c3 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBAuthorizingRealm.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collection;
import java.util.Set;
@@ -32,10 +32,10 @@ import org.apache.shiro.authz.SimpleAuthorizationInfo;
import org.apache.shiro.realm.AuthorizingRealm;
import org.apache.shiro.subject.PrincipalCollection;
-public class CaosDBAuthorizingRealm extends AuthorizingRealm {
+public class LinkAheadAuthorizingRealm extends AuthorizingRealm {
- private static final CaosDBRolePermissionResolver role_permission_resolver =
- new CaosDBRolePermissionResolver();
+ private static final LinkAheadRolePermissionResolver role_permission_resolver =
+ new LinkAheadRolePermissionResolver();
public Collection<String> getSessionRoles(SelfValidatingAuthenticationToken token) {
return token.getRoles();
@@ -77,7 +77,7 @@ public class CaosDBAuthorizingRealm extends AuthorizingRealm {
return authzInfo;
}
- public CaosDBAuthorizingRealm() {
+ public LinkAheadAuthorizingRealm() {
setCachingEnabled(false);
setAuthorizationCachingEnabled(false);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java b/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
index 47fe71fd..9be19663 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBDefaultRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
@@ -28,7 +28,7 @@ import org.apache.shiro.authc.SimpleAuthenticationInfo;
import org.apache.shiro.authc.credential.AllowAllCredentialsMatcher;
import org.apache.shiro.realm.AuthenticatingRealm;
-public class CaosDBDefaultRealm extends AuthenticatingRealm {
+public class LinkAheadDefaultRealm extends AuthenticatingRealm {
@Override
protected AuthenticationInfo doGetAuthenticationInfo(final AuthenticationToken token) {
@@ -43,7 +43,7 @@ public class CaosDBDefaultRealm extends AuthenticatingRealm {
}
}
- public CaosDBDefaultRealm() {
+ public LinkAheadDefaultRealm() {
setCredentialsMatcher(new AllowAllCredentialsMatcher());
setCachingEnabled(false);
diff --git a/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java b/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
index 5bc711e1..53878fa4 100644
--- a/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
+++ b/src/main/java/org/caosdb/server/accessControl/CaosDBRolePermissionResolver.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.authc.AuthenticationException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.CaosPermission;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.transaction.RetrievePermissionRulesTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.LinkAheadPermission;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.transaction.RetrievePermissionRulesTransaction;
+import org.linkahead.server.utils.ServerMessages;
-public class CaosDBRolePermissionResolver {
+public class LinkAheadRolePermissionResolver {
- /** Return CaosPermission with the rules which are associated with the roles. */
- public CaosPermission resolvePermissionsInRole(final Set<String> roles) {
+ /** Return LinkAheadPermission with the rules which are associated with the roles. */
+ public LinkAheadPermission resolvePermissionsInRole(final Set<String> roles) {
final HashSet<PermissionRule> rules = new HashSet<PermissionRule>();
for (final String role : roles) {
final RetrievePermissionRulesTransaction t = new RetrievePermissionRulesTransaction(role);
@@ -50,6 +50,6 @@ public class CaosDBRolePermissionResolver {
}
}
- return new CaosPermission(rules);
+ return new LinkAheadPermission(rules);
}
}
diff --git a/src/main/java/org/caosdb/server/accessControl/Config.java b/src/main/java/org/caosdb/server/accessControl/Config.java
index 4c50b445..9350897d 100644
--- a/src/main/java/org/caosdb/server/accessControl/Config.java
+++ b/src/main/java/org/caosdb/server/accessControl/Config.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public class Config {
private String[] permissions = {};
diff --git a/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java b/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
index b5945c5c..8167f72f 100644
--- a/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
+++ b/src/main/java/org/caosdb/server/accessControl/ConsumedInfoCleanupJob.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
import org.quartz.CronScheduleBuilder;
import org.quartz.Job;
import org.quartz.JobBuilder;
@@ -19,7 +19,7 @@ public class ConsumedInfoCleanupJob implements Job {
TriggerBuilder.newTrigger()
.withSchedule(CronScheduleBuilder.dailyAtHourAndMinute(0, 0))
.build();
- CaosDBServer.scheduleJob(job, trigger);
+ LinkAheadServer.scheduleJob(job, trigger);
}
@Override
diff --git a/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java b/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
index dfcbe8df..52c52d95 100644
--- a/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
+++ b/src/main/java/org/caosdb/server/accessControl/CredentialsValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public interface CredentialsValidator<T> {
diff --git a/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java b/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
index dcf1e3fe..47432ce7 100644
--- a/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
+++ b/src/main/java/org/caosdb/server/accessControl/HashPasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.utils.Utils;
public class HashPasswordValidator implements CredentialsValidator<String> {
diff --git a/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java b/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
index 23f772df..0e1fb296 100644
--- a/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
+++ b/src/main/java/org/caosdb/server/accessControl/InternalUserSource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.RetrievePasswordValidatorTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.RetrievePasswordValidatorTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class InternalUserSource implements UserSource {
diff --git a/src/main/java/org/caosdb/server/accessControl/Mode.java b/src/main/java/org/caosdb/server/accessControl/Mode.java
index 8f91a9ba..d8afc538 100644
--- a/src/main/java/org/caosdb/server/accessControl/Mode.java
+++ b/src/main/java/org/caosdb/server/accessControl/Mode.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public enum Mode {
ONETIME,
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
index f87dd0da..9f7627c4 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectReader;
@@ -36,9 +36,9 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.quartz.SchedulerException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -48,10 +48,11 @@ public class OneTimeAuthenticationToken extends SelfValidatingAuthenticationToke
public static final long DEFAULT_MAX_REPLAYS = 1L;
public static final int DEFAULT_REPLAYS_TIMEOUT_MS =
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_REPLAYS_TIMEOUT_MS));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_ONE_TIME_TOKEN_REPLAYS_TIMEOUT_MS));
public static final int DEFAULT_TIMEOUT_MS =
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS));
public static final String REALM_NAME = "OneTimeAuthenticationToken"; // TODO move to UserSources
public static final Logger LOGGER = LoggerFactory.getLogger(OneTimeAuthenticationToken.class);
@@ -204,7 +205,7 @@ public class OneTimeAuthenticationToken extends SelfValidatingAuthenticationToke
resetConfig();
try (FileInputStream f =
new FileInputStream(
- CaosDBServer.getServerProperty(ServerProperties.KEY_AUTHTOKEN_CONFIG))) {
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTHTOKEN_CONFIG))) {
initConfig(f);
} catch (IOException e) {
LOGGER.error("Could not load the auth token configuration", e);
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
index 20c648b2..1f55d822 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenConsumedInfo.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashMap;
import java.util.Iterator;
diff --git a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
index 46017701..409395ba 100644
--- a/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
+++ b/src/main/java/org/caosdb/server/accessControl/OneTimeTokenToFile.java
@@ -1,10 +1,10 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import com.google.common.io.Files;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
import org.quartz.CronScheduleBuilder;
import org.quartz.Job;
import org.quartz.JobBuilder;
@@ -63,7 +63,7 @@ public class OneTimeTokenToFile implements Job {
.withIdentity(config.toString())
.withSchedule(CronScheduleBuilder.cronSchedule(this.schedule))
.build();
- CaosDBServer.scheduleJob(outputJob, trigger);
+ LinkAheadServer.scheduleJob(outputJob, trigger);
} else {
output(OneTimeAuthenticationToken.generate(config), file);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/Pam.java b/src/main/java/org/caosdb/server/accessControl/Pam.java
index 992665c1..a4d1f99a 100644
--- a/src/main/java/org/caosdb/server/accessControl/Pam.java
+++ b/src/main/java/org/caosdb/server/accessControl/Pam.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,7 +23,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.File;
import java.io.IOException;
@@ -35,9 +35,9 @@ import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.caching.Cache;
import org.jvnet.libpam.PAMException;
import org.jvnet.libpam.UnixUser;
+import org.linkahead.server.caching.Cache;
/**
* PAM UserSource for authenticating users via the Host's pam module.
diff --git a/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java b/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
index dc9137e0..e906a9aa 100644
--- a/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
+++ b/src/main/java/org/caosdb/server/accessControl/PamScriptCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public interface PamScriptCaller {
public boolean isValid(String username, String password);
diff --git a/src/main/java/org/caosdb/server/accessControl/Principal.java b/src/main/java/org/caosdb/server/accessControl/Principal.java
index 7d414455..b0b6e7bb 100644
--- a/src/main/java/org/caosdb/server/accessControl/Principal.java
+++ b/src/main/java/org/caosdb/server/accessControl/Principal.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.HashMap;
-import org.caosdb.server.permissions.ResponsibleAgent;
import org.jdom2.Element;
+import org.linkahead.server.permissions.ResponsibleAgent;
public class Principal implements ResponsibleAgent {
diff --git a/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java b/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
index 1d934310..1b6e4cbd 100644
--- a/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/RealmUsernamePasswordToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/Role.java b/src/main/java/org/caosdb/server/accessControl/Role.java
index d1b04918..5a4035e5 100644
--- a/src/main/java/org/caosdb/server/accessControl/Role.java
+++ b/src/main/java/org/caosdb/server/accessControl/Role.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.Serializable;
import java.util.LinkedList;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.permissions.PermissionRule;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.permissions.PermissionRule;
public class Role implements Serializable {
diff --git a/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java b/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
index 1832563f..842514fd 100644
--- a/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/SelfValidatingAuthenticationToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Arrays;
import java.util.Collection;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.AuthenticationToken;
-import org.caosdb.server.utils.Utils;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.utils.Utils;
/**
* These AuthenticationTokens are characterized by the following properties:
diff --git a/src/main/java/org/caosdb/server/accessControl/SessionToken.java b/src/main/java/org/caosdb/server/accessControl/SessionToken.java
index 760f1195..aa02c5c8 100644
--- a/src/main/java/org/caosdb/server/accessControl/SessionToken.java
+++ b/src/main/java/org/caosdb/server/accessControl/SessionToken.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,12 +23,12 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
/**
* Session tokens are formatted as JSON arrays with the following elements:
@@ -82,7 +82,8 @@ public class SessionToken extends SelfValidatingAuthenticationToken {
private static SessionToken generate(
final Principal principal, final String[] permissions, final String[] roles) {
int timeout =
- Integer.parseInt(CaosDBServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
+ Integer.parseInt(
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
return new SessionToken(principal, timeout, permissions, roles);
}
diff --git a/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java b/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
index 270565be..afe01b91 100644
--- a/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
+++ b/src/main/java/org/caosdb/server/accessControl/SessionTokenRealm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import org.apache.shiro.authc.AuthenticationInfo;
import org.apache.shiro.authc.AuthenticationToken;
diff --git a/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java b/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
index 2c3a3479..9d8936dd 100644
--- a/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
+++ b/src/main/java/org/caosdb/server/accessControl/SinglePermissionSubject.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Collection;
import java.util.Iterator;
diff --git a/src/main/java/org/caosdb/server/accessControl/UserSource.java b/src/main/java/org/caosdb/server/accessControl/UserSource.java
index ff9882bf..204fecb7 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserSource.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserSource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.util.Map;
import java.util.Set;
@@ -37,8 +37,8 @@ import java.util.Set;
* <li>get the default {@link UserStatus} - {@link #getDefaultUserStatus(String)}
* <li>get the default email address - {@link #getDefaultUserEmail(String)}
* <li>retrieve a users roles - {@link #resolveRolesForUsername(String)} The default email and
- * default {@link UserStatus} might be overridden by other settings in CaosDB - that's why they
- * are called "default".
+ * default {@link UserStatus} might be overridden by other settings in LinkAhead - that's why
+ * they are called "default".
*
* <p>Also, the user's roles might be overridden by the internal user source {@link
* InternalUserSource}.
@@ -50,7 +50,7 @@ import java.util.Set;
public interface UserSource {
/**
- * Every UserSource has a unique name, e.g. PAM, CaosDB (which is default name of the internal
+ * Every UserSource has a unique name, e.g. PAM, LinkAhead (which is default name of the internal
* user source {@link InternalUserSource}).
*
* @return name
diff --git a/src/main/java/org/caosdb/server/accessControl/UserSources.java b/src/main/java/org/caosdb/server/accessControl/UserSources.java
index 04c2ecab..7eb945f9 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserSources.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserSources.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import java.io.FileInputStream;
import java.io.IOException;
@@ -34,14 +34,14 @@ import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.config.Ini;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.Role;
-import org.caosdb.server.transaction.LogUserVisitTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.Role;
+import org.linkahead.server.transaction.LogUserVisitTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -53,7 +53,7 @@ import org.slf4j.LoggerFactory;
*
* <ul>
* <li>User name: A string which identifies a user uniquely across one realm. Why is this so?
- * Because it is possible, that two different people from collaborating work groups with
+ * Because it is possible that two different people from collaborating work groups with
* similar names have the same user name in their group e.g. "mueller@uni1.de" and
* "mueller@uni2.de" or two people from different user groups use the name "admin". In the
* "mueller" example the domain name of the email is the realm of authentication.
@@ -95,7 +95,7 @@ public class UserSources extends HashMap<String, UserSource> {
return true;
}
if (principal.toString().equals(AnonymousAuthenticationToken.PRINCIPAL.toString())
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return true;
}
@@ -162,7 +162,7 @@ public class UserSources extends HashMap<String, UserSource> {
this.map = new Ini();
try (final FileInputStream f =
new FileInputStream(
- CaosDBServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE))) {
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE))) {
this.map.load(f);
} catch (final IOException e) {
logger.debug("could not load usersources.ini", e);
@@ -196,6 +196,11 @@ public class UserSources extends HashMap<String, UserSource> {
return null;
}
+ /**
+ * Guess the realm for a user name.
+ *
+ * <p>Returns null if the name can not be found in any UserSource.
+ */
public static String guessRealm(final String username) {
String found = null;
for (final UserSource u : instance.values()) {
@@ -324,7 +329,7 @@ public class UserSources extends HashMap<String, UserSource> {
}
if (principal.getUsername().equals(AnonymousAuthenticationToken.PRINCIPAL.getUsername())
&& principal.getRealm().equals(AnonymousAuthenticationToken.PRINCIPAL.getRealm())
- && CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ && LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true")) {
return true;
}
diff --git a/src/main/java/org/caosdb/server/accessControl/UserStatus.java b/src/main/java/org/caosdb/server/accessControl/UserStatus.java
index 6091d3e1..73859071 100644
--- a/src/main/java/org/caosdb/server/accessControl/UserStatus.java
+++ b/src/main/java/org/caosdb/server/accessControl/UserStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
public enum UserStatus {
ACTIVE,
diff --git a/src/main/java/org/caosdb/server/caching/Cache.java b/src/main/java/org/caosdb/server/caching/Cache.java
index fe5e12c5..9600071d 100644
--- a/src/main/java/org/caosdb/server/caching/Cache.java
+++ b/src/main/java/org/caosdb/server/caching/Cache.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,13 +22,13 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
/**
- * Caching Helper Class used for all caches in the CaosDB Server.
+ * Caching Helper Class used for all caches in the LinkAhead Server.
*
* <p>The actual work is delegated to an instance of {@link JCSCacheHelper}. However, the delegate
* {@link #DELEGATE} can be be overridden for testing purposes with {@link #setDelegate(Cache)}.
diff --git a/src/main/java/org/caosdb/server/caching/CacheHelper.java b/src/main/java/org/caosdb/server/caching/CacheHelper.java
index 0dfd32da..bd21dfc5 100644
--- a/src/main/java/org/caosdb/server/caching/CacheHelper.java
+++ b/src/main/java/org/caosdb/server/caching/CacheHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 IndiScale GmbH
* Copyright (C) 2019 Timm Fitschen (t.fitschen@indiscale.com)
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
diff --git a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
index 1613b8be..176c8909 100644
--- a/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
+++ b/src/main/java/org/caosdb/server/caching/JCSCacheHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@@ -34,8 +34,8 @@ import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
/**
* A CacheHelper implementation which is configured statically via the {@link
@@ -63,8 +63,8 @@ public class JCSCacheHelper implements CacheHelper {
public static void init() {
final boolean disabled =
- Boolean.parseBoolean(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
- init(CaosDBServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC), disabled);
+ Boolean.parseBoolean(LinkAheadServer.getServerProperty(ServerProperties.KEY_CACHE_DISABLE));
+ init(LinkAheadServer.getServerProperty(ServerProperties.KEY_CACHE_CONF_LOC), disabled);
}
public static void init(String configFileLocation, boolean disabled) {
diff --git a/src/main/java/org/caosdb/server/database/BackendTransaction.java b/src/main/java/org/caosdb/server/database/BackendTransaction.java
index 05ea26c2..16b0912f 100644
--- a/src/main/java/org/caosdb/server/database/BackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/BackendTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,119 +19,119 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.HashMap;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteEntityProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeletePassword;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLDeleteUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetAllNames;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetChildren;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetDependentEntities;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetFileRecordByPath;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetIDByName;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetInfo;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLGetUpdateableChecksums;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityDatatype;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertEntityProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLinCon;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertLogRecord;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertParents;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLInsertTransactionHistory;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLIsSubType;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLListRoles;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLListUsers;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveEntityACL;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveLogRecord;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveParents;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePasswordValidator;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrievePermissionRules;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveProperties;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveQueryTemplateDefinition;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetFileCheckedTimestampImpl;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetFileChecksum;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetPassword;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetPermissionRules;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSetQueryTemplateDefinition;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLSyncStats;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateSparseEntity;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateUser;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLUpdateUserRoles;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.utils.UndoHandler;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteEntityProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeletePassword;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLDeleteUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetAllNames;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetChildren;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetDependentEntities;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetFileRecordByPath;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetIDByName;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetInfo;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLGetUpdateableChecksums;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertEntityDatatype;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertEntityProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertLinCon;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertLogRecord;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertParents;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLInsertTransactionHistory;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLIsSubType;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLListRoles;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLListUsers;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLLogUserVisit;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveAll;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveAllUncheckedFiles;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveDatatypes;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveEntityACL;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveLogRecord;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveParents;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrievePasswordValidator;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrievePermissionRules;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveProperties;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveQueryTemplateDefinition;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveRole;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLRetrieveVersionHistory;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetFileCheckedTimestampImpl;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetFileChecksum;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetPassword;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetPermissionRules;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSetQueryTemplateDefinition;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLSyncStats;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateSparseEntity;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateUser;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLUpdateUserRoles;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.utils.UndoHandler;
+import org.linkahead.server.utils.Undoable;
public abstract class BackendTransaction implements Undoable {
diff --git a/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java b/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
index 621fa31c..8fad626c 100644
--- a/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
+++ b/src/main/java/org/caosdb/server/database/CacheableBackendTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.io.Serializable;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public abstract class CacheableBackendTransaction<K, V extends Serializable>
extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/ChainTransaction.java b/src/main/java/org/caosdb/server/database/ChainTransaction.java
index 6adee64a..472ffa7e 100644
--- a/src/main/java/org/caosdb/server/database/ChainTransaction.java
+++ b/src/main/java/org/caosdb/server/database/ChainTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.LinkedList;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
public class ChainTransaction<T extends BackendTransactionImpl> {
private final LinkedList<T> chain = new LinkedList<T>();
diff --git a/src/main/java/org/caosdb/server/database/Database.java b/src/main/java/org/caosdb/server/database/Database.java
index 797aadcc..808b4937 100644
--- a/src/main/java/org/caosdb/server/database/Database.java
+++ b/src/main/java/org/caosdb/server/database/Database.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
public class Database {
diff --git a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
index f12c78e3..002670c9 100644
--- a/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
+++ b/src/main/java/org/caosdb/server/database/DatabaseAccessManager.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -23,22 +23,22 @@
*
* ** end header
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import java.util.concurrent.Semaphore;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.locks.ReentrantLock;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.access.AccessControlAccess;
-import org.caosdb.server.database.access.InfoAccess;
-import org.caosdb.server.database.access.InitAccess;
-import org.caosdb.server.database.access.TransactionAccess;
-import org.caosdb.server.transaction.AccessControlTransaction;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.Initialization;
-import org.caosdb.server.utils.Releasable;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.access.AccessControlAccess;
+import org.linkahead.server.database.access.InfoAccess;
+import org.linkahead.server.database.access.InitAccess;
+import org.linkahead.server.database.access.TransactionAccess;
+import org.linkahead.server.transaction.AccessControlTransaction;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.Initialization;
+import org.linkahead.server.utils.Releasable;
/**
* Acquire and release read access. {@link DatabaseAccessManager} uses this class for managing
@@ -307,7 +307,7 @@ public class DatabaseAccessManager {
}
/**
- * Special access to be used during the {@link Initialization} of the caosdb server.
+ * Special access to be used during the {@link Initialization} of the LinkAhead server.
*
* @param initialization
* @return
diff --git a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
index 1d30bd3f..4e97117d 100644
--- a/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/AbstractAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.util.HashMap;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.transaction.TransactionInterface;
public abstract class AbstractAccess<T extends TransactionInterface> implements Access {
diff --git a/src/main/java/org/caosdb/server/database/access/Access.java b/src/main/java/org/caosdb/server/database/access/Access.java
index 228e8e00..b6fc8a8e 100644
--- a/src/main/java/org/caosdb/server/database/access/Access.java
+++ b/src/main/java/org/caosdb/server/database/access/Access.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.DBHelper;
public interface Access {
diff --git a/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java b/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
index 450f0c61..bc223166 100644
--- a/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/AccessControlAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.transaction.AccessControlTransaction;
+import org.linkahead.server.transaction.AccessControlTransaction;
public class AccessControlAccess extends AbstractAccess<AccessControlTransaction> {
diff --git a/src/main/java/org/caosdb/server/database/access/InfoAccess.java b/src/main/java/org/caosdb/server/database/access/InfoAccess.java
index 3d66e67a..78b7c63e 100644
--- a/src/main/java/org/caosdb/server/database/access/InfoAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/InfoAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.sql.SQLException;
-import org.caosdb.server.utils.Info;
+import org.linkahead.server.utils.Info;
public class InfoAccess extends AbstractAccess<Info> {
diff --git a/src/main/java/org/caosdb/server/database/access/InitAccess.java b/src/main/java/org/caosdb/server/database/access/InitAccess.java
index 1a6108cc..0de69202 100644
--- a/src/main/java/org/caosdb/server/database/access/InitAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/InitAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
import java.sql.SQLException;
-import org.caosdb.server.utils.Initialization;
+import org.linkahead.server.utils.Initialization;
public class InitAccess extends AbstractAccess<Initialization> {
diff --git a/src/main/java/org/caosdb/server/database/access/TransactionAccess.java b/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
index 406d0fb6..2a71659e 100644
--- a/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
+++ b/src/main/java/org/caosdb/server/database/access/TransactionAccess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.access;
+package org.linkahead.server.database.access;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.utils.Releasable;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.utils.Releasable;
public class TransactionAccess extends AbstractAccess<TransactionInterface> {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
index 83c334ac..164101e7 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/ConnectionException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
public class ConnectionException extends Exception {
private static final long serialVersionUID = 6119424337789255870L;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
index 997de314..647b0b06 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseConnectionPool.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.CallableStatement;
@@ -29,9 +29,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import snaq.db.ConnectionPool;
@@ -76,21 +76,21 @@ class DatabaseConnectionPool {
private static synchronized ConnectionPool createConnectionPool()
throws ClassNotFoundException, InstantiationException, IllegalAccessException, SQLException,
- ConnectionException, CaosDBException {
+ ConnectionException, LinkAheadException {
final String url =
"jdbc:mysql://"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_HOST)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_HOST)
+ ":"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_PORT)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_PORT)
+ "/"
- + CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_DATABASE_NAME)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_DATABASE_NAME)
+ "?noAccessToProcedureBodies=true&autoReconnect=true&serverTimezone=UTC&characterEncoding=UTF-8";
- final String user = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_NAME);
- final String pwd = CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_PASSWORD);
+ final String user = LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_NAME);
+ final String pwd = LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_USER_PASSWORD);
final ConnectionPool pool = new ConnectionPool("MySQL Pool", 2, 5, 0, 0, url, user, pwd);
pool.removeShutdownHook();
- CaosDBServer.addPostShutdownHook(
+ LinkAheadServer.addPostShutdownHook(
new Thread("SHUTDOWN_MYSQL_CONNECTION_POOL") {
@Override
public void run() {
@@ -185,10 +185,10 @@ class DatabaseConnectionPool {
* <p>@todo Patch versions are not handled yet.
*/
private static void checkVersion(final Connection con)
- throws SQLException, ConnectionException, CaosDBException {
+ throws SQLException, ConnectionException, LinkAheadException {
try {
final String[] expected_version =
- CaosDBServer.getServerProperty(ServerProperties.KEY_MYSQL_SCHEMA_VERSION)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_MYSQL_SCHEMA_VERSION)
.toLowerCase()
.split("\\.");
final String expected_major = expected_version[0];
@@ -215,7 +215,7 @@ class DatabaseConnectionPool {
actual_version);
} else {
logger.error(
- "Version of the MySQL/MariaDB schema is incompatible.\n\tExpected: {}.{}\n\tActual: {}\nPlease upgrade the CaosDB server.\n\n",
+ "Version of the MySQL/MariaDB schema is incompatible.\n\tExpected: {}.{}\n\tActual: {}\nPlease upgrade the LinkAhead server.\n\n",
expected_major,
expected_minor,
actual_version);
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
index f7d364ae..ae8d77dd 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/DatabaseUtils.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import com.google.common.base.Objects;
import java.sql.ResultSet;
@@ -34,19 +34,19 @@ import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Collectors;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.database.proto.FlatProperty;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Property;
public class DatabaseUtils {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
index f8cba7d4..91f9527f 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLDeleteEntityProperties extends MySQLTransaction
implements DeleteEntityPropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
index 2569226e..fa9228f9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeletePassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLDeletePassword extends MySQLTransaction implements DeletePasswordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
index b0faa45f..770b6832 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteRole.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,15 +21,15 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerMessages;
public class MySQLDeleteRole extends MySQLTransaction implements DeleteRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
index 7fe8ac30..f1e5caba 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLDeleteSparseEntity extends MySQLTransaction implements DeleteSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
index 88b20e4a..2424c468 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLDeleteUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLDeleteUser extends MySQLTransaction implements DeleteUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
index 474048f1..c544f2c5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetAllNames.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
/** Retrieve name, role and acl of all entities from the MySQL backend. */
public class MySQLGetAllNames extends MySQLTransaction implements GetAllNamesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
index 3c1cebf1..c16f5ed3 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetChildren.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetChildren extends MySQLTransaction implements GetChildrenImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
index 9384c8a0..6145b7f5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetDependentEntities.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetDependentEntities extends MySQLTransaction
implements GetDependentEntitiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
index 9b147d28..80dc7aa4 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetFileRecordByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLGetFileRecordByPath extends MySQLTransaction implements GetFileRecordByPathImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
index c2e28cd3..e3eb38c2 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetIDByName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetIDByName extends MySQLTransaction implements GetIDByNameImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
index 2e7a110c..62b1e425 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public class MySQLGetInfo extends MySQLTransaction implements GetInfoImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
index 28c55032..1b270d16 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLGetUpdateableChecksums.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLGetUpdateableChecksums extends MySQLTransaction
implements GetUpdateableChecksumsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
index 568e0e53..503ea244 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.UnsupportedEncodingException;
import java.sql.CallableStatement;
@@ -31,11 +31,11 @@ import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.transaction.ChecksumUpdater;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.transaction.ChecksumUpdater;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransactionInterface;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
index c4cb7cf9..a19490eb 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityDatatype.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLIntegrityConstraintViolationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLInsertEntityDatatype extends MySQLTransaction
implements InsertEntityDatatypeImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
index becb56a2..60dc5d3c 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import static java.sql.Types.BIGINT;
@@ -33,20 +33,20 @@ import java.util.Deque;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.FlatProperty;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.FlatProperty;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Property;
public class MySQLInsertEntityProperties extends MySQLTransaction
implements InsertEntityPropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
index b8ea7872..479c6d9e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
public class MySQLInsertLinCon extends MySQLTransaction implements InsertLinConImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
index 6807808d..5ebfb430 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLInsertLogRecord extends MySQLTransaction implements InsertLogRecordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
index 61a5e8c4..56821b0e 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLInsertParents extends MySQLTransaction implements InsertParentsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
index 66f5a888..1700c7ae 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLInsertRole extends MySQLTransaction implements InsertRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
index 27227926..62bde118 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLInsertSparseEntity extends MySQLTransaction implements InsertSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
index 0832790a..d0e48e3d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLInsertTransactionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLInsertTransactionHistory extends MySQLTransaction
implements InsertTransactionHistoryImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
index f6c2daf8..6304b0f0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLIsSubType.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLIsSubType extends MySQLTransaction implements IsSubTypeImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
index 69ac524e..dce046a9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,17 +19,17 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLListRoles extends MySQLTransaction implements ListRolesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
index 83ebffe6..b9658ae5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLListUsers.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,18 +19,18 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLListUsers extends MySQLTransaction implements ListUsersImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
index 23050da8..9b866ddd 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLLogUserVisit.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,14 +19,14 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLLogUserVisit extends MySQLTransaction implements LogUserVisitImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
index 9a2ea816..f82082d6 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAll.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
@@ -27,13 +27,13 @@ import java.sql.SQLException;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
public class MySQLRetrieveAll extends MySQLTransaction implements RetrieveAllImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
index 09a4e7c2..1a5f151b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveAllUncheckedFiles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Iterator;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLRetrieveAllUncheckedFiles extends MySQLTransaction
implements RetrieveAllUncheckedFilesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
index 68524941..d3f41cc8 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveDatatypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public class MySQLRetrieveDatatypes extends MySQLTransaction implements RetrieveDatatypesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
index 5db8ed75..8a8947ea 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveEntityACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,15 +19,15 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public class MySQLRetrieveEntityACL extends MySQLTransaction implements RetrieveEntityACLImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
index bba36d2e..bec4c245 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.ByteArrayInputStream;
import java.io.IOException;
@@ -32,9 +32,9 @@ import java.util.LinkedList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLRetrieveLogRecord extends MySQLTransaction implements RetrieveLogRecordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
index 1e2a6621..5fdb944a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
import java.util.LinkedList;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveParents extends MySQLTransaction implements RetrieveParentsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
index 9fd7e0a8..144fb524 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.security.NoSuchAlgorithmException;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.HashPasswordValidator;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.HashPasswordValidator;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLRetrievePasswordValidator extends MySQLTransaction
implements RetrievePasswordValidatorImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
index 40767db3..21e407f9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrievePermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Map;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLRetrievePermissionRules extends MySQLTransaction
implements RetrievePermissionRulesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
index 100df4ce..d9ebb771 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
@@ -28,11 +28,11 @@ import java.sql.SQLException;
import java.sql.Types;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveProperties extends MySQLTransaction implements RetrievePropertiesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
index 1ab95ae7..7db88b13 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLRetrieveQueryTemplateDefinition extends MySQLTransaction
implements RetrieveQueryTemplateDefinitionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
index e9ee37c9..f5e56c6b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveRole.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,20 +21,20 @@
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.LinkedList;
import java.util.Map;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLRetrieveRole extends MySQLTransaction implements RetrieveRoleImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
index 48cd84b3..0ff92298 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
/**
* Retrieve a single SparseEntity by id.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
index 40f036f1..85d9ac26 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashSet;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLRetrieveUser extends MySQLTransaction implements RetrieveUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
index 6c4c2629..d7c3b9f6 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLRetrieveVersionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.LinkedList;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
/**
* Transaction to retrieve all versions of an entity.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
index 18d7d9b7..448c1f81 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileCheckedTimestampImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLSetFileCheckedTimestampImpl extends MySQLTransaction
implements SetFileCheckedTimestampImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
index fb6d4188..bcec7504 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetFileChecksum.java
@@ -1,11 +1,11 @@
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
/**
* Implements {@link SetFileChecksumImpl} for a MySQL/MariaDB back-end.
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
index 9972c3af..47dc173d 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.math.BigInteger;
import java.security.MessageDigest;
@@ -28,10 +28,10 @@ import java.security.NoSuchAlgorithmException;
import java.security.SecureRandom;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Utils;
public class MySQLSetPassword extends MySQLTransaction implements SetPasswordImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
index 1569cd49..0cbc11ee 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetPermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
import org.eclipse.jetty.util.ajax.JSON;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class MySQLSetPermissionRules extends MySQLTransaction implements SetPermissionRulesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
index f3ded949..226bd410 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSetQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class MySQLSetQueryTemplateDefinition extends MySQLTransaction
implements SetQueryTemplateDefinitionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
index c874f21b..077c0aef 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLSyncStats.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
@@ -32,10 +32,10 @@ import java.io.ObjectOutputStream;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public class MySQLSyncStats extends MySQLTransaction implements SyncStatsImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
index 5b46579e..f86001b5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public class MySQLTransaction implements BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
index b2d0fb9e..492ab7cb 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.SQLIntegrityConstraintViolationException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class MySQLUpdateSparseEntity extends MySQLTransaction implements UpdateSparseEntityImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
index bd368698..e9ab293c 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class MySQLUpdateUser extends MySQLTransaction implements UpdateUserImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
index 6a52ab9d..590ec57a 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/MySQLUpdateUserRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.Set;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class MySQLUpdateUserRoles extends MySQLTransaction implements UpdateUserRolesImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
index 61e431ba..e604d3b9 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/MySQL/Replacement.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,13 +17,13 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.wrapper.Property;
enum ReplacementStatus implements StatementStatusInterface {
REPLACEMENT
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
index e6b95a99..ab7ddbb0 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckHash.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.Hasher;
public class UnixFileSystemCheckHash extends UnixFileSystemTransaction implements FileCheckHash {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
index c695ff58..4b7d46c5 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemCheckSize.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemCheckSize extends UnixFileSystemTransaction implements FileCheckSize {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
index 908d917c..cd508e17 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileExists.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemFileExists extends UnixFileSystemTransaction implements FileExists {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
index 70c97fec..145df874 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemFileWasModifiedAfter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemFileWasModifiedAfter extends UnixFileSystemTransaction
implements FileWasModifiedAfter {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
index 89c275dd..a98c7f0b 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.util.Arrays;
import java.util.Iterator;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class UnixFileSystemGetFileIterator extends UnixFileSystemTransaction
implements GetFileIteratorImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
index 260a401f..4d2ba2aa 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.transaction.TransactionInterface;
public class UnixFileSystemHelper implements DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
index ccf13744..b1a03f07 100644
--- a/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.UnixFileSystem;
+package org.linkahead.server.database.backend.implementation.UnixFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.BackendTransactionImpl;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.BackendTransactionImpl;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.Message;
public abstract class UnixFileSystemTransaction implements BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
index 8a2dbb0c..b63a2216 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/BackendTransactionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public interface BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
index 1c271bcc..911e015a 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteEntityPropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface DeleteEntityPropertiesImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
index 32c485a9..3f0866aa 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeletePasswordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeletePasswordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
index 0bd6c5c7..bb8b09df 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeleteRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
index 5f1d2ec2..fd7c234b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface DeleteSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
index 3ee0a1e4..05b76cc4 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/DeleteUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface DeleteUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
index edd0718c..6b5f85c5 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckHash.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Hasher;
public interface FileCheckHash extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
index bce32498..9de1c9c3 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileCheckSize.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileCheckSize extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
index 9a5ab664..df0029ce 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileExists.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileExists extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java b/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
index 08fccc58..dad501ed 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/FileWasModifiedAfter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface FileWasModifiedAfter extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
index 9ca7a040..67961f05 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetAllNamesImpl.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.SparseEntity;
/**
* Interface for the retrieval of all known names from the backend.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
index 8b0211a0..2d388a51 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetChildrenImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetChildrenImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
index 00c533df..8a7797dc 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetDependentEntitiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetDependentEntitiesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
index 0b7e4570..32ad37ae 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileIteratorImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Iterator;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface GetFileIteratorImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
index e7f69667..17ad3cdb 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetFileRecordByPathImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public interface GetFileRecordByPathImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
index 02cbc807..8902224f 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetIDByNameImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetIDByNameImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
index d2bb1326..134fecf1 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetInfoImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public interface GetInfoImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
index 762fa2d3..2cd5dadd 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/GetUpdateableChecksumsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface GetUpdateableChecksumsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
index 6da8d5cf..b9f98c5e 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityDatatypeImpl.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface InsertEntityDatatypeImpl extends BackendTransactionImpl, Undoable {
public abstract void execute(SparseEntity entity);
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
index f17643fd..a7f0888b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertEntityPropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.Undoable;
public interface InsertEntityPropertiesImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
index 98ba022e..651ab863 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLinConImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
+import org.linkahead.server.utils.Undoable;
public interface InsertLinConImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
index 78bab8e2..5382f9ea 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertLogRecordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface InsertLogRecordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
index 890ed642..4eae2db1 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertParentsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface InsertParentsImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
index ff305cab..59252dda 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface InsertRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
index 33f46e97..c87f8463 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface InsertSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
index 927238e6..c15bbc16 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/InsertTransactionHistoryImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.utils.Undoable;
public interface InsertTransactionHistoryImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
index 10c18e43..d1c312dc 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/IsSubTypeImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface IsSubTypeImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
index aab9041a..b5f63d0b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/ListRolesImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,10 +19,10 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
+import org.linkahead.server.accessControl.Role;
public interface ListRolesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
index 6bdfda92..a72d5721 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/ListUsersImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,10 +19,10 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.proto.ProtoUser;
public interface ListUsersImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
index 38c253e2..253a6e83 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/LogUserVisitImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,7 +17,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
public interface LogUserVisitImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
index 8e5a5594..869b6089 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveAllImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
index dc247bf6..e9a4d3a2 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveAllUncheckedFilesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Iterator;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
/**
* Retrieve an iterator which iterates over all File entities which need to be consistency-checked.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
index 0886ff43..c3d94ce9 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveDatatypesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
public interface RetrieveDatatypesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
index 230d4d34..3717f5a8 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveEntityACLImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,9 +19,9 @@
*
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.proto.VerySparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
public interface RetrieveEntityACLImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
index b6646d26..e1d09963 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveLogRecordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrieveLogRecordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
index 9f7eba82..6007efb3 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveParentsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.LinkedList;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveParentsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
index 3b3c2851..5c0054af 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePasswordValidatorImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrievePasswordValidatorImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
index cdbb5eb9..40f44c68 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePermissionRulesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.HashSet;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public interface RetrievePermissionRulesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
index 6bf2051a..f65ff2d9 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrievePropertiesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.LinkedList;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityID;
public interface RetrievePropertiesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
index 485b6289..6f6be810 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveQueryTemplateDefinitionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveQueryTemplateDefinitionImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
index 92fde36b..3ba60e18 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveRoleImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface RetrieveRoleImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
index 8b5c516b..e1c26acf 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveSparseEntityImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
index 2ff82863..3dfa0cc5 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public interface RetrieveUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
index 1dbcbfb0..aaff748d 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/RetrieveVersionHistoryImpl.java
@@ -1,8 +1,8 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.HashMap;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
public interface RetrieveVersionHistoryImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
index 8e6a6f2b..989d2dff 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileCheckedTimestampImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public interface SetFileCheckedTimestampImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
index 26cb7ce1..5d1a317b 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetFileChecksumImpl.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
/**
* Store the checksum and timestamp of the checksum for a File entity.
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
index e60f5788..8ef9407f 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPasswordImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface SetPasswordImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
index 89ab9bd1..cf756c2e 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetPermissionRulesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Set;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public interface SetPermissionRulesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
index 53a0032f..9b18dadb 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SetQueryTemplateDefinitionImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public interface SetQueryTemplateDefinitionImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
index d5a15f0e..0192f3a7 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/SyncStatsImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public interface SyncStatsImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
index e7cb2612..9310d97e 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateSparseEntityImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.utils.Undoable;
public interface UpdateSparseEntityImpl extends BackendTransactionImpl, Undoable {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
index eb26002c..2f36361c 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public interface UpdateUserImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
index 891df301..9e04d176 100644
--- a/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
+++ b/src/main/java/org/caosdb/server/database/backend/interfaces/UpdateUserRolesImpl.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.interfaces;
+package org.linkahead.server.database.backend.interfaces;
import java.util.Set;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.exceptions.TransactionException;
public interface UpdateUserRolesImpl extends BackendTransactionImpl {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
index 4072c1b2..628c4c62 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteEntityProperties extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
index f8ebcd2a..122c14a5 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteEntityTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
public class DeleteEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
index 254e4e70..5226c498 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteFile.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.io.IOException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
public class DeleteFile extends BackendTransaction {
@@ -43,7 +43,7 @@ public class DeleteFile extends BackendTransaction {
getUndoHandler().append(this.entity.getFileProperties().deleteFile());
} catch (final IOException e) {
throw new TransactionException(e);
- } catch (final CaosDBException e) {
+ } catch (final LinkAheadException e) {
throw new TransactionException(e);
} catch (final InterruptedException e) {
throw new TransactionException(e);
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
index 402726a9..ba6f3292 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeletePassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeletePasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeletePasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeletePassword extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
index eab8f6f3..117e852a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeleteRole extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
index e371cfe1..697fcc0e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
index 13ea8744..4c64c2d3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/DeleteUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.DeleteUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.DeleteUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class DeleteUser extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java b/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
index 5cece246..1b3436d8 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/FileConsistencyCheck.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.Hasher;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.Hasher;
public class FileConsistencyCheck extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
index 5db82a5e..603dd344 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetAllNames.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
public class GetAllNames extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
index d0e2a809..26d9885b 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetChildren.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetChildrenImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetChildrenImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetChildren extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
index 421fcaae..f5608e9f 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetDependentEntities.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetDependentEntitiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetDependentEntitiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetDependentEntities extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
index c5db6bef..9a391891 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileIterator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Iterator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class GetFileIterator extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
index 8ce0e0e2..1564b35d 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetFileRecordByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,16 +22,16 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetFileRecordByPathImpl;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetFileRecordByPathImpl;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
public class GetFileRecordByPath extends CacheableBackendTransaction<String, SparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
index 7855af4a..057b16e1 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetIDByName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetIDByNameImpl;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetIDByNameImpl;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetIDByName extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
index a1662ec0..337504d3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetInfoImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetInfoImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
public class GetInfo extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java b/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
index a9a8d280..7018628e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/GetUpdateableChecksums.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.GetUpdateableChecksumsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class GetUpdateableChecksums extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
index 382dde55..46641455 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityDatatype.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertEntityDatatypeImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertEntityDatatypeImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.ServerMessages;
public class InsertEntityDatatype extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
index 8de8afc0..c0cbcc7e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertEntityPropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertEntityPropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class InsertEntityProperties extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
index 2846fa64..1c16626f 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertEntityTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,12 +19,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public class InsertEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
index f92dc62b..558458de 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertFile.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.io.IOException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.EntityStatus;
public class InsertFile extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
index 68555010..58844b30 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertLinConImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.LinCon;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertLinConImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.LinCon;
public class InsertLinCon extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
index 3ce27add..fc54582c 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class InsertLogRecord extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
index d71fec92..949981b1 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.utils.EntityStatus;
public class InsertParents extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
index 4ffa7d68..179f3490 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class InsertRole extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
index 9c9c1902..4ece81f8 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertSparseEntityImpl;
-import org.caosdb.server.database.exceptions.IntegrityException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
-import org.caosdb.server.utils.ServerMessages;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertSparseEntityImpl;
+import org.linkahead.server.database.exceptions.IntegrityException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
+import org.linkahead.server.utils.ServerMessages;
public class InsertSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
index 32f62845..866d85c4 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/InsertTransactionHistory.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,17 +19,17 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.InsertTransactionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.InsertTransactionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
/**
* Record the current transaction in the entities transaction history.
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java b/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
index 74045721..be3fad99 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/IsSubType.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.IsSubTypeImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.IsSubTypeImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class IsSubType extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java b/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
index 75792475..83187edd 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/ListRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,12 +19,12 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.ListRolesImpl;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.ListRolesImpl;
public class ListRoles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java b/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
index 9f29a3c5..51f46eb0 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/ListUsers.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,12 +19,12 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.ListUsersImpl;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.ListUsersImpl;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListUsers extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java b/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
index 43fd8749..1a73dfd1 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/LogUserVisit.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,16 +19,16 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashSet;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.LogUserVisitImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.LogUserVisitImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class LogUserVisit extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
index e7f27afc..44357973 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAll.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
public class RetrieveAll extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
index 655e47b8..e261dd41 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveAllUncheckedFiles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Iterator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveAllUncheckedFilesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
public class RetrieveAllUncheckedFiles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
index 1ca9f60e..82698207 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveDatatypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveDatatypesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.Container;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveDatatypesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.Container;
public class RetrieveDatatypes extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
index 8ef143b4..3f97dc41 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveEntityACLTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,14 +19,14 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveEntityACLImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.permissions.EntityACL;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveEntityACLImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.permissions.EntityACL;
public class RetrieveEntityACLTransaction
extends CacheableBackendTransaction<EntityID, VerySparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
index eee73735..4bd29d4e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,25 +22,25 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.container.Container;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.container.Container;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
/**
* Retrieve the full entity from the backend - with all parents, properties, file properties and so
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
index eae8a965..9de77339 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveLogRecord.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveLogRecordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveLogRecordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrieveLogRecord extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
index 262ee271..49aa672a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveParents.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveParentsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.wrapper.Parent;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveParentsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.wrapper.Parent;
// TODO Problem with the caching.
// When an old entity version has a parent which is deleted, the name is
@@ -47,7 +47,7 @@ import org.caosdb.server.entity.wrapper.Parent;
// Changes are necessary in the backend-api, i.e. mysqlbackend and the
// interfaces as well.
//
-// See also a failing test in caosdb-pyinttest:
+// See also a failing test in linkahead-pyinttest:
// tests/test_version.py::test_bug_cached_parent_name_in_old_version
public class RetrieveParents
extends CacheableBackendTransaction<String, LinkedList<VerySparseEntity>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
index d8ea908d..396bbdeb 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePasswordValidator.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrievePasswordValidator extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
index 0ec67561..4cd626f5 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrievePermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashSet;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class RetrievePermissionRules
extends CacheableBackendTransaction<String, HashSet<PermissionRule>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
index f9c11303..c1b2ae94 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,20 +22,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils;
-import org.caosdb.server.database.backend.interfaces.RetrievePropertiesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils;
+import org.linkahead.server.database.backend.interfaces.RetrievePropertiesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
public class RetrieveProperties
extends CacheableBackendTransaction<String, LinkedList<ProtoProperty>> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
index 90a8ac27..47907de3 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class RetrieveQueryTemplateDefinition extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
index f4059832..c44f1852 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveRole.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class RetrieveRole extends CacheableBackendTransaction<String, Role> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
index f1ba8354..a6fbfdf2 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,18 +22,18 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.utils.EntityStatus;
public class RetrieveSparseEntity extends CacheableBackendTransaction<String, SparseEntity> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
index 3ffdee13..8f30b9f1 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,15 +22,15 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class RetrieveUser extends CacheableBackendTransaction<Principal, ProtoUser> {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
index a5079c4e..b1010ee0 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionHistory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class RetrieveVersionHistory extends VersionTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
index 8d0e54c9..aec177ea 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/RetrieveVersionInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class RetrieveVersionInfo extends VersionTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
index a96c0286..e7819305 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileCheckedTimestamp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetFileCheckedTimestampImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
public class SetFileCheckedTimestamp extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
index afca8be4..233b6b94 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetFileChecksum.java
@@ -1,8 +1,8 @@
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetFileChecksumImpl;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetFileChecksumImpl;
+import org.linkahead.server.entity.EntityInterface;
public class SetFileChecksum extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
index a22815ab..0929960e 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetPassword.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetPasswordImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetPasswordImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class SetPassword extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
index 30986303..fbc6d61a 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetPermissionRules.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetPermissionRulesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.permissions.PermissionRule;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetPermissionRulesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.permissions.PermissionRule;
public class SetPermissionRules extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java b/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
index b697b04f..d1ba53da 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SetQueryTemplateDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SetQueryTemplateDefinitionImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
public class SetQueryTemplateDefinition extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java b/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
index d2650aff..3b3c4dff 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/SyncStats.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.SyncStatsImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.utils.ServerStat;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.SyncStatsImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.utils.ServerStat;
public class SyncStats extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
index 39d1c76b..28fa575b 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateEntityTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,13 +19,13 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateEntityTransaction extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
index 837f64b3..c854c2bc 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateSparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
-
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateSparseEntityImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+package org.linkahead.server.database.backend.transaction;
+
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateSparseEntityImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
public class UpdateSparseEntity extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
index 07740f88..9ded2834 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUser.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
public class UpdateUser extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
index bbd23aa9..c90ca027 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/UpdateUserRoles.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.Set;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.UpdateUserRolesImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.UpdateUserRolesImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
public class UpdateUserRoles extends BackendTransaction {
diff --git a/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
index 568528f8..edfde326 100644
--- a/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
+++ b/src/main/java/org/caosdb/server/database/backend/transaction/VersionTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.CacheableBackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.VersionHistoryItem;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Version;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.CacheableBackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrieveVersionHistoryImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.VersionHistoryItem;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Version;
/**
* Abstract base class which retrieves and caches the full, but flat version history. The
diff --git a/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java b/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
index f282a355..a373e3ec 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/EntityDoesNotExistException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class EntityDoesNotExistException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java b/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
index b792cd45..bb84a994 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/EntityWasNotUniqueException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class EntityWasNotUniqueException extends TransactionException {
private static final long serialVersionUID = 5181653214330392866L;
diff --git a/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java b/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
index 440c1e57..2bb55f8e 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/IntegrityException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class IntegrityException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java b/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
index c99fcbbd..45fb8871 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/RolledBackException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class RolledBackException extends TransactionException {
diff --git a/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java b/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
index 6564ed49..7ef4c561 100644
--- a/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
+++ b/src/main/java/org/caosdb/server/database/exceptions/TransactionException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.exceptions;
+package org.linkahead.server.database.exceptions;
public class TransactionException extends RuntimeException {
diff --git a/src/main/java/org/caosdb/server/database/misc/DBHelper.java b/src/main/java/org/caosdb/server/database/misc/DBHelper.java
index 27bd1d08..31304d7e 100644
--- a/src/main/java/org/caosdb/server/database/misc/DBHelper.java
+++ b/src/main/java/org/caosdb/server/database/misc/DBHelper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.TransactionInterface;
public interface DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java b/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
index 1591d858..164d674c 100644
--- a/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
+++ b/src/main/java/org/caosdb/server/database/misc/RollBackHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.utils.UndoHandler;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.utils.UndoHandler;
public class RollBackHandler extends UndoHandler implements DBHelper {
diff --git a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
index 397a1f52..ae3f9c13 100644
--- a/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
+++ b/src/main/java/org/caosdb/server/database/misc/TransactionBenchmark.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.misc;
+package org.linkahead.server.database.misc;
import java.io.Serializable;
import java.util.ArrayList;
@@ -33,15 +33,15 @@ import java.util.Map;
import java.util.Map.Entry;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.utils.CronJob;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.ServerStat;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.utils.CronJob;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.ServerStat;
class Counter implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private int c;
public Counter(int initial) {
@@ -58,7 +58,7 @@ class Counter implements Serializable {
}
class Timer implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private long c;
public Timer(long initial) {
@@ -80,7 +80,7 @@ class Timer implements Serializable {
* Measurement object knows nothing about other Measurement objects.
*/
class Measurement implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private final Timer timer;
private final Counter counter;
private final String name;
@@ -130,7 +130,7 @@ class Measurement implements Serializable {
class RootBenchmark extends TransactionBenchmark implements ServerStat {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private transient boolean synced = false;
/**
* Fetch old data (from before last shutdown) and fill it into this instance.
@@ -208,7 +208,7 @@ class RootBenchmark extends TransactionBenchmark implements ServerStat {
class SubBenchmark extends TransactionBenchmark {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private final String name;
public SubBenchmark(String name) {
@@ -270,12 +270,12 @@ class JdomConverter {
*/
public abstract class TransactionBenchmark implements Serializable {
- private static final long serialVersionUID = -95212746021180579L;
+ private static final long serialVersionUID = -4023348648910860772L;
private static final TransactionBenchmark rootService = new RootBenchmark().init();
public final transient Logger logger = LogManager.getLogger(getClass());
protected static final transient boolean isActive =
Boolean.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_TRANSACTION_BENCHMARK_ENABLED)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_TRANSACTION_BENCHMARK_ENABLED)
.toLowerCase());
protected StackTraceElement[] stackTraceElements;
@@ -459,11 +459,11 @@ public abstract class TransactionBenchmark implements Serializable {
/**
* Return a nice String for the StackTraceElement.
*
- * <p>The String is composed like this: CLASS::METHOD [LINE_NUMBER], with "org.caosdb.server."
+ * <p>The String is composed like this: CLASS::METHOD [LINE_NUMBER], with "org.linkahead.server."
* removed from the class name.
*/
private static String prettifyStackTraceElement(final StackTraceElement ste) {
- return ste.getClassName().replaceFirst("caosdb\\.server\\.", "")
+ return ste.getClassName().replaceFirst("linkahead\\.server\\.", "")
+ "::"
+ ste.getMethodName().replaceAll("[<>]", "")
+ " ["
diff --git a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
index b92d3def..3acee6d4 100644
--- a/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/FlatProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/database/proto/LinCon.java b/src/main/java/org/caosdb/server/database/proto/LinCon.java
index 719e7602..041fc420 100644
--- a/src/main/java/org/caosdb/server/database/proto/LinCon.java
+++ b/src/main/java/org/caosdb/server/database/proto/LinCon.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
public class LinCon {
public final long signature_from;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java b/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
index 31d58986..e3a2da8e 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoGroup.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.HashSet;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java b/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
index e8486e2f..c0521170 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
public class ProtoInfo {
public Integer recordsCount = null;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
index 7a11cd4d..d0dae166 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.List;
diff --git a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
index 643f4250..67f7306d 100644
--- a/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
+++ b/src/main/java/org/caosdb/server/database/proto/ProtoUser.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,11 +21,11 @@
*
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.HashSet;
-import org.caosdb.server.accessControl.UserStatus;
+import org.linkahead.server.accessControl.UserStatus;
public class ProtoUser implements Serializable {
diff --git a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
index d2292c58..82e3905a 100644
--- a/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/SparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
/**
* Rather abstract representation of a sparse Entity used by the data base abstraction layer.
diff --git a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
index 4c0a60ce..37db0947 100644
--- a/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
+++ b/src/main/java/org/caosdb/server/database/proto/VersionHistoryItem.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
import java.util.List;
diff --git a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
index 8f32bf52..e39f5211 100644
--- a/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
+++ b/src/main/java/org/caosdb/server/database/proto/VerySparseEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.proto;
+package org.linkahead.server.database.proto;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java b/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
index cbd822ee..15469495 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractCollectionDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.HashMap;
import java.util.regex.Matcher;
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java b/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
index 583145fb..15c2a1c0 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.HashMap;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.Container;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.Container;
import org.reflections.Reflections;
public abstract class AbstractDatatype {
@@ -87,7 +87,7 @@ public abstract class AbstractDatatype {
}
private static void loadClasses() throws Exception {
- final Reflections datatypePackage = new Reflections("org.caosdb.server.datatype");
+ final Reflections datatypePackage = new Reflections("org.linkahead.server.datatype");
for (final Class<? extends AbstractDatatype> c :
datatypePackage.getSubTypesOf(AbstractDatatype.class)) {
if (c.isAnnotationPresent(DatatypeDefinition.class)) {
diff --git a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
index be880025..16b3721e 100644
--- a/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
+++ b/src/main/java/org/caosdb/server/datatype/AbstractEnumValue.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public abstract class AbstractEnumValue implements SingleValue {
diff --git a/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java b/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
index 366b7793..a1fcac3c 100644
--- a/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/BooleanDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Boolean")
public class BooleanDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/BooleanValue.java b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
index 2bcbb48b..eb312f58 100644
--- a/src/main/java/org/caosdb/server/datatype/BooleanValue.java
+++ b/src/main/java/org/caosdb/server/datatype/BooleanValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public class BooleanValue extends AbstractEnumValue {
- private static CaosEnum caosEnum = new CaosEnum("TRUE", "FALSE");
+ private static LinkAheadEnum linkAheadEnum = new LinkAheadEnum("TRUE", "FALSE");
private BooleanValue(final EnumElement e) {
super(e);
}
public static BooleanValue valueOf(final String s) {
- return new BooleanValue(caosEnum.valueOf(s));
+ return new BooleanValue(linkAheadEnum.valueOf(s));
}
public static BooleanValue valueOf(final boolean b) {
diff --git a/src/main/java/org/caosdb/server/datatype/CaosEnum.java b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
index 00d8cb16..03f4afd9 100644
--- a/src/main/java/org/caosdb/server/datatype/CaosEnum.java
+++ b/src/main/java/org/caosdb/server/datatype/CaosEnum.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
import java.util.TreeSet;
@@ -59,15 +59,15 @@ class EnumElement implements Comparable<EnumElement> {
}
}
-public class CaosEnum {
+public class LinkAheadEnum {
final boolean case_sensitive; // for string operations
- public CaosEnum(final String... values) {
+ public LinkAheadEnum(final String... values) {
this(false, values);
}
- public CaosEnum(final boolean case_sensitive, final String... values) {
+ public LinkAheadEnum(final boolean case_sensitive, final String... values) {
this.case_sensitive = case_sensitive;
int index = 0;
for (String v : values) {
diff --git a/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java b/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
index 1f80d937..21a946ab 100644
--- a/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
+++ b/src/main/java/org/caosdb/server/datatype/CollectionDatatypeFactory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public interface CollectionDatatypeFactory {
diff --git a/src/main/java/org/caosdb/server/datatype/CollectionValue.java b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
index fc94f660..f81e0af5 100644
--- a/src/main/java/org/caosdb/server/datatype/CollectionValue.java
+++ b/src/main/java/org/caosdb/server/datatype/CollectionValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.ArrayList;
import java.util.Collections;
diff --git a/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java b/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
index b28ce312..81d27fa3 100644
--- a/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
+++ b/src/main/java/org/caosdb/server/datatype/DatatypeDefinition.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
diff --git a/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java b/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
index 9c66f425..2b55ad06 100644
--- a/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/DateTimeDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.datetime.Date;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.datetime.Date;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "DateTime")
public class DateTimeDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java b/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
index f3f17ace..f20a56f7 100644
--- a/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/DoubleDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,10 +21,10 @@
* ** end header
*/
// Copyright (c) 2019 Daniel Hornung
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Double")
public class DoubleDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/FileDatatype.java b/src/main/java/org/caosdb/server/datatype/FileDatatype.java
index febc317d..30d2c9ae 100644
--- a/src/main/java/org/caosdb/server/datatype/FileDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/FileDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
@DatatypeDefinition(name = "File")
public class FileDatatype extends ReferenceDatatype {}
diff --git a/src/main/java/org/caosdb/server/datatype/GenericValue.java b/src/main/java/org/caosdb/server/datatype/GenericValue.java
index a4b1b0b1..c9962c90 100644
--- a/src/main/java/org/caosdb/server/datatype/GenericValue.java
+++ b/src/main/java/org/caosdb/server/datatype/GenericValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import com.google.common.base.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class GenericValue implements SingleValue {
Object value;
diff --git a/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java b/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
index ec9280c3..e69bca17 100644
--- a/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
+++ b/src/main/java/org/caosdb/server/datatype/IndexedSingleValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
public class IndexedSingleValue implements SingleValue, Comparable<IndexedSingleValue> {
diff --git a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
index f3a58a4a..90bc4c7c 100644
--- a/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/IntegerDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Integer")
public class IntegerDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ListDatatype.java b/src/main/java/org/caosdb/server/datatype/ListDatatype.java
index bdf148e6..8ee15b8f 100644
--- a/src/main/java/org/caosdb/server/datatype/ListDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/ListDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
public class ListDatatype extends AbstractCollectionDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java b/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
index d1999f13..15dc3218 100644
--- a/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
+++ b/src/main/java/org/caosdb/server/datatype/ListDatatypeFactory.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public class ListDatatypeFactory implements CollectionDatatypeFactory {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
index 769d3ebd..1ab0ab00 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
@DatatypeDefinition(name = "Reference")
public class ReferenceDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
index 503e4679..1711ccb0 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceDatatype2.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
public class ReferenceDatatype2 extends ReferenceDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
index a24e2ddf..3655af9c 100644
--- a/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
+++ b/src/main/java/org/caosdb/server/datatype/ReferenceValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -25,15 +25,15 @@
*/
/** @review Daniel Hornung 2022-03-04 */
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import java.util.Objects;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
/**
* A ReferenceValue represents the value of a reference property to another entity.
diff --git a/src/main/java/org/caosdb/server/datatype/SingleValue.java b/src/main/java/org/caosdb/server/datatype/SingleValue.java
index cfe2b640..7d96d6fc 100644
--- a/src/main/java/org/caosdb/server/datatype/SingleValue.java
+++ b/src/main/java/org/caosdb/server/datatype/SingleValue.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
public interface SingleValue extends Value {
diff --git a/src/main/java/org/caosdb/server/datatype/TextDatatype.java b/src/main/java/org/caosdb/server/datatype/TextDatatype.java
index 3b32fadc..49b226e4 100644
--- a/src/main/java/org/caosdb/server/datatype/TextDatatype.java
+++ b/src/main/java/org/caosdb/server/datatype/TextDatatype.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
@DatatypeDefinition(name = "Text")
public class TextDatatype extends AbstractDatatype {
diff --git a/src/main/java/org/caosdb/server/datatype/Value.java b/src/main/java/org/caosdb/server/datatype/Value.java
index a2612fb3..d7e7c64a 100644
--- a/src/main/java/org/caosdb/server/datatype/Value.java
+++ b/src/main/java/org/caosdb/server/datatype/Value.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/Affiliation.java b/src/main/java/org/caosdb/server/entity/Affiliation.java
index f3e5ec73..4bd145bb 100644
--- a/src/main/java/org/caosdb/server/entity/Affiliation.java
+++ b/src/main/java/org/caosdb/server/entity/Affiliation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public enum Affiliation {
INSTANTIATION, // RECORD is-a RECORD TYPE
diff --git a/src/main/java/org/caosdb/server/entity/ClientMessage.java b/src/main/java/org/caosdb/server/entity/ClientMessage.java
index f6b99677..41780d51 100644
--- a/src/main/java/org/caosdb/server/entity/ClientMessage.java
+++ b/src/main/java/org/caosdb/server/entity/ClientMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -21,7 +21,7 @@
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Map;
diff --git a/src/main/java/org/caosdb/server/entity/DeleteEntity.java b/src/main/java/org/caosdb/server/entity/DeleteEntity.java
index 38e8385a..05e5eba3 100644
--- a/src/main/java/org/caosdb/server/entity/DeleteEntity.java
+++ b/src/main/java/org/caosdb/server/entity/DeleteEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class DeleteEntity extends Entity {
diff --git a/src/main/java/org/caosdb/server/entity/Entity.java b/src/main/java/org/caosdb/server/entity/Entity.java
index 614397c5..dee98676 100644
--- a/src/main/java/org/caosdb/server/entity/Entity.java
+++ b/src/main/java/org/caosdb/server/entity/Entity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.ArrayList;
import java.util.HashMap;
@@ -34,33 +34,33 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.EntityToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.EntityToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public abstract class Entity extends AbstractObservable implements EntityInterface {
@@ -290,7 +290,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
return;
}
if (this.entityStatus == EntityStatus.UNQUALIFIED) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"It is not allowed to change the state again, once an UNQUALIFIED state has been reached.");
}
this.entityStatus = entityStatus;
@@ -488,7 +488,7 @@ public abstract class Entity extends AbstractObservable implements EntityInterfa
* cuid setter.
*
* @param cuid
- * @throws CaosDBException if one tried to set it once again.
+ * @throws LinkAheadException if one tried to set it once again.
*/
@Override
public final void setCuid(final String cuid) {
diff --git a/src/main/java/org/caosdb/server/entity/EntityID.java b/src/main/java/org/caosdb/server/entity/EntityID.java
index 6a2d2ca3..2c3aa186 100644
--- a/src/main/java/org/caosdb/server/entity/EntityID.java
+++ b/src/main/java/org/caosdb/server/entity/EntityID.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.io.Serializable;
import java.util.Objects;
diff --git a/src/main/java/org/caosdb/server/entity/EntityInterface.java b/src/main/java/org/caosdb/server/entity/EntityInterface.java
index ba77b5c4..85d24734 100644
--- a/src/main/java/org/caosdb/server/entity/EntityInterface.java
+++ b/src/main/java/org/caosdb/server/entity/EntityInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobTarget;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobTarget;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public interface EntityInterface
extends JobTarget, Observable, ToElementable, WriteEntity, TransactionEntity {
diff --git a/src/main/java/org/caosdb/server/entity/FileProperties.java b/src/main/java/org/caosdb/server/entity/FileProperties.java
index eaf4246f..b985e6ec 100644
--- a/src/main/java/org/caosdb/server/entity/FileProperties.java
+++ b/src/main/java/org/caosdb/server/entity/FileProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.io.File;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.UndoHandler;
-import org.caosdb.server.utils.Undoable;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.UndoHandler;
+import org.linkahead.server.utils.Undoable;
public class FileProperties {
private File thumbnail = null;
@@ -176,7 +176,8 @@ public class FileProperties {
return ret;
}
- public Undoable deleteFile() throws Message, IOException, InterruptedException, CaosDBException {
+ public Undoable deleteFile()
+ throws Message, IOException, InterruptedException, LinkAheadException {
final File file = new File(FileSystem.getPath(this.path));
final File thumbnail = new File(getThumbnailPath(file));
@@ -210,7 +211,7 @@ public class FileProperties {
} else if (file.getCanonicalPath().startsWith(FileSystem.getBasepath())) {
d = FileUtils.delete(file, file.isDirectory());
} else {
- throw new CaosDBException(
+ throw new LinkAheadException(
"File is in Filesystem, but it is neither a normal file nor a symlink.");
}
if (parent != null && parent.listFiles() != null && parent.listFiles().length == 0) {
@@ -226,14 +227,14 @@ public class FileProperties {
}
public File retrieveFromFileSystem()
- throws IOException, CaosDBException, NoSuchAlgorithmException {
+ throws IOException, LinkAheadException, NoSuchAlgorithmException {
if (this.file != null) {
return this.file;
}
if (hasPath()) {
final File f = FileSystem.getFromFileSystem(getPath());
if (f == null) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"File not in file system. File system is not consistent with the data base!!! "
+ getPath());
}
diff --git a/src/main/java/org/caosdb/server/entity/InsertEntity.java b/src/main/java/org/caosdb/server/entity/InsertEntity.java
index b88b319f..57cd43eb 100644
--- a/src/main/java/org/caosdb/server/entity/InsertEntity.java
+++ b/src/main/java/org/caosdb/server/entity/InsertEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/MagicTypes.java b/src/main/java/org/caosdb/server/entity/MagicTypes.java
index 39556385..fcc4d251 100644
--- a/src/main/java/org/caosdb/server/entity/MagicTypes.java
+++ b/src/main/java/org/caosdb/server/entity/MagicTypes.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Objects;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.transaction.Retrieve;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.transaction.Retrieve;
/** Some types correspond to entities in the database with magic IDs. */
public enum MagicTypes {
diff --git a/src/main/java/org/caosdb/server/entity/Message.java b/src/main/java/org/caosdb/server/entity/Message.java
index fca60245..e85d874b 100644
--- a/src/main/java/org/caosdb/server/entity/Message.java
+++ b/src/main/java/org/caosdb/server/entity/Message.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.ServerMessages;
public class Message extends Exception implements Comparable<Message>, ToElementable {
diff --git a/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java b/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
index 31d79a6d..ad2738b0 100644
--- a/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
+++ b/src/main/java/org/caosdb/server/entity/NoSuchRoleException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class NoSuchRoleException extends IllegalArgumentException {
diff --git a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
index 2d1ca6f2..a61b87ba 100644
--- a/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
+++ b/src/main/java/org/caosdb/server/entity/RetrieveEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
public class RetrieveEntity extends Entity {
diff --git a/src/main/java/org/caosdb/server/entity/Role.java b/src/main/java/org/caosdb/server/entity/Role.java
index f86158a9..1e2cc28a 100644
--- a/src/main/java/org/caosdb/server/entity/Role.java
+++ b/src/main/java/org/caosdb/server/entity/Role.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.HashMap;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.entity.xml.EntityToElementStrategy;
-import org.caosdb.server.entity.xml.FileToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.entity.xml.EntityToElementStrategy;
+import org.linkahead.server.entity.xml.FileToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
public enum Role {
RecordType,
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatus.java b/src/main/java/org/caosdb/server/entity/StatementStatus.java
index 83d0c57e..92840787 100644
--- a/src/main/java/org/caosdb/server/entity/StatementStatus.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
/**
* The statement status has two purposes:
diff --git a/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
index d1596afd..102802fc 100644
--- a/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
+++ b/src/main/java/org/caosdb/server/entity/StatementStatusInterface.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2023 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2023 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,12 +17,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
/**
* Interface for the StatementStatus. This may be used by back-end implementations to use back-end
* specific implementations (e.g.
- * org.caosdb.server.database.backend.implementation.MySQL.ReplacementStatus).
+ * org.linkahead.server.database.backend.implementation.MySQL.ReplacementStatus).
*/
public interface StatementStatusInterface {
public String name();
diff --git a/src/main/java/org/caosdb/server/entity/TransactionEntity.java b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
index 97610622..8e450f19 100644
--- a/src/main/java/org/caosdb/server/entity/TransactionEntity.java
+++ b/src/main/java/org/caosdb/server/entity/TransactionEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
public interface TransactionEntity {
diff --git a/src/main/java/org/caosdb/server/entity/UpdateEntity.java b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
index 45df0aba..17fe68c0 100644
--- a/src/main/java/org/caosdb/server/entity/UpdateEntity.java
+++ b/src/main/java/org/caosdb/server/entity/UpdateEntity.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,11 +19,11 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
/**
* UpdateEntity class represents entities which are to be updated. The previous version is appeded
diff --git a/src/main/java/org/caosdb/server/entity/Version.java b/src/main/java/org/caosdb/server/entity/Version.java
index 5529c7c5..e1005828 100644
--- a/src/main/java/org/caosdb/server/entity/Version.java
+++ b/src/main/java/org/caosdb/server/entity/Version.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,10 +18,10 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import java.util.List;
-import org.caosdb.datetime.UTCDateTime;
+import org.linkahead.datetime.UTCDateTime;
/**
* Plain old java object (POJO) for an entity's version.
diff --git a/src/main/java/org/caosdb/server/entity/WritableEntity.java b/src/main/java/org/caosdb/server/entity/WritableEntity.java
index 6c967cc4..42e5e72c 100644
--- a/src/main/java/org/caosdb/server/entity/WritableEntity.java
+++ b/src/main/java/org/caosdb/server/entity/WritableEntity.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/WriteEntity.java b/src/main/java/org/caosdb/server/entity/WriteEntity.java
index 64cbbee8..6aea615f 100644
--- a/src/main/java/org/caosdb/server/entity/WriteEntity.java
+++ b/src/main/java/org/caosdb/server/entity/WriteEntity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/container/Container.java b/src/main/java/org/caosdb/server/entity/container/Container.java
index 1618fbed..0231f149 100644
--- a/src/main/java/org/caosdb/server/entity/container/Container.java
+++ b/src/main/java/org/caosdb/server/entity/container/Container.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.ArrayList;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
public class Container<T extends EntityInterface> extends ArrayList<T> {
diff --git a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
index a8c3e6a8..c6b84e1a 100644
--- a/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/EntityByIdContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.EntityID;
+import org.linkahead.server.entity.EntityID;
public abstract class EntityByIdContainer extends TransactionContainer {
private static final long serialVersionUID = 7997517210502207523L;
diff --git a/src/main/java/org/caosdb/server/entity/container/ParentContainer.java b/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
index 896a355c..6a6b36f5 100644
--- a/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/ParentContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.xml.ParentToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.xml.ParentToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
public class ParentContainer extends Container<Parent> {
diff --git a/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java b/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
index 2a6593d1..67d779bc 100644
--- a/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/PropertyContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,22 +22,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategy;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategy;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
public class PropertyContainer extends Container<Property> {
diff --git a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
index bc0da7c1..0016820c 100644
--- a/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/RetrieveContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
public class RetrieveContainer extends EntityByIdContainer {
diff --git a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
index d3963455..be259468 100644
--- a/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/TransactionContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobTarget;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobTarget;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
public class TransactionContainer extends Container<EntityInterface>
implements ToElementable, JobTarget {
@@ -106,7 +106,7 @@ public class TransactionContainer extends Container<EntityInterface>
@Override
public void addToElement(final Element element) {
element.setAttribute("count", Integer.toString(size()));
- if (this.benchmark != null && CaosDBServer.isDebugMode()) {
+ if (this.benchmark != null && LinkAheadServer.isDebugMode()) {
element.addContent(this.benchmark.toElement());
}
for (final ToElementable m : this.messages) {
diff --git a/src/main/java/org/caosdb/server/entity/container/WritableContainer.java b/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
index fcc8de4e..a8c43f99 100644
--- a/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
+++ b/src/main/java/org/caosdb/server/entity/container/WritableContainer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,12 +19,12 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import java.util.HashMap;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.server.entity.FileProperties;
public class WritableContainer extends TransactionContainer {
private static final long serialVersionUID = -4097777313518959519L;
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
index b294a17e..ec8b5a85 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/EntityWrapper.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,36 +22,36 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.database.proto.VerySparseEntity;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.Version;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.PropertyContainer;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.entity.xml.ToElementStrategy;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query.Selection;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.TransactionLogMessage;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.database.proto.VerySparseEntity;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.Version;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.PropertyContainer;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.entity.xml.ToElementStrategy;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query.Selection;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.TransactionLogMessage;
+import org.linkahead.unit.Unit;
public abstract class EntityWrapper implements EntityInterface {
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Parent.java b/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
index a2116ac3..4cec7739 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Parent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
-import org.caosdb.server.entity.Affiliation;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.xml.ParentToElementStrategy;
+import org.linkahead.server.entity.Affiliation;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.xml.ParentToElementStrategy;
public class Parent extends EntityWrapper {
diff --git a/src/main/java/org/caosdb/server/entity/wrapper/Property.java b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
index 9268d7f3..0755928a 100644
--- a/src/main/java/org/caosdb/server/entity/wrapper/Property.java
+++ b/src/main/java/org/caosdb/server/entity/wrapper/Property.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.entity.wrapper;
+package org.linkahead.server.entity.wrapper;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.proto.ProtoProperty;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.xml.PropertyToElementStrategy;
+import org.linkahead.server.database.proto.ProtoProperty;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.xml.PropertyToElementStrategy;
public class Property extends EntityWrapper {
diff --git a/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
index 94801192..d6a223a7 100644
--- a/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/DomainToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,10 +22,10 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
/**
* Generates a JDOM (XML) representation of an entity with role "Domain".
diff --git a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
index 35d94aa7..a98969a4 100644
--- a/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/EntityToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,18 +22,18 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.TransactionLogMessage;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.TransactionLogMessage;
/**
* Base class for the generation of a JDOM (XML) representation for entities.
diff --git a/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
index 28815980..fca711d2 100644
--- a/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/FileToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
public class FileToElementStrategy extends EntityToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java b/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
index 42f7eef9..fa2ec298 100644
--- a/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/IdAndServerMessagesOnlyStrategy.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
/**
* Special purpose subclass of {@link SerializeFieldStrategy} which only serializes the id and the
diff --git a/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
index 2556fdb2..a61597f4 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ParentToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.wrapper.Parent;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.wrapper.Parent;
/**
* Generates a JDOM (XML) representation of an entity's parent.
diff --git a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
index 7109a0d8..ab5b60b8 100644
--- a/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/PropertyToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
import org.jdom2.Attribute;
import org.jdom2.Element;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
public class PropertyToElementStrategy extends EntityToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java b/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
index 30210118..fcca353d 100644
--- a/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/SerializeFieldStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,14 +22,14 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
/**
* A class which decides whether the properties, parents, name, etc. of an entity are to be included
diff --git a/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java b/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
index 01e114a2..79359cbf 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ToElementStrategy.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
public interface ToElementStrategy {
diff --git a/src/main/java/org/caosdb/server/entity/xml/ToElementable.java b/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
index 4202111b..82b110b2 100644
--- a/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
+++ b/src/main/java/org/caosdb/server/entity/xml/ToElementable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
index 40d19a5f..8184b6c6 100644
--- a/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
+++ b/src/main/java/org/caosdb/server/entity/xml/VersionXMLSerializer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,11 +18,11 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import java.util.TimeZone;
-import org.caosdb.server.entity.Version;
import org.jdom2.Element;
+import org.linkahead.server.entity.Version;
/**
* Creates a JDOM Element for a Version instance.
diff --git a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
index 88429828..417dc2cd 100644
--- a/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/AccessControlManagementServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Status;
import io.grpc.StatusException;
@@ -30,56 +30,56 @@ import java.util.List;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.UnauthorizedException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.acm.v1alpha1.AccessControlManagementServiceGrpc.AccessControlManagementServiceImplBase;
-import org.caosdb.api.acm.v1alpha1.CreateSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.CreateSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.CreateSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.CreateSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.DeleteSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.EmailSetting;
-import org.caosdb.api.acm.v1alpha1.EntitySetting;
-import org.caosdb.api.acm.v1alpha1.ListKnownPermissionsRequest;
-import org.caosdb.api.acm.v1alpha1.ListKnownPermissionsResponse;
-import org.caosdb.api.acm.v1alpha1.ListRoleItem;
-import org.caosdb.api.acm.v1alpha1.ListRolesRequest;
-import org.caosdb.api.acm.v1alpha1.ListRolesResponse;
-import org.caosdb.api.acm.v1alpha1.ListUsersRequest;
-import org.caosdb.api.acm.v1alpha1.ListUsersResponse;
-import org.caosdb.api.acm.v1alpha1.PermissionDescription;
-import org.caosdb.api.acm.v1alpha1.PermissionRule;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.RetrieveSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.RoleCapabilities;
-import org.caosdb.api.acm.v1alpha1.RolePermissions;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleRoleRequest;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleRoleResponse;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleUserRequest;
-import org.caosdb.api.acm.v1alpha1.UpdateSingleUserResponse;
-import org.caosdb.api.acm.v1alpha1.User;
-import org.caosdb.api.acm.v1alpha1.UserCapabilities;
-import org.caosdb.api.acm.v1alpha1.UserPermissions;
-import org.caosdb.api.acm.v1alpha1.UserStatus;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.transaction.DeleteRoleTransaction;
-import org.caosdb.server.transaction.DeleteUserTransaction;
-import org.caosdb.server.transaction.InsertRoleTransaction;
-import org.caosdb.server.transaction.InsertUserTransaction;
-import org.caosdb.server.transaction.ListRolesTransaction;
-import org.caosdb.server.transaction.ListUsersTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.transaction.UpdateRoleTransaction;
-import org.caosdb.server.transaction.UpdateUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.acm.v1alpha1.AccessControlManagementServiceGrpc.AccessControlManagementServiceImplBase;
+import org.linkahead.api.acm.v1alpha1.CreateSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.CreateSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.CreateSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.CreateSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.DeleteSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.EmailSetting;
+import org.linkahead.api.acm.v1alpha1.EntitySetting;
+import org.linkahead.api.acm.v1alpha1.ListKnownPermissionsRequest;
+import org.linkahead.api.acm.v1alpha1.ListKnownPermissionsResponse;
+import org.linkahead.api.acm.v1alpha1.ListRoleItem;
+import org.linkahead.api.acm.v1alpha1.ListRolesRequest;
+import org.linkahead.api.acm.v1alpha1.ListRolesResponse;
+import org.linkahead.api.acm.v1alpha1.ListUsersRequest;
+import org.linkahead.api.acm.v1alpha1.ListUsersResponse;
+import org.linkahead.api.acm.v1alpha1.PermissionDescription;
+import org.linkahead.api.acm.v1alpha1.PermissionRule;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.RetrieveSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.RoleCapabilities;
+import org.linkahead.api.acm.v1alpha1.RolePermissions;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleRoleRequest;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleRoleResponse;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleUserRequest;
+import org.linkahead.api.acm.v1alpha1.UpdateSingleUserResponse;
+import org.linkahead.api.acm.v1alpha1.User;
+import org.linkahead.api.acm.v1alpha1.UserCapabilities;
+import org.linkahead.api.acm.v1alpha1.UserPermissions;
+import org.linkahead.api.acm.v1alpha1.UserStatus;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.transaction.DeleteRoleTransaction;
+import org.linkahead.server.transaction.DeleteUserTransaction;
+import org.linkahead.server.transaction.InsertRoleTransaction;
+import org.linkahead.server.transaction.InsertUserTransaction;
+import org.linkahead.server.transaction.ListRolesTransaction;
+import org.linkahead.server.transaction.ListUsersTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.transaction.UpdateRoleTransaction;
+import org.linkahead.server.transaction.UpdateUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class AccessControlManagementServiceImpl extends AccessControlManagementServiceImplBase {
@@ -98,16 +98,16 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private org.caosdb.server.accessControl.UserStatus convert(UserStatus status) {
+ private org.linkahead.server.accessControl.UserStatus convert(UserStatus status) {
switch (status) {
case USER_STATUS_ACTIVE:
- return org.caosdb.server.accessControl.UserStatus.ACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.ACTIVE;
case USER_STATUS_INACTIVE:
- return org.caosdb.server.accessControl.UserStatus.INACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.INACTIVE;
default:
break;
}
- return org.caosdb.server.accessControl.UserStatus.INACTIVE;
+ return org.linkahead.server.accessControl.UserStatus.INACTIVE;
}
private ListUsersResponse convertUsers(List<ProtoUser> users) {
@@ -138,7 +138,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private UserStatus convert(org.caosdb.server.accessControl.UserStatus status) {
+ private UserStatus convert(org.linkahead.server.accessControl.UserStatus status) {
switch (status) {
case ACTIVE:
return UserStatus.USER_STATUS_ACTIVE;
@@ -149,7 +149,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
}
}
- private Role convert(org.caosdb.api.acm.v1alpha1.Role role) {
+ private Role convert(org.linkahead.api.acm.v1alpha1.Role role) {
Role result = new Role();
result.name = role.getName();
@@ -158,18 +158,18 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
return result;
}
- private LinkedList<org.caosdb.server.permissions.PermissionRule> convertPermissionRules(
+ private LinkedList<org.linkahead.server.permissions.PermissionRule> convertPermissionRules(
List<PermissionRule> permissionRulesList) {
- LinkedList<org.caosdb.server.permissions.PermissionRule> result = new LinkedList<>();
+ LinkedList<org.linkahead.server.permissions.PermissionRule> result = new LinkedList<>();
permissionRulesList.forEach((r) -> result.add(convert(r)));
return result;
}
- private org.caosdb.server.permissions.PermissionRule convert(PermissionRule r) {
+ private org.linkahead.server.permissions.PermissionRule convert(PermissionRule r) {
boolean grant = r.getGrant();
boolean priority = r.getPriority();
String permission = r.getPermission();
- return new org.caosdb.server.permissions.PermissionRule(grant, priority, permission);
+ return new org.linkahead.server.permissions.PermissionRule(grant, priority, permission);
}
private ListRolesResponse convert(List<Role> roles) {
@@ -193,15 +193,16 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
.build();
}
- private org.caosdb.api.acm.v1alpha1.Role.Builder convert(Role role) {
- org.caosdb.api.acm.v1alpha1.Role.Builder result = org.caosdb.api.acm.v1alpha1.Role.newBuilder();
+ private org.linkahead.api.acm.v1alpha1.Role.Builder convert(Role role) {
+ org.linkahead.api.acm.v1alpha1.Role.Builder result =
+ org.linkahead.api.acm.v1alpha1.Role.newBuilder();
result.setDescription(role.description);
result.setName(role.name);
if (role.permission_rules != null) result.addAllPermissionRules(convert(role.permission_rules));
return result;
}
- private PermissionRule convert(org.caosdb.server.permissions.PermissionRule rule) {
+ private PermissionRule convert(org.linkahead.server.permissions.PermissionRule rule) {
PermissionRule.Builder result = PermissionRule.newBuilder();
result.setGrant(rule.isGrant());
result.setPriority(rule.isPriority());
@@ -210,7 +211,7 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
}
private Iterable<PermissionRule> convert(
- LinkedList<org.caosdb.server.permissions.PermissionRule> permission_rules) {
+ LinkedList<org.linkahead.server.permissions.PermissionRule> permission_rules) {
List<PermissionRule> result = new LinkedList<>();
permission_rules.forEach(
@@ -281,10 +282,10 @@ public class AccessControlManagementServiceImpl extends AccessControlManagementS
/** What can be done with this role. */
private Iterable<? extends RoleCapabilities> getRoleCapabilities(Role role) {
List<RoleCapabilities> result = new LinkedList<>();
- if (org.caosdb.server.permissions.Role.ADMINISTRATION.toString().equals(role.name)) {
+ if (org.linkahead.server.permissions.Role.ADMINISTRATION.toString().equals(role.name)) {
// administration cannot be deleted and the permissions cannot be changed (from *)
result.add(RoleCapabilities.ROLE_CAPABILITIES_ASSIGN);
- } else if (org.caosdb.server.permissions.Role.ANONYMOUS_ROLE.toString().equals(role.name)) {
+ } else if (org.linkahead.server.permissions.Role.ANONYMOUS_ROLE.toString().equals(role.name)) {
// anonymous cannot be deleted or assigned to any user
result.add(RoleCapabilities.ROLE_CAPABILITIES_UPDATE_PERMISSION_RULES);
} else {
diff --git a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
index ce8a6221..90a83ce9 100644
--- a/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/AuthInterceptor.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,9 +19,9 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
-import static org.caosdb.server.utils.Utils.URLDecodeWithUTF8;
+import static org.linkahead.server.utils.Utils.URLDecodeWithUTF8;
import io.grpc.Context;
import io.grpc.Contexts;
@@ -40,15 +40,15 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.util.ThreadContext;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.RealmUsernamePasswordToken;
-import org.caosdb.server.accessControl.SelfValidatingAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.RealmUsernamePasswordToken;
+import org.linkahead.server.accessControl.SelfValidatingAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.CookieSetting;
/**
@@ -97,7 +97,7 @@ public class AuthInterceptor implements ServerInterceptor {
/** Whether the anonymous login is possible or not. */
private final boolean isAuthOptional() {
- return CaosDBServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
+ return LinkAheadServer.getServerProperty(ServerProperties.KEY_AUTH_OPTIONAL)
.equalsIgnoreCase("true");
}
@@ -272,7 +272,8 @@ final class CookieSetter<ReqT, RespT>
String getSessionTimeoutSeconds() {
int ms =
- Integer.parseInt(CaosDBServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
+ Integer.parseInt(
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SESSION_TIMEOUT_MS));
int seconds = (int) Math.floor(ms / 1000);
return Integer.toString(seconds);
}
diff --git a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
index 8ab8b057..b8322668 100644
--- a/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/CaosDBToGrpcConverters.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.Iterator;
import java.util.LinkedList;
@@ -27,69 +27,69 @@ import java.util.List;
import java.util.NoSuchElementException;
import java.util.Objects;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.AtomicDataType;
-import org.caosdb.api.entity.v1.CollectionValues;
-import org.caosdb.api.entity.v1.DataType;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.Entity.Builder;
-import org.caosdb.api.entity.v1.EntityACL;
-import org.caosdb.api.entity.v1.EntityAclPermission;
-import org.caosdb.api.entity.v1.EntityPermissionRule;
-import org.caosdb.api.entity.v1.EntityPermissionRuleCapability;
-import org.caosdb.api.entity.v1.EntityResponse;
-import org.caosdb.api.entity.v1.EntityRole;
-import org.caosdb.api.entity.v1.FileDescriptor;
-import org.caosdb.api.entity.v1.Importance;
-import org.caosdb.api.entity.v1.ListDataType;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.api.entity.v1.Parent;
-import org.caosdb.api.entity.v1.ReferenceDataType;
-import org.caosdb.api.entity.v1.ScalarValue;
-import org.caosdb.api.entity.v1.SelectQueryColumn;
-import org.caosdb.api.entity.v1.SelectQueryHeader;
-import org.caosdb.api.entity.v1.SelectQueryResult;
-import org.caosdb.api.entity.v1.SelectQueryRow;
-import org.caosdb.api.entity.v1.SpecialValue;
-import org.caosdb.api.entity.v1.Version;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.BooleanDatatype;
-import org.caosdb.server.datatype.BooleanValue;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.DateTimeDatatype;
-import org.caosdb.server.datatype.DoubleDatatype;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.IntegerDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.TextDatatype;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.StatementStatusInterface;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
-
-public class CaosDBToGrpcConverters {
+import org.linkahead.api.entity.v1.AtomicDataType;
+import org.linkahead.api.entity.v1.CollectionValues;
+import org.linkahead.api.entity.v1.DataType;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.Entity.Builder;
+import org.linkahead.api.entity.v1.EntityACL;
+import org.linkahead.api.entity.v1.EntityAclPermission;
+import org.linkahead.api.entity.v1.EntityPermissionRule;
+import org.linkahead.api.entity.v1.EntityPermissionRuleCapability;
+import org.linkahead.api.entity.v1.EntityResponse;
+import org.linkahead.api.entity.v1.EntityRole;
+import org.linkahead.api.entity.v1.FileDescriptor;
+import org.linkahead.api.entity.v1.Importance;
+import org.linkahead.api.entity.v1.ListDataType;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.api.entity.v1.Parent;
+import org.linkahead.api.entity.v1.ReferenceDataType;
+import org.linkahead.api.entity.v1.ScalarValue;
+import org.linkahead.api.entity.v1.SelectQueryColumn;
+import org.linkahead.api.entity.v1.SelectQueryHeader;
+import org.linkahead.api.entity.v1.SelectQueryResult;
+import org.linkahead.api.entity.v1.SelectQueryRow;
+import org.linkahead.api.entity.v1.SpecialValue;
+import org.linkahead.api.entity.v1.Version;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.BooleanDatatype;
+import org.linkahead.server.datatype.BooleanValue;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.DateTimeDatatype;
+import org.linkahead.server.datatype.DoubleDatatype;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.IntegerDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.TextDatatype;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.StatementStatusInterface;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
+
+public class LinkAheadToGrpcConverters {
private TimeZone timeZone;
- public CaosDBToGrpcConverters(TimeZone timeZone) {
+ public LinkAheadToGrpcConverters(TimeZone timeZone) {
this.timeZone = timeZone;
}
@@ -194,18 +194,18 @@ public class CaosDBToGrpcConverters {
}
}
- public Iterable<? extends org.caosdb.api.entity.v1.Message> convert(
+ public Iterable<? extends org.linkahead.api.entity.v1.Message> convert(
final List<Message> messages) {
- final List<org.caosdb.api.entity.v1.Message> result = new LinkedList<>();
+ final List<org.linkahead.api.entity.v1.Message> result = new LinkedList<>();
for (final Message m : messages) {
result.add(convert(m));
}
return result;
}
- public org.caosdb.api.entity.v1.Message convert(final Message m) {
- final org.caosdb.api.entity.v1.Message.Builder builder =
- org.caosdb.api.entity.v1.Message.newBuilder();
+ public org.linkahead.api.entity.v1.Message convert(final Message m) {
+ final org.linkahead.api.entity.v1.Message.Builder builder =
+ org.linkahead.api.entity.v1.Message.newBuilder();
final MessageCode code = getMessageCode(m);
builder.setCode(code.getNumber());
builder.setDescription(m.getDescription());
@@ -216,15 +216,15 @@ public class CaosDBToGrpcConverters {
return m.getCode();
}
- public Version convert(final org.caosdb.server.entity.Version from) {
- final org.caosdb.api.entity.v1.Version.Builder builder = Version.newBuilder();
+ public Version convert(final org.linkahead.server.entity.Version from) {
+ final org.linkahead.api.entity.v1.Version.Builder builder = Version.newBuilder();
builder.setId(from.getId());
return builder.build();
}
- public Parent convert(final org.caosdb.server.entity.wrapper.Parent from) {
- final org.caosdb.api.entity.v1.Parent.Builder builder = Parent.newBuilder();
+ public Parent convert(final org.linkahead.server.entity.wrapper.Parent from) {
+ final org.linkahead.api.entity.v1.Parent.Builder builder = Parent.newBuilder();
if (from.hasId()) {
builder.setId(from.getId().toString());
}
@@ -238,10 +238,10 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- public org.caosdb.api.entity.v1.Property convert(final Property from) {
+ public org.linkahead.api.entity.v1.Property convert(final Property from) {
// @review Florian Spreckelsen 2022-03-22
- final org.caosdb.api.entity.v1.Property.Builder builder =
- org.caosdb.api.entity.v1.Property.newBuilder();
+ final org.linkahead.api.entity.v1.Property.Builder builder =
+ org.linkahead.api.entity.v1.Property.newBuilder();
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasId() && s.isToBeSet("id")) {
@@ -276,12 +276,12 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- private org.caosdb.api.entity.v1.Value.Builder convert(final Value value) {
+ private org.linkahead.api.entity.v1.Value.Builder convert(final Value value) {
if (value instanceof CollectionValue) {
return convertCollectionValue((CollectionValue) value);
}
- final org.caosdb.api.entity.v1.Value.Builder builder =
- org.caosdb.api.entity.v1.Value.newBuilder();
+ final org.linkahead.api.entity.v1.Value.Builder builder =
+ org.linkahead.api.entity.v1.Value.newBuilder();
builder.setScalarValue(convertScalarValue(value));
return builder;
}
@@ -316,19 +316,19 @@ public class CaosDBToGrpcConverters {
}
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertStringValue(final String value) {
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertStringValue(final String value) {
if (value.isEmpty()) {
return ScalarValue.newBuilder().setSpecialValue(SpecialValue.SPECIAL_VALUE_EMPTY_STRING);
}
return ScalarValue.newBuilder().setStringValue(value);
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertDateTimeInterface(
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertDateTimeInterface(
final DateTimeInterface value) {
return convertStringValue(value.toDateTimeString(timeZone));
}
- private org.caosdb.api.entity.v1.ScalarValue.Builder convertBooleanValue(
+ private org.linkahead.api.entity.v1.ScalarValue.Builder convertBooleanValue(
final BooleanValue value) {
return ScalarValue.newBuilder().setBooleanValue(value.getValue());
}
@@ -337,11 +337,11 @@ public class CaosDBToGrpcConverters {
return convertStringValue(value.toString());
}
- private org.caosdb.api.entity.v1.Value.Builder convertCollectionValue(
+ private org.linkahead.api.entity.v1.Value.Builder convertCollectionValue(
final CollectionValue value) {
- final org.caosdb.api.entity.v1.Value.Builder builder =
- org.caosdb.api.entity.v1.Value.newBuilder();
+ final org.linkahead.api.entity.v1.Value.Builder builder =
+ org.linkahead.api.entity.v1.Value.newBuilder();
final List<ScalarValue> values = new LinkedList<>();
value.forEach(
(v) -> {
@@ -375,7 +375,7 @@ public class CaosDBToGrpcConverters {
}
}
- private org.caosdb.api.entity.v1.DataType.Builder convert(final AbstractDatatype datatype) {
+ private org.linkahead.api.entity.v1.DataType.Builder convert(final AbstractDatatype datatype) {
if (datatype instanceof ReferenceDatatype2) {
return DataType.newBuilder()
.setReferenceDataType(convertReferenceDatatype((ReferenceDatatype2) datatype));
@@ -431,10 +431,10 @@ public class CaosDBToGrpcConverters {
return AtomicDataType.ATOMIC_DATA_TYPE_BOOLEAN;
}
- private org.caosdb.api.entity.v1.ListDataType.Builder convertAbstractCollectionDatatype(
+ private org.linkahead.api.entity.v1.ListDataType.Builder convertAbstractCollectionDatatype(
final AbstractCollectionDatatype collectionDatatype) {
- final org.caosdb.api.entity.v1.ListDataType.Builder listBuilder = ListDataType.newBuilder();
+ final org.linkahead.api.entity.v1.ListDataType.Builder listBuilder = ListDataType.newBuilder();
final AbstractDatatype datatype = collectionDatatype.getDatatype();
if (datatype instanceof ReferenceDatatype) {
listBuilder.setReferenceDataType(convertReferenceDatatype((ReferenceDatatype) datatype));
@@ -456,15 +456,15 @@ public class CaosDBToGrpcConverters {
return listBuilder;
}
- private org.caosdb.api.entity.v1.ReferenceDataType.Builder convertReferenceDatatype(
+ private org.linkahead.api.entity.v1.ReferenceDataType.Builder convertReferenceDatatype(
final ReferenceDatatype datatype) {
return ReferenceDataType.newBuilder().setName(datatype.getName());
}
- public Iterable<? extends org.caosdb.api.entity.v1.Property> convertProperties(
+ public Iterable<? extends org.linkahead.api.entity.v1.Property> convertProperties(
final EntityInterface from) {
// @review Florian Spreckelsen 2022-03-22
- final Iterator<org.caosdb.server.entity.wrapper.Property> iterator =
+ final Iterator<org.linkahead.server.entity.wrapper.Property> iterator =
from.getProperties().iterator();
return () ->
new Iterator<>() {
@@ -485,7 +485,7 @@ public class CaosDBToGrpcConverters {
}
@Override
- public org.caosdb.api.entity.v1.Property next() {
+ public org.linkahead.api.entity.v1.Property next() {
if (this.property == null) {
// trigger this.property to be non-null
if (!hasNext()) {
@@ -502,7 +502,7 @@ public class CaosDBToGrpcConverters {
}
public Iterable<? extends Parent> convert(final ParentContainer from) {
- final Iterator<org.caosdb.server.entity.wrapper.Parent> iterator = from.iterator();
+ final Iterator<org.linkahead.server.entity.wrapper.Parent> iterator = from.iterator();
return () ->
new Iterator<>() {
@@ -519,7 +519,8 @@ public class CaosDBToGrpcConverters {
}
public void appendMessages(
- final EntityInterface from, final org.caosdb.api.entity.v1.EntityResponse.Builder builder) {
+ final EntityInterface from,
+ final org.linkahead.api.entity.v1.EntityResponse.Builder builder) {
// @review Florian Spreckelsen 2022-03-22
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasMessage(Message.MessageType.Error.toString()) && s.isToBeSet("error")) {
@@ -534,7 +535,7 @@ public class CaosDBToGrpcConverters {
}
public void appendMessages(
- final EntityInterface from, final org.caosdb.api.entity.v1.IdResponse.Builder builder) {
+ final EntityInterface from, final org.linkahead.api.entity.v1.IdResponse.Builder builder) {
// @review Florian Spreckelsen 2022-03-22
SerializeFieldStrategy s = from.getSerializeFieldStrategy();
if (from.hasMessage(Message.MessageType.Error.toString()) && s.isToBeSet("error")) {
@@ -554,7 +555,8 @@ public class CaosDBToGrpcConverters {
if (e.hasEntityACL()) {
builder.addAllRules(convert(e.getEntityACL(), true));
}
- builder.addAllRules(convert(org.caosdb.server.permissions.EntityACL.GLOBAL_PERMISSIONS, false));
+ builder.addAllRules(
+ convert(org.linkahead.server.permissions.EntityACL.GLOBAL_PERMISSIONS, false));
EntityAclPermission entityAclPermission = getCurrentACLPermission(e);
if (entityAclPermission != null) {
builder.setPermission(entityAclPermission);
@@ -562,7 +564,8 @@ public class CaosDBToGrpcConverters {
return builder.build();
}
- private org.caosdb.api.entity.v1.EntityAclPermission getCurrentACLPermission(EntityInterface e) {
+ private org.linkahead.api.entity.v1.EntityAclPermission getCurrentACLPermission(
+ EntityInterface e) {
if (e.hasPermission(EntityPermission.EDIT_PRIORITY_ACL)) {
return EntityAclPermission.ENTITY_ACL_PERMISSION_EDIT_PRIORITY_ACL;
}
@@ -573,7 +576,7 @@ public class CaosDBToGrpcConverters {
}
private Iterable<? extends EntityPermissionRule> convert(
- org.caosdb.server.permissions.EntityACL entityACL, boolean deletable) {
+ org.linkahead.server.permissions.EntityACL entityACL, boolean deletable) {
List<EntityPermissionRule> result = new LinkedList<>();
for (EntityACI aci : entityACL.getRules()) {
EntityPermissionRule.Builder builder =
@@ -591,8 +594,8 @@ public class CaosDBToGrpcConverters {
return result;
}
- private Iterable<org.caosdb.api.entity.v1.EntityPermission> convert(EntityACI aci) {
- List<org.caosdb.api.entity.v1.EntityPermission> result = new LinkedList<>();
+ private Iterable<org.linkahead.api.entity.v1.EntityPermission> convert(EntityACI aci) {
+ List<org.linkahead.api.entity.v1.EntityPermission> result = new LinkedList<>();
for (EntityPermission p : aci.getPermission()) {
result.add(p.getMapping());
@@ -600,7 +603,7 @@ public class CaosDBToGrpcConverters {
return result;
}
- public org.caosdb.api.entity.v1.SelectQueryResult.Builder convertSelectResult(
+ public org.linkahead.api.entity.v1.SelectQueryResult.Builder convertSelectResult(
RetrieveContainer container) {
SelectQueryResult.Builder result = SelectQueryResult.newBuilder();
result.setHeader(convertSelectQueryHeader(container));
@@ -614,7 +617,7 @@ public class CaosDBToGrpcConverters {
SelectQueryRow.Builder result = SelectQueryRow.newBuilder();
for (Selection s : selections) {
- org.caosdb.api.entity.v1.Value.Builder value = getSelectedValue(s, e);
+ org.linkahead.api.entity.v1.Value.Builder value = getSelectedValue(s, e);
result.addCells(value);
}
return result;
@@ -623,12 +626,12 @@ public class CaosDBToGrpcConverters {
/**
* Handle special selectors like "id", "name", "value", "parent",...
*
- * @return a {@link org.caosdb.api.entity.v1.Value.Builder}, if the selector has been handled.
+ * @return a {@link org.linkahead.api.entity.v1.Value.Builder}, if the selector has been handled.
* Return null when the caller must handle the selector otherwise.
*/
- private org.caosdb.api.entity.v1.Value.Builder handleSpecialSelectors(
+ private org.linkahead.api.entity.v1.Value.Builder handleSpecialSelectors(
String selector, EntityInterface e) {
- org.caosdb.api.entity.v1.Value.Builder result = null;
+ org.linkahead.api.entity.v1.Value.Builder result = null;
switch (selector) {
case "value":
try {
@@ -642,27 +645,27 @@ public class CaosDBToGrpcConverters {
break;
case "version":
if (e.hasVersion()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getVersion().getId()));
return result;
}
break;
case "name":
if (e.hasName()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getName()));
return result;
}
break;
case "id":
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getId().toString()));
return result;
case "description":
if (e.hasDescription()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getDescription()));
return result;
}
@@ -671,30 +674,30 @@ public class CaosDBToGrpcConverters {
case "unit":
final String unit = getStringUnit(e);
if (unit != null) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(unit));
return result;
}
break;
case "datatype":
if (e.hasDatatype()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getDatatype().toString()));
return result;
}
break;
case "path":
if (e.hasFileProperties() && e.getFileProperties().hasPath()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setScalarValue(convertStringValue(e.getFileProperties().getPath()));
return result;
}
break;
case "parent":
if (e.hasParents()) {
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
CollectionValues.Builder parents = CollectionValues.newBuilder();
- for (org.caosdb.server.entity.wrapper.Parent p : e.getParents()) {
+ for (org.linkahead.server.entity.wrapper.Parent p : e.getParents()) {
parents.addValues(ScalarValue.newBuilder().setStringValue(p.getName()));
}
result.setListValues(parents);
@@ -707,13 +710,13 @@ public class CaosDBToGrpcConverters {
return null;
}
- org.caosdb.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
- org.caosdb.api.entity.v1.Value.Builder result = null;
+ org.linkahead.api.entity.v1.Value.Builder getSelectedValue(Selection s, EntityInterface e) {
+ org.linkahead.api.entity.v1.Value.Builder result = null;
String selector = s.getSelector();
result = handleSpecialSelectors(selector, e);
if (result == null) {
// selector for a normal property
- List<org.caosdb.api.entity.v1.Value.Builder> results = new LinkedList<>();
+ List<org.linkahead.api.entity.v1.Value.Builder> results = new LinkedList<>();
for (Property p : e.getProperties()) {
if (p.getName() != null && p.getName().equals(selector)) {
if (s.getSubselection() == null) {
@@ -765,7 +768,7 @@ public class CaosDBToGrpcConverters {
if (results.size() > 1) {
// There have been multiple matching properties
CollectionValues.Builder values = CollectionValues.newBuilder();
- for (org.caosdb.api.entity.v1.Value.Builder v : results) {
+ for (org.linkahead.api.entity.v1.Value.Builder v : results) {
// Concatenate all found values to a list
if (v.hasScalarValue()) {
values.addValues(v.getScalarValueBuilder());
@@ -773,7 +776,7 @@ public class CaosDBToGrpcConverters {
values.addAllValues(v.getListValuesBuilder().getValuesList());
}
}
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
result.setListValues(values);
} else if (results.size() == 1) {
// There has been exactly one matching property
@@ -783,7 +786,7 @@ public class CaosDBToGrpcConverters {
if (result == null) {
// no matching property found
- result = org.caosdb.api.entity.v1.Value.newBuilder();
+ result = org.linkahead.api.entity.v1.Value.newBuilder();
}
return result;
}
diff --git a/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
index 06c38762..a502682e 100644
--- a/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
+++ b/src/main/java/org/caosdb/server/grpc/DownloadBuffer.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.FileInputStream;
@@ -7,10 +7,10 @@ import java.io.IOException;
import java.nio.MappedByteBuffer;
import java.nio.channels.FileChannel;
import java.nio.channels.FileChannel.MapMode;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.entity.FileProperties;
public class DownloadBuffer {
diff --git a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
index 030b5254..f72f0e7a 100644
--- a/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/EntityTransactionServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.util.HashMap;
@@ -27,53 +27,53 @@ import java.util.TimeZone;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
-import org.caosdb.api.entity.v1.DeleteRequest;
-import org.caosdb.api.entity.v1.DeleteResponse;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.EntityRequest;
-import org.caosdb.api.entity.v1.EntityResponse;
-import org.caosdb.api.entity.v1.EntityTransactionServiceGrpc.EntityTransactionServiceImplBase;
-import org.caosdb.api.entity.v1.FindQueryResult;
-import org.caosdb.api.entity.v1.IdResponse;
-import org.caosdb.api.entity.v1.InsertRequest;
-import org.caosdb.api.entity.v1.InsertResponse;
-import org.caosdb.api.entity.v1.MultiRetrieveEntityACLRequest;
-import org.caosdb.api.entity.v1.MultiRetrieveEntityACLResponse;
-import org.caosdb.api.entity.v1.MultiTransactionRequest;
-import org.caosdb.api.entity.v1.MultiTransactionResponse;
-import org.caosdb.api.entity.v1.MultiUpdateEntityACLRequest;
-import org.caosdb.api.entity.v1.MultiUpdateEntityACLResponse;
-import org.caosdb.api.entity.v1.RetrieveResponse;
-import org.caosdb.api.entity.v1.SelectQueryResult;
-import org.caosdb.api.entity.v1.TransactionRequest;
-import org.caosdb.api.entity.v1.TransactionRequest.WrappedRequestsCase;
-import org.caosdb.api.entity.v1.TransactionResponse;
-import org.caosdb.api.entity.v1.UpdateRequest;
-import org.caosdb.api.entity.v1.UpdateResponse;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.RetrieveACL;
-import org.caosdb.server.transaction.UpdateACL;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.DeleteRequest;
+import org.linkahead.api.entity.v1.DeleteResponse;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.EntityRequest;
+import org.linkahead.api.entity.v1.EntityResponse;
+import org.linkahead.api.entity.v1.EntityTransactionServiceGrpc.EntityTransactionServiceImplBase;
+import org.linkahead.api.entity.v1.FindQueryResult;
+import org.linkahead.api.entity.v1.IdResponse;
+import org.linkahead.api.entity.v1.InsertRequest;
+import org.linkahead.api.entity.v1.InsertResponse;
+import org.linkahead.api.entity.v1.MultiRetrieveEntityACLRequest;
+import org.linkahead.api.entity.v1.MultiRetrieveEntityACLResponse;
+import org.linkahead.api.entity.v1.MultiTransactionRequest;
+import org.linkahead.api.entity.v1.MultiTransactionResponse;
+import org.linkahead.api.entity.v1.MultiUpdateEntityACLRequest;
+import org.linkahead.api.entity.v1.MultiUpdateEntityACLResponse;
+import org.linkahead.api.entity.v1.RetrieveResponse;
+import org.linkahead.api.entity.v1.SelectQueryResult;
+import org.linkahead.api.entity.v1.TransactionRequest;
+import org.linkahead.api.entity.v1.TransactionRequest.WrappedRequestsCase;
+import org.linkahead.api.entity.v1.TransactionResponse;
+import org.linkahead.api.entity.v1.UpdateRequest;
+import org.linkahead.api.entity.v1.UpdateResponse;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.RetrieveACL;
+import org.linkahead.server.transaction.UpdateACL;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ServerMessages;
public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBase {
// TODO(tf) let the clients define the time zone of the date time values which are being returned.
- private final CaosDBToGrpcConverters caosdbToGrpc =
- new CaosDBToGrpcConverters(TimeZone.getDefault());
- private final GrpcToCaosDBConverters grpcToCaosdb = new GrpcToCaosDBConverters();
+ private final LinkAheadToGrpcConverters linkaheadToGrpc =
+ new LinkAheadToGrpcConverters(TimeZone.getDefault());
+ private final GrpcToLinkAheadConverters grpcToLinkAhead = new GrpcToLinkAheadConverters();
private final FileTransmissionServiceImpl fileTransmissionService;
public EntityTransactionServiceImpl(final FileTransmissionServiceImpl fileTransmissionService) {
@@ -93,8 +93,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
fileTransmissionService.registerFileDownload(
fileDownload.getId(), entity.getFileProperties()));
} catch (AuthenticationException exc) {
- entityResponse.addErrors(caosdbToGrpc.convert(ServerMessages.AUTHORIZATION_ERROR));
- entityResponse.addInfos(caosdbToGrpc.convert(new Message(exc.getMessage())));
+ entityResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.AUTHORIZATION_ERROR));
+ entityResponse.addInfos(linkaheadToGrpc.convert(new Message(exc.getMessage())));
}
}
@@ -116,7 +116,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
for (final TransactionRequest sub_request : request.getRequestsList()) {
if (sub_request.getWrappedRequestsCase() != WrappedRequestsCase.RETRIEVE_REQUEST) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ sub_request.getWrappedRequestsCase().name()
+ " in a read-only request.");
@@ -126,7 +126,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
&& !sub_request.getRetrieveRequest().getQuery().getQuery().isBlank()) {
final String query = sub_request.getRetrieveRequest().getQuery().getQuery();
if (container.getFlags().containsKey("query")) { // Check for more than one query request.
- throw new CaosDBException("Cannot process more than one query request.");
+ throw new LinkAheadException("Cannot process more than one query request.");
}
container.getFlags().put("query", query);
if (isFileDownload) {
@@ -136,7 +136,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final String id = sub_request.getRetrieveRequest().getId();
if (!id.isBlank()) {
try {
- final RetrieveEntity entity = new RetrieveEntity(grpcToCaosdb.getId(id));
+ final RetrieveEntity entity = new RetrieveEntity(grpcToLinkAhead.getId(id));
if (isFileDownload) {
entity.setFlag("download_files", "true");
}
@@ -159,7 +159,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
} else if (container.getQuery() != null
&& container.getQuery().getType() == Query.Type.SELECT) {
// this was a select query
- SelectQueryResult.Builder selectResult = caosdbToGrpc.convertSelectResult(container);
+ SelectQueryResult.Builder selectResult = linkaheadToGrpc.convertSelectResult(container);
builder
.addResponsesBuilder()
.setRetrieveResponse(RetrieveResponse.newBuilder().setSelectResult(selectResult));
@@ -168,7 +168,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final boolean download_files_container = container.getFlags().containsKey("download_files");
FindQueryResult.Builder findResult = FindQueryResult.newBuilder();
for (final EntityInterface entity : container) {
- final EntityResponse.Builder entityResponse = caosdbToGrpc.convert(entity);
+ final EntityResponse.Builder entityResponse = linkaheadToGrpc.convert(entity);
if ((download_files_container || entity.getFlags().containsKey("download_files"))
&& entity.hasFileProperties()) {
prepareDownload(entityResponse, entity, fileDownload);
@@ -182,7 +182,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
// normal retrieval via id
final boolean download_files_container = container.getFlags().containsKey("download_files");
for (final EntityInterface entity : container) {
- final EntityResponse.Builder entityResponse = caosdbToGrpc.convert(entity);
+ final EntityResponse.Builder entityResponse = linkaheadToGrpc.convert(entity);
if ((download_files_container || entity.getFlags().containsKey("download_files"))
&& entity.hasFileProperties()) {
prepareDownload(entityResponse, entity, fileDownload);
@@ -198,7 +198,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final String id = sub_request.getRetrieveRequest().getId();
if (!id.isBlank()) {
try {
- grpcToCaosdb.getId(id);
+ grpcToLinkAhead.getId(id);
} catch (final NumberFormatException e) {
// ID wasn't an integer - the server doesn't support string ids yet, so that entity
// cannot exist.
@@ -214,7 +214,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
private EntityResponse entityDoesNotExist(final String id) {
return EntityResponse.newBuilder()
- .addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
+ .addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST))
.setEntity(Entity.newBuilder().setId(id))
.build();
}
@@ -285,8 +285,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final InsertEntity entity =
new InsertEntity(
insertEntity.getName().isEmpty() ? null : insertEntity.getName(),
- grpcToCaosdb.convert(insertEntity.getRole()));
- grpcToCaosdb.convert(insertEntity, entity);
+ grpcToLinkAhead.convert(insertEntity.getRole()));
+ grpcToLinkAhead.convert(insertEntity, entity);
addFileUpload(container, entity, insertRequest.getEntityRequest());
container.add(entity);
}
@@ -298,9 +298,10 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
try {
final UpdateEntity entity =
new UpdateEntity(
- grpcToCaosdb.getId(updateEntity.getId()), // ID is not handled by grpc convert
- grpcToCaosdb.convert(updateEntity.getRole()));
- grpcToCaosdb.convert(updateEntity, entity);
+ grpcToLinkAhead.getId(
+ updateEntity.getId()), // ID is not handled by grpc convert
+ grpcToLinkAhead.convert(updateEntity.getRole()));
+ grpcToLinkAhead.convert(updateEntity, entity);
addFileUpload(container, entity, updateRequest.getEntityRequest());
container.add(entity);
} catch (final NumberFormatException e) {
@@ -311,7 +312,8 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
case DELETE_REQUEST:
final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
try {
- final DeleteEntity entity = new DeleteEntity(grpcToCaosdb.getId(deleteRequest.getId()));
+ final DeleteEntity entity =
+ new DeleteEntity(grpcToLinkAhead.getId(deleteRequest.getId()));
container.add(entity);
} catch (final NumberFormatException e) {
@@ -320,7 +322,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
}
break;
default:
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ subRequest.getWrappedRequestsCase().name()
+ " in a write request.");
@@ -338,7 +340,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
if (entity.hasId()) {
idResponse.setId(entity.getId().toString());
}
- caosdbToGrpc.appendMessages(entity, idResponse);
+ linkaheadToGrpc.appendMessages(entity, idResponse);
if (entity instanceof InsertEntity) {
builder
@@ -367,7 +369,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
* @return
*/
private MultiTransactionResponse failedWriteDueToStringId(final MultiTransactionRequest request) {
- final org.caosdb.api.entity.v1.MultiTransactionResponse.Builder builder =
+ final org.linkahead.api.entity.v1.MultiTransactionResponse.Builder builder =
MultiTransactionResponse.newBuilder();
for (final TransactionRequest subRequest : request.getRequestsList()) {
final IdResponse.Builder idResponse = IdResponse.newBuilder();
@@ -384,10 +386,10 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
idResponse.setId(updateEntity.getId());
try {
- grpcToCaosdb.getId(updateEntity.getId());
+ grpcToLinkAhead.getId(updateEntity.getId());
} catch (final NumberFormatException e) {
// ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ idResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
}
builder
.addResponsesBuilder()
@@ -397,17 +399,17 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
final DeleteRequest deleteRequest = subRequest.getDeleteRequest();
idResponse.setId(deleteRequest.getId());
try {
- grpcToCaosdb.getId(deleteRequest.getId());
+ grpcToLinkAhead.getId(deleteRequest.getId());
} catch (final NumberFormatException e) {
// ID wasn't an integer
- idResponse.addErrors(caosdbToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
+ idResponse.addErrors(linkaheadToGrpc.convert(ServerMessages.ENTITY_DOES_NOT_EXIST));
}
builder
.addResponsesBuilder()
.setDeleteResponse(DeleteResponse.newBuilder().setIdResponse(idResponse));
break;
default:
- throw new CaosDBException(
+ throw new LinkAheadException(
"Cannot process a "
+ subRequest.getWrappedRequestsCase().name()
+ " in a write request.");
@@ -438,7 +440,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
RetrieveACL transaction = new RetrieveACL(request.getIdList());
transaction.execute();
for (EntityInterface e : transaction.getContainer()) {
- builder.addAcls(caosdbToGrpc.convertACL(e));
+ builder.addAcls(linkaheadToGrpc.convertACL(e));
}
return builder.build();
}
@@ -446,7 +448,7 @@ public class EntityTransactionServiceImpl extends EntityTransactionServiceImplBa
private MultiUpdateEntityACLResponse multiUpdateEntityACL(MultiUpdateEntityACLRequest request)
throws Exception {
MultiUpdateEntityACLResponse.Builder builder = MultiUpdateEntityACLResponse.newBuilder();
- UpdateACL transaction = new UpdateACL(grpcToCaosdb.convertAcls(request.getAclsList()));
+ UpdateACL transaction = new UpdateACL(grpcToLinkAhead.convertAcls(request.getAclsList()));
transaction.execute();
return builder.build();
}
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownload.java b/src/main/java/org/caosdb/server/grpc/FileDownload.java
index 2f3c7989..fb0b5b58 100644
--- a/src/main/java/org/caosdb/server/grpc/FileDownload.java
+++ b/src/main/java/org/caosdb/server/grpc/FileDownload.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileDownload extends FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
index 51304040..e0da93ce 100644
--- a/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
+++ b/src/main/java/org/caosdb/server/grpc/FileDownloadRegistration.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.io.FileNotFoundException;
import java.io.IOException;
@@ -7,11 +7,11 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileDownloadRegistration {
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmission.java b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
index 67eca23a..7e65faab 100644
--- a/src/main/java/org/caosdb/server/grpc/FileTransmission.java
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmission.java
@@ -1,9 +1,9 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.concurrent.locks.ReentrantLock;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.RegistrationStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.RegistrationStatus;
+import org.linkahead.server.entity.FileProperties;
public abstract class FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
index 1f549b37..57fd49b8 100644
--- a/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/FileTransmissionServiceImpl.java
@@ -1,24 +1,24 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.io.IOException;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileDownloadRequest;
-import org.caosdb.api.entity.v1.FileDownloadResponse;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.api.entity.v1.FileTransmissionServiceGrpc.FileTransmissionServiceImplBase;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.FileUploadRequest;
-import org.caosdb.api.entity.v1.FileUploadResponse;
-import org.caosdb.api.entity.v1.RegisterFileUploadRequest;
-import org.caosdb.api.entity.v1.RegisterFileUploadResponse;
-import org.caosdb.api.entity.v1.RegisterFileUploadResponse.Builder;
-import org.caosdb.api.entity.v1.RegistrationStatus;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.CronJob;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileDownloadRequest;
+import org.linkahead.api.entity.v1.FileDownloadResponse;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.api.entity.v1.FileTransmissionServiceGrpc.FileTransmissionServiceImplBase;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.FileUploadRequest;
+import org.linkahead.api.entity.v1.FileUploadResponse;
+import org.linkahead.api.entity.v1.RegisterFileUploadRequest;
+import org.linkahead.api.entity.v1.RegisterFileUploadResponse;
+import org.linkahead.api.entity.v1.RegisterFileUploadResponse.Builder;
+import org.linkahead.api.entity.v1.RegistrationStatus;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.CronJob;
+import org.linkahead.server.utils.Utils;
public class FileTransmissionServiceImpl extends FileTransmissionServiceImplBase {
@@ -68,7 +68,7 @@ public class FileTransmissionServiceImpl extends FileTransmissionServiceImplBase
}
public FileTransmissionServiceImpl() {
- CaosDBServer.addPreShutdownHook(
+ LinkAheadServer.addPreShutdownHook(
() -> {
fileDownloadRegistration.cleanUp(true);
fileUploadRegistration.cleanUp(true);
diff --git a/src/main/java/org/caosdb/server/grpc/FileUpload.java b/src/main/java/org/caosdb/server/grpc/FileUpload.java
index 2ec4ca3d..5100f06f 100644
--- a/src/main/java/org/caosdb/server/grpc/FileUpload.java
+++ b/src/main/java/org/caosdb/server/grpc/FileUpload.java
@@ -1,16 +1,16 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
-import org.caosdb.api.entity.v1.FileChunk;
-import org.caosdb.api.entity.v1.FileTransmissionSettings;
-import org.caosdb.api.entity.v1.FileTransmissionSettings.Builder;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.FileChunk;
+import org.linkahead.api.entity.v1.FileTransmissionSettings;
+import org.linkahead.api.entity.v1.FileTransmissionSettings.Builder;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.FileProperties;
public class FileUpload extends FileTransmission {
diff --git a/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
index bfb25be2..dbb782e1 100644
--- a/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
+++ b/src/main/java/org/caosdb/server/grpc/FileUploadRegistration.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import org.caosdb.api.entity.v1.FileTransmissionId;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.FileTransmissionId;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.utils.Utils;
public class FileUploadRegistration {
diff --git a/src/main/java/org/caosdb/server/grpc/GRPCServer.java b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
index 73356140..096d46fa 100644
--- a/src/main/java/org/caosdb/server/grpc/GRPCServer.java
+++ b/src/main/java/org/caosdb/server/grpc/GRPCServer.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Server;
import io.grpc.ServerInterceptors;
@@ -43,8 +43,8 @@ import java.util.LinkedList;
import java.util.List;
import java.util.concurrent.TimeUnit;
import javax.net.ssl.KeyManagerFactory;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -59,7 +59,7 @@ public class GRPCServer {
private static GRPCServer instance = new GRPCServer();
private static String getServerProperty(final String key) {
- return CaosDBServer.getServerProperty(key);
+ return LinkAheadServer.getServerProperty(key);
}
private static final Logger logger = LoggerFactory.getLogger(GRPCServer.class.getName());
@@ -190,7 +190,7 @@ public class GRPCServer {
if (port_https_str != null && !port_https_str.isEmpty()) {
final Integer port_https = Integer.parseInt(port_https_str);
final Server server = instance.buildServer(port_https, true);
- CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ LinkAheadServer.addPreShutdownHook(new ServerStopper(server));
server.start();
started = true;
logger.info("Started GRPC (HTTPS) on port {}", port_https);
@@ -201,7 +201,7 @@ public class GRPCServer {
final Integer port_http = Integer.parseInt(port_http_str);
final Server server = instance.buildServer(port_http, false);
- CaosDBServer.addPreShutdownHook(new ServerStopper(server));
+ LinkAheadServer.addPreShutdownHook(new ServerStopper(server));
server.start();
logger.info("Started GRPC (HTTP) on port {}", port_http);
diff --git a/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
index e47bda9c..8393c014 100644
--- a/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
+++ b/src/main/java/org/caosdb/server/grpc/GeneralInfoServiceImpl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.stub.StreamObserver;
import java.util.Collection;
@@ -27,17 +27,17 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationInfo;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.info.v1.GeneralInfoServiceGrpc.GeneralInfoServiceImplBase;
-import org.caosdb.api.info.v1.GetSessionInfoRequest;
-import org.caosdb.api.info.v1.GetSessionInfoResponse;
-import org.caosdb.api.info.v1.GetVersionInfoRequest;
-import org.caosdb.api.info.v1.GetVersionInfoResponse;
-import org.caosdb.api.info.v1.VersionInfo;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.permissions.CaosPermission;
+import org.linkahead.api.info.v1.GeneralInfoServiceGrpc.GeneralInfoServiceImplBase;
+import org.linkahead.api.info.v1.GetSessionInfoRequest;
+import org.linkahead.api.info.v1.GetSessionInfoResponse;
+import org.linkahead.api.info.v1.GetVersionInfoRequest;
+import org.linkahead.api.info.v1.GetVersionInfoResponse;
+import org.linkahead.api.info.v1.VersionInfo;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.permissions.LinkAheadPermission;
/**
* Implementation of the GeneralInfoService.
@@ -53,12 +53,12 @@ public class GeneralInfoServiceImpl extends GeneralInfoServiceImplBase {
private GetVersionInfoResponse getVersionInfo(GetVersionInfoRequest request) {
final String version[] =
- CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_VERSION).split("[\\.-]", 4);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_PROJECT_VERSION).split("[\\.-]", 4);
final Integer major = Integer.parseInt(version[0]);
final Integer minor = Integer.parseInt(version[1]);
final Integer patch = Integer.parseInt(version[2]);
final String pre_release = version.length > 3 ? version[3] : "";
- final String build = CaosDBServer.getServerProperty(ServerProperties.KEY_PROJECT_REVISTION);
+ final String build = LinkAheadServer.getServerProperty(ServerProperties.KEY_PROJECT_REVISTION);
final VersionInfo versionInfo =
VersionInfo.newBuilder()
@@ -110,8 +110,8 @@ public class GeneralInfoServiceImpl extends GeneralInfoServiceImplBase {
}
for (Permission p : authorizationInfo.getObjectPermissions()) {
- if (p instanceof CaosPermission) {
- permissions.addAll(((CaosPermission) p).getStringPermissions(subject));
+ if (p instanceof LinkAheadPermission) {
+ permissions.addAll(((LinkAheadPermission) p).getStringPermissions(subject));
} else {
permissions.add(p.toString());
}
diff --git a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
index 0430a795..09b3fc3c 100644
--- a/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
+++ b/src/main/java/org/caosdb/server/grpc/GrpcToCaosDBConverters.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,7 +19,7 @@
*
*/
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import java.util.ArrayList;
import java.util.Collection;
@@ -27,44 +27,44 @@ import java.util.LinkedList;
import java.util.List;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.api.entity.v1.AtomicDataType;
-import org.caosdb.api.entity.v1.CollectionValues;
-import org.caosdb.api.entity.v1.DataType;
-import org.caosdb.api.entity.v1.Entity;
-import org.caosdb.api.entity.v1.EntityACL;
-import org.caosdb.api.entity.v1.EntityPermission;
-import org.caosdb.api.entity.v1.EntityPermissionRule;
-import org.caosdb.api.entity.v1.EntityRole;
-import org.caosdb.api.entity.v1.FileDescriptor;
-import org.caosdb.api.entity.v1.Importance;
-import org.caosdb.api.entity.v1.ListDataType;
-import org.caosdb.api.entity.v1.Parent;
-import org.caosdb.api.entity.v1.ReferenceDataType;
-import org.caosdb.api.entity.v1.SpecialValue;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.BooleanValue;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ListDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.permissions.EntityACLFactory;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.AtomicDataType;
+import org.linkahead.api.entity.v1.CollectionValues;
+import org.linkahead.api.entity.v1.DataType;
+import org.linkahead.api.entity.v1.Entity;
+import org.linkahead.api.entity.v1.EntityACL;
+import org.linkahead.api.entity.v1.EntityPermission;
+import org.linkahead.api.entity.v1.EntityPermissionRule;
+import org.linkahead.api.entity.v1.EntityRole;
+import org.linkahead.api.entity.v1.FileDescriptor;
+import org.linkahead.api.entity.v1.Importance;
+import org.linkahead.api.entity.v1.ListDataType;
+import org.linkahead.api.entity.v1.Parent;
+import org.linkahead.api.entity.v1.ReferenceDataType;
+import org.linkahead.api.entity.v1.SpecialValue;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.BooleanValue;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ListDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.permissions.EntityACLFactory;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
-public class GrpcToCaosDBConverters {
+public class GrpcToLinkAheadConverters {
public EntityID getId(final String id) {
return new EntityID(Integer.parseInt(id));
@@ -133,7 +133,7 @@ public class GrpcToCaosDBConverters {
return entity;
}
- private Value convert(final org.caosdb.api.entity.v1.Value value) {
+ private Value convert(final org.linkahead.api.entity.v1.Value value) {
switch (value.getValueCase()) {
case LIST_VALUES:
return convertListValue(value.getListValues());
@@ -156,7 +156,7 @@ public class GrpcToCaosDBConverters {
return result;
}
- private Value convertScalarValue(final org.caosdb.api.entity.v1.ScalarValue value) {
+ private Value convertScalarValue(final org.linkahead.api.entity.v1.ScalarValue value) {
switch (value.getScalarValueCase()) {
case BOOLEAN_VALUE:
return BooleanValue.valueOf(value.getBooleanValue());
@@ -241,7 +241,7 @@ public class GrpcToCaosDBConverters {
}
private Collection<Property> convertProperties(
- final List<org.caosdb.api.entity.v1.Property> propertiesList,
+ final List<org.linkahead.api.entity.v1.Property> propertiesList,
final StatementStatus defaultImportance) {
final Collection<Property> result = new LinkedList<>();
propertiesList.forEach(
@@ -252,7 +252,7 @@ public class GrpcToCaosDBConverters {
}
private Property convert(
- final org.caosdb.api.entity.v1.Property e, final StatementStatus defaultImportance) {
+ final org.linkahead.api.entity.v1.Property e, final StatementStatus defaultImportance) {
final Property result = new Property(new RetrieveEntity());
try {
@@ -299,9 +299,9 @@ public class GrpcToCaosDBConverters {
}
}
- private Collection<org.caosdb.server.entity.wrapper.Parent> convertParents(
+ private Collection<org.linkahead.server.entity.wrapper.Parent> convertParents(
final List<Parent> parentsList) {
- final Collection<org.caosdb.server.entity.wrapper.Parent> result = new LinkedList<>();
+ final Collection<org.linkahead.server.entity.wrapper.Parent> result = new LinkedList<>();
parentsList.forEach(
e -> {
result.add(convert(e));
@@ -309,9 +309,9 @@ public class GrpcToCaosDBConverters {
return result;
}
- private org.caosdb.server.entity.wrapper.Parent convert(final Parent e) {
- final org.caosdb.server.entity.wrapper.Parent result =
- new org.caosdb.server.entity.wrapper.Parent(new RetrieveEntity());
+ private org.linkahead.server.entity.wrapper.Parent convert(final Parent e) {
+ final org.linkahead.server.entity.wrapper.Parent result =
+ new org.linkahead.server.entity.wrapper.Parent(new RetrieveEntity());
try {
result.setId(e.getId().isBlank() ? null : getId(e.getId()));
@@ -347,32 +347,32 @@ public class GrpcToCaosDBConverters {
}
}
- private org.caosdb.server.permissions.EntityACL convertAcl(EntityACL acl) {
+ private org.linkahead.server.permissions.EntityACL convertAcl(EntityACL acl) {
EntityACLFactory fac = new EntityACLFactory();
for (EntityPermissionRule rule : acl.getRulesList()) {
if (rule.getGrant()) {
fac.grant(
- org.caosdb.server.permissions.Role.create(rule.getRole()),
+ org.linkahead.server.permissions.Role.create(rule.getRole()),
rule.getPriority(),
convert(rule.getPermissionsList()));
} else {
fac.deny(
- org.caosdb.server.permissions.Role.create(rule.getRole()),
+ org.linkahead.server.permissions.Role.create(rule.getRole()),
rule.getPriority(),
convert(rule.getPermissionsList()));
}
}
- return fac.remove(org.caosdb.server.permissions.EntityACL.GLOBAL_PERMISSIONS).create();
+ return fac.remove(org.linkahead.server.permissions.EntityACL.GLOBAL_PERMISSIONS).create();
}
- private org.caosdb.server.permissions.EntityPermission[] convert(
+ private org.linkahead.server.permissions.EntityPermission[] convert(
List<EntityPermission> permissionsList) {
- ArrayList<org.caosdb.server.permissions.EntityPermission> result =
+ ArrayList<org.linkahead.server.permissions.EntityPermission> result =
new ArrayList<>(permissionsList.size());
permissionsList.forEach(
(p) -> {
- result.add(org.caosdb.server.permissions.EntityPermission.getEntityPermission(p));
+ result.add(org.linkahead.server.permissions.EntityPermission.getEntityPermission(p));
});
- return result.toArray(new org.caosdb.server.permissions.EntityPermission[0]);
+ return result.toArray(new org.linkahead.server.permissions.EntityPermission[0]);
}
}
diff --git a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
index 4e52485d..a0efc8b7 100644
--- a/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
+++ b/src/main/java/org/caosdb/server/grpc/LoggingInterceptor.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import io.grpc.Attributes.Key;
import io.grpc.Context;
@@ -9,8 +9,8 @@ import io.grpc.ServerCall.Listener;
import io.grpc.ServerCallHandler;
import io.grpc.ServerInterceptor;
import java.net.SocketAddress;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.routing.Template;
import org.restlet.util.Resolver;
import org.slf4j.Logger;
@@ -56,7 +56,8 @@ public class LoggingInterceptor implements ServerInterceptor {
private Template template;
public LoggingInterceptor() {
- String format = CaosDBServer.getServerProperty(ServerProperties.KEY_GRPC_RESPONSE_LOG_FORMAT);
+ String format =
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_GRPC_RESPONSE_LOG_FORMAT);
if ("OFF".equalsIgnoreCase(format)) {
this.template = null;
} else if (format != null) {
diff --git a/src/main/java/org/caosdb/server/grpc/UploadBuffer.java b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
index b341c33c..a3dbc074 100644
--- a/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
+++ b/src/main/java/org/caosdb/server/grpc/UploadBuffer.java
@@ -1,11 +1,11 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import com.google.protobuf.ByteString;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
-import org.caosdb.api.entity.v1.TransmissionStatus;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.api.entity.v1.TransmissionStatus;
+import org.linkahead.server.entity.FileProperties;
public class UploadBuffer {
diff --git a/src/main/java/org/caosdb/server/jobs/ContainerJob.java b/src/main/java/org/caosdb/server/jobs/ContainerJob.java
index 205b28f6..e35828dc 100644
--- a/src/main/java/org/caosdb/server/jobs/ContainerJob.java
+++ b/src/main/java/org/caosdb/server/jobs/ContainerJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.utils.EntityStatus;
public abstract class ContainerJob extends Job {
diff --git a/src/main/java/org/caosdb/server/jobs/EntityJob.java b/src/main/java/org/caosdb/server/jobs/EntityJob.java
index b0dd8ecc..18cf983e 100644
--- a/src/main/java/org/caosdb/server/jobs/EntityJob.java
+++ b/src/main/java/org/caosdb/server/jobs/EntityJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityInterface;
public abstract class EntityJob extends Job {
diff --git a/src/main/java/org/caosdb/server/jobs/FilesJob.java b/src/main/java/org/caosdb/server/jobs/FilesJob.java
index 43c89be9..05936afc 100644
--- a/src/main/java/org/caosdb/server/jobs/FilesJob.java
+++ b/src/main/java/org/caosdb/server/jobs/FilesJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.FileProperties;
+import org.linkahead.server.entity.FileProperties;
public abstract class FilesJob extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/jobs/FlagJob.java b/src/main/java/org/caosdb/server/jobs/FlagJob.java
index 5c039bb3..f10de844 100644
--- a/src/main/java/org/caosdb/server/jobs/FlagJob.java
+++ b/src/main/java/org/caosdb/server/jobs/FlagJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
public abstract class FlagJob extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/Job.java b/src/main/java/org/caosdb/server/jobs/Job.java
index 9da74edd..5ddcd4b4 100644
--- a/src/main/java/org/caosdb/server/jobs/Job.java
+++ b/src/main/java/org/caosdb/server/jobs/Job.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
@@ -29,28 +29,28 @@ import java.util.List;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.database.backend.transaction.IsSubType;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveParents;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.ParentContainer;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.database.backend.transaction.IsSubType;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveParents;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.ParentContainer;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
import org.reflections.Reflections;
/**
@@ -104,7 +104,7 @@ public abstract class Job {
| InvocationTargetException
| NoSuchMethodException
| SecurityException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
}
@@ -335,7 +335,7 @@ public abstract class Job {
if (allClasses == null || loadAlways == null) {
allClasses = new HashMap<>();
loadAlways = new ArrayList<>();
- Reflections jobPackage = new Reflections("org.caosdb.server.jobs.core");
+ Reflections jobPackage = new Reflections("org.linkahead.server.jobs.core");
Set<Class<? extends Job>> allClassesSet = jobPackage.getSubTypesOf(Job.class);
allClassesSet.addAll(jobPackage.getSubTypesOf(FlagJob.class));
for (final Class<? extends Job> c : allClassesSet) {
@@ -351,7 +351,7 @@ public abstract class Job {
}
}
// TODO merge these two parts of this function. Its the same!
- jobPackage = new Reflections("org.caosdb.server.jobs.extension");
+ jobPackage = new Reflections("org.linkahead.server.jobs.extension");
allClassesSet = jobPackage.getSubTypesOf(Job.class);
for (final Class<? extends Job> c : allClassesSet) {
allClasses.put(c.getSimpleName().toLowerCase(), c);
diff --git a/src/main/java/org/caosdb/server/jobs/JobAnnotation.java b/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
index bebebd75..19dd0337 100644
--- a/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
+++ b/src/main/java/org/caosdb/server/jobs/JobAnnotation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.TransactionInterface;
/**
* Jobs may be annotated with @JobAnnotation(...).
*
* <p>Without a JobAnnotation, the Job will run at the default {@link
- * org.caosdb.server.transaction.Transaction#check() CHECK} stage.
+ * org.linkahead.server.transaction.Transaction#check() CHECK} stage.
*
* @see {@link TransactionStage}
*/
diff --git a/src/main/java/org/caosdb/server/jobs/JobConfig.java b/src/main/java/org/caosdb/server/jobs/JobConfig.java
index 40917b36..6b6db3eb 100644
--- a/src/main/java/org/caosdb/server/jobs/JobConfig.java
+++ b/src/main/java/org/caosdb/server/jobs/JobConfig.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.io.BufferedReader;
import java.io.File;
@@ -30,16 +30,16 @@ import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.ConfigurationException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.ConfigurationException;
/**
* Configuration of the jobs which have to run during all entity transactions with "job rules".
@@ -68,7 +68,7 @@ public class JobConfig {
instance = new JobConfig();
} catch (final Exception e) {
e.printStackTrace();
- // CaosDB Server cannot work without a proper job configuration.
+ // LinkAhead Server cannot work without a proper job configuration.
System.exit(1);
}
}
@@ -80,7 +80,7 @@ public class JobConfig {
private final Map<String, List<Object[]>> rules;
public JobConfig() throws FileNotFoundException, IOException {
- this(new File(CaosDBServer.getServerProperty(ServerProperties.KEY_JOB_RULES_CONFIG)));
+ this(new File(LinkAheadServer.getServerProperty(ServerProperties.KEY_JOB_RULES_CONFIG)));
}
public JobConfig(final File config) throws FileNotFoundException, IOException {
diff --git a/src/main/java/org/caosdb/server/jobs/JobTarget.java b/src/main/java/org/caosdb/server/jobs/JobTarget.java
index 27aa0d91..c9e1754a 100644
--- a/src/main/java/org/caosdb/server/jobs/JobTarget.java
+++ b/src/main/java/org/caosdb/server/jobs/JobTarget.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
public interface JobTarget {
diff --git a/src/main/java/org/caosdb/server/jobs/Schedule.java b/src/main/java/org/caosdb/server/jobs/Schedule.java
index 57474da5..dd8dccc9 100644
--- a/src/main/java/org/caosdb/server/jobs/Schedule.java
+++ b/src/main/java/org/caosdb/server/jobs/Schedule.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import java.util.ArrayList;
import java.util.Collection;
@@ -27,7 +27,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.CopyOnWriteArrayList;
-import org.caosdb.server.entity.EntityInterface;
+import org.linkahead.server.entity.EntityInterface;
/**
* Keeps track of Jobs.
diff --git a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
index 2122b34d..40ad96ad 100644
--- a/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
+++ b/src/main/java/org/caosdb/server/jobs/ScheduledJob.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,9 +18,9 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.entity.Message;
+import org.linkahead.server.entity.Message;
/**
* ScheduledJob is a wrapper class for jobs held by the Scheduler.
diff --git a/src/main/java/org/caosdb/server/jobs/TransactionStage.java b/src/main/java/org/caosdb/server/jobs/TransactionStage.java
index 9e15b4e5..edf6233c 100644
--- a/src/main/java/org/caosdb/server/jobs/TransactionStage.java
+++ b/src/main/java/org/caosdb/server/jobs/TransactionStage.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,11 +19,11 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
-import org.caosdb.server.jobs.core.Strict;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.UndoHandler;
+import org.linkahead.server.jobs.core.Strict;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.UndoHandler;
/**
* Any {@link Transaction} of an Entity consists of sequence of stages. Jobs which have a {@link
diff --git a/src/main/java/org/caosdb/server/jobs/core/AccessControl.java b/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
index ede76585..a3ea1050 100644
--- a/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
+++ b/src/main/java/org/caosdb/server/jobs/core/AccessControl.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,22 +19,22 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Checks the TRANSACTION:* permissions before a transaction begins.
diff --git a/src/main/java/org/caosdb/server/jobs/core/Atomic.java b/src/main/java/org/caosdb/server/jobs/core/Atomic.java
index 8639615e..df79df64 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Atomic.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Atomic.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.PRE_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
index d60db5a3..32e7179c 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckChildDependencyExistent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.database.backend.transaction.GetChildren;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetChildren;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether any children of this entity do exist. There must not be any children left when an
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
index 40e01d26..3d4a2452 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDatatypePresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether the entity has a data type. Assign the data type of the abstract property if
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
index e430a081..352b75ac 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckDescPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has a description.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java b/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
index 037b38b9..d75f0f56 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckEntityACLRoles.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class CheckEntityACLRoles extends ContainerJob {
@@ -42,7 +42,7 @@ public class CheckEntityACLRoles extends ContainerJob {
&& entity.getEntityACL() != null) {
for (final EntityACI aci : entity.getEntityACL().getRules()) {
if (!AuthenticationUtils.isResponsibleAgentExistent(aci.getResponsibleAgent())) {
- if (CaosDBServer.getServerProperty(ServerProperties.KEY_CHECK_ENTITY_ACL_ROLES_MODE)
+ if (LinkAheadServer.getServerProperty(ServerProperties.KEY_CHECK_ENTITY_ACL_ROLES_MODE)
.equalsIgnoreCase("MUST")) {
entity.addError(ServerMessages.ROLE_DOES_NOT_EXIST);
entity.setEntityStatus(EntityStatus.UNQUALIFIED);
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
index e425649b..01ab9e2f 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckFileStorageConsistency.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
import java.io.FileNotFoundException;
@@ -28,22 +28,22 @@ import java.io.IOException;
import java.io.PrintStream;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.transaction.FileStorageConsistencyCheck;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.Transaction;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.Undoable;
import org.jdom2.Document;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.transaction.FileStorageConsistencyCheck;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.Transaction;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.Undoable;
@JobAnnotation(
flag = "fileStorageConsistency",
@@ -55,7 +55,7 @@ import org.jdom2.output.XMLOutputter;
+ " - a test case which can be run if the server is in debug mode (prefixed\n"
+ " -c)\n"
+ " - a filesystem location whose children are checked recursively,\n"
- + " relative to the caosroot dilesystem location.\n")
+ + " relative to the linkaheadroot file system location.\n")
public class CheckFileStorageConsistency extends FlagJob {
public static final Pattern parseArgs =
@@ -81,7 +81,7 @@ public class CheckFileStorageConsistency extends FlagJob {
} catch (final NumberFormatException e) {
}
}
- if (matcher.group(2) != null && CaosDBServer.isDebugMode()) {
+ if (matcher.group(2) != null && LinkAheadServer.isDebugMode()) {
// group two is TestCase (-c$testcase)
try {
test(TestCase.valueOf(matcher.group(2)));
@@ -208,7 +208,7 @@ public class CheckFileStorageConsistency extends FlagJob {
+ "test_file_storage_consistecy"
+ Integer.toString(hashCode()));
- final Undoable undo2 = org.caosdb.server.utils.FileUtils.rename(f2, tmp2);
+ final Undoable undo2 = org.linkahead.server.utils.FileUtils.rename(f2, tmp2);
final File overridden = new File(oldPath2);
overridden.createNewFile();
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
index 3166057c..60084194 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNamePresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has a name.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
index fb691964..3cd840c5 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNoAdditionalPropertiesPresent.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.HashSet;
import java.util.Objects;
import java.util.Set;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
flag = "noAdditionalProperties",
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
index d6cae3ee..d7967f38 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckNoOverridesPresent.java
@@ -1,10 +1,10 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
flag = "noOverrides",
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
index e6ba9da4..46ea9ee7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParOblPropPresent.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,17 +19,17 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity implements all obligatory properties of all parents.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
index 058710c6..7bd12207 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity has at least one parent.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
index 8895ae9a..64affc9b 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckParValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,24 +20,24 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import com.google.common.base.Objects;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.Affiliation;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.Affiliation;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether all parents of an entity are valid/qualified.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
index cc23d980..e7a81089 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckPropPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether at least one property is present.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
index 23a92340..835fb1b7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckPropValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import static org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST;
+import static org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST;
import com.google.common.base.Objects;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether all properties of an entity are valid or qualified.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java b/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
index 42dccf55..9d7579cc 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckQueryTemplate.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.ParsingException;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.ParsingException;
+import org.linkahead.server.utils.ServerMessages;
public class CheckQueryTemplate extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java b/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
index 2edbc5a2..ff72e207 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckReferenceDependencyExistent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.database.backend.transaction.GetDependentEntities;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetDependentEntities;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether an entity is referenced by other entities. In the event that someone wants to
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
index 0b8ba45b..f2f556df 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidIsaParRefid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.FileDatatype;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.FileDatatype;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check if the referenced entity is in the scope of the data type. E.g. if the data type is
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
index 17d9bc7c..346290ee 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.jobs.EntityJob;
public class CheckRefidPresent extends EntityJob {
@Override
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
index 12b545b8..fdba6643 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckRefidValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,23 +22,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether a reference property is pointing to a valid entity.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java b/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
index a43face9..381dd72d 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckStateTransition.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,19 +18,19 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.Map;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check if the attempted state transition is allowed.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
index 28b914e6..e13007b9 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckTargetPathValid.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether the target path of a file entity is valid. That is, the target path is in the file
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
index 85eb3259..19195c47 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckUnitPresent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Check whether this entity has a unit property.
diff --git a/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java b/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
index 1dd45714..b1af70a4 100644
--- a/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
+++ b/src/main/java/org/caosdb/server/jobs/core/CheckValueParsable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
/**
* Check whether the value of an entity is parsable according to the entity's data type. This job
diff --git a/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java b/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
index 8e0ae743..e3822608 100644
--- a/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
+++ b/src/main/java/org/caosdb/server/jobs/core/DebugCalls.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(
flag = "debug",
@@ -40,7 +40,7 @@ public class DebugCalls extends FlagJob {
@Override
protected void job(final String value) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
if (value != null) {
if (value.equalsIgnoreCase(ex_null_p)) {
throw new NullPointerException();
diff --git a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
index a4c50f88..4dc817c7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
+++ b/src/main/java/org/caosdb/server/jobs/core/EntityStateJob.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -18,7 +18,7 @@
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.HashMap;
@@ -33,31 +33,31 @@ import java.util.Map.Entry;
import java.util.Objects;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.datatype.AbstractCollectionDatatype;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.IndexedSingleValue;
-import org.caosdb.server.datatype.ReferenceDatatype;
-import org.caosdb.server.datatype.ReferenceDatatype2;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.TextDatatype;
-import org.caosdb.server.entity.ClientMessage;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.permissions.EntityACI;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.datatype.AbstractCollectionDatatype;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.IndexedSingleValue;
+import org.linkahead.server.datatype.ReferenceDatatype;
+import org.linkahead.server.datatype.ReferenceDatatype2;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.TextDatatype;
+import org.linkahead.server.entity.ClientMessage;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.permissions.EntityACI;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
/**
* The EntityStateJob is the abstract base class for four EntityJobs:
@@ -338,7 +338,7 @@ public abstract class EntityStateJob extends EntityJob {
final int end = aci.getResponsibleAgent().toString().length() - 1;
final String role = aci.getResponsibleAgent().toString().substring(7, end);
rules.add(
- new EntityACI(org.caosdb.server.permissions.Role.create(role), aci.getBitSet()));
+ new EntityACI(org.linkahead.server.permissions.Role.create(role), aci.getBitSet()));
}
}
return new EntityACL(rules);
diff --git a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
index 2d7a45d0..ce0ca985 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ExecuteQuery.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.ParsingException;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.ParsingException;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(flag = "query", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class ExecuteQuery extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/History.java b/src/main/java/org/caosdb/server/jobs/core/History.java
index c1215db5..16872e49 100644
--- a/src/main/java/org/caosdb/server/jobs/core/History.java
+++ b/src/main/java/org/caosdb/server/jobs/core/History.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveVersionHistory;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.RetrieveVersionHistory;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* Retrieves the complete version history of each entity and appends it to the entity.
diff --git a/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java b/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
index b905bfa0..353bae3f 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InheritInitialState.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,15 +17,15 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(stage = TransactionStage.CHECK)
public class InheritInitialState extends EntityStateJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
index a1bd800c..35e94ad2 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Inheritance.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,23 +22,23 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.utils.EntityStatus;
/**
* Add all those properties from the parent to the child which have the same importance (or higher).
diff --git a/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java b/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
index 5cd6d67a..f687b1b1 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InitEntityStateJobs.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,29 +17,29 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.ClientMessage;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.WritableEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.ClientMessage;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.WritableEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
/**
* Initialize the other entity jobs by converting the client message with type "State" or
@@ -59,7 +59,7 @@ public class InitEntityStateJobs extends EntityStateJob implements Observer {
@Override
protected void run() {
- if ("ENABLED".equals(CaosDBServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
+ if ("ENABLED".equals(LinkAheadServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
State newState = handleNewState();
State oldState = handleOldState(newState);
if (newState != null || oldState != null) {
diff --git a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
index 6390ad7c..13dd3466 100644
--- a/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
+++ b/src/main/java/org/caosdb/server/jobs/core/InsertFilesInDir.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
import java.io.IOException;
@@ -30,30 +30,30 @@ import java.util.LinkedList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.Undoable;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.Undoable;
+import org.linkahead.server.utils.Utils;
@JobAnnotation(
flag = "InsertFilesInDir",
@@ -80,7 +80,7 @@ public class InsertFilesInDir extends FlagJob {
private static LinkedList<File> getAllowedFolders() {
final String[] dirs =
- CaosDBServer.getServerProperty(ServerProperties.KEY_INSERT_FILES_IN_DIR_ALLOWED_DIRS)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_INSERT_FILES_IN_DIR_ALLOWED_DIRS)
.split("\\s*,?\\s*");
final LinkedList<File> ret = new LinkedList<File>();
for (final String dir : dirs) {
@@ -174,7 +174,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException | CaosDBException | InterruptedException e) {
+ } catch (final IOException | LinkAheadException | InterruptedException e) {
e.printStackTrace();
}
}
@@ -184,7 +184,7 @@ public class InsertFilesInDir extends FlagJob {
try {
final Undoable delete = FileUtils.delete(InsertFilesInDir.this.tmp, true);
delete.cleanUp();
- } catch (final IOException | CaosDBException | InterruptedException e) {
+ } catch (final IOException | LinkAheadException | InterruptedException e) {
e.printStackTrace();
}
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java b/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
index e95bef34..843c0fae 100644
--- a/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
+++ b/src/main/java/org/caosdb/server/jobs/core/JobFailureSeverity.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
/**
* Describes the severity of a failure of a job (esp. consitency checks).
diff --git a/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java b/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
index a07862c0..417281d7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
+++ b/src/main/java/org/caosdb/server/jobs/core/LoadContainerFlagJobs.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.Map.Entry;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(stage = TransactionStage.INIT)
public class LoadContainerFlagJobs extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java b/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
index d497a2ab..a5093717 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MakeStateMessage.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,18 +17,18 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import java.util.Map;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
/**
* Remove the state property from the entity and, iff necessary, convert it into a State instance
@@ -50,7 +50,7 @@ public class MakeStateMessage extends EntityStateJob {
@Override
protected void run() {
- if ("ENABLED".equals(CaosDBServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
+ if ("ENABLED".equals(LinkAheadServer.getServerProperty(SERVER_PROPERTY_EXT_ENTITY_STATE))) {
try {
// fetch all state properties and remove them from the entity (indicated by "true")
List<Property> stateProperties = getStateProperties(true);
diff --git a/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java b/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
index c2aebc68..0b0a8f54 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MakeStateProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
@@ -21,12 +21,12 @@
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.WriteTransaction;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.WriteTransaction;
/**
* This job constructs an ordinary Property from the State right before the entity is being written
diff --git a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
index 249fc0b1..0866e661 100644
--- a/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/MatchFileProp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.jobs.FilesJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.jobs.FilesJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
/**
* Match the checksum and the size of a file record to the uploaded file's checksum and size.
diff --git a/src/main/java/org/caosdb/server/jobs/core/NoCache.java b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
index e408330e..e22f3df6 100644
--- a/src/main/java/org/caosdb/server/jobs/core/NoCache.java
+++ b/src/main/java/org/caosdb/server/jobs/core/NoCache.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
@JobAnnotation(
flag = "cache",
diff --git a/src/main/java/org/caosdb/server/jobs/core/Paging.java b/src/main/java/org/caosdb/server/jobs/core/Paging.java
index aa918ecf..b390cf32 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Paging.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Paging.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(flag = "P", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class Paging extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java b/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
index 8e0a7818..57b78ef7 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ParseUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import de.timmfitschen.easyunits.parser.ParserException;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.MagicTypes;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.unit.CaosDBSystemOfUnits;
-import org.caosdb.unit.Unit;
-import org.caosdb.unit.UnknownUnit;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.MagicTypes;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.unit.LinkAheadSystemOfUnits;
+import org.linkahead.unit.Unit;
+import org.linkahead.unit.UnknownUnit;
public class ParseUnit extends EntityJob {
@@ -43,7 +43,7 @@ public class ParseUnit extends EntityJob {
try {
Unit unit;
- unit = CaosDBSystemOfUnits.getUnit(unitStr);
+ unit = LinkAheadSystemOfUnits.getUnit(unitStr);
if (unit instanceof UnknownUnit) {
getEntity().addWarning(ServerMessages.UNKNOWN_UNIT);
}
diff --git a/src/main/java/org/caosdb/server/jobs/core/PickUp.java b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
index b0e04529..deba4b92 100644
--- a/src/main/java/org/caosdb/server/jobs/core/PickUp.java
+++ b/src/main/java/org/caosdb/server/jobs/core/PickUp.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.io.File;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.Observable;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.Observable;
+import org.linkahead.server.utils.Observer;
@JobAnnotation(stage = TransactionStage.INIT)
public class PickUp extends EntityJob implements Observer {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
index 7196f04e..085562b5 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ProcessNameProperties.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import static org.caosdb.server.entity.MagicTypes.NAME;
+import static org.linkahead.server.entity.MagicTypes.NAME;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.Set;
-import org.caosdb.server.datatype.AbstractDatatype;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.datatype.AbstractDatatype;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* To be called after CheckPropValid and Inheritance.
diff --git a/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java b/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
index 3d3adcc1..92e57e19 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RemoveDuplicates.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.HashSet;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.ContainerJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.ContainerJob;
public class RemoveDuplicates extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
index 5ab722c7..79ecf341 100644
--- a/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
+++ b/src/main/java/org/caosdb/server/jobs/core/ResolveNames.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.database.backend.transaction.GetIDByName;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.GetIDByName;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class ResolveNames extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
index 0f250718..69021f5f 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveACL.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.POST_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
index a89385e2..8112dcda 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveAllJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.RetrieveAll;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveAll;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
@JobAnnotation(flag = "all", stage = TransactionStage.INIT, transaction = Retrieve.class)
public class RetrieveAllJob extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java b/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
index fa094b28..1712e17f 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetrieveOwner.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import java.util.List;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.ResponsibleAgent;
-import org.caosdb.server.transaction.Retrieve;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.ResponsibleAgent;
+import org.linkahead.server.transaction.Retrieve;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(
stage = TransactionStage.POST_TRANSACTION,
diff --git a/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java b/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
index b5787246..ef15f9cf 100644
--- a/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
+++ b/src/main/java/org/caosdb/server/jobs/core/RetriveAllNames.java
@@ -1,12 +1,12 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.GetAllNames;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.GetAllNames;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
/**
* A jobs which retrieves all known names for which the requesting user has the RETRIEVE_ENTITY
diff --git a/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java b/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
index f0047d02..e6624a78 100644
--- a/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
+++ b/src/main/java/org/caosdb/server/jobs/core/SetImpToFix.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.jobs.EntityJob;
/**
* Set the statement status of all properties of an entity to the value "FIX".
diff --git a/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java b/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
index dd6cfc08..93d551b5 100644
--- a/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
+++ b/src/main/java/org/caosdb/server/jobs/core/SetImpToRecByDefault.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.jobs.EntityJob;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.jobs.EntityJob;
/**
* Set the statement status of all properties of an entity which do not have a statement status to
diff --git a/src/main/java/org/caosdb/server/jobs/core/Strict.java b/src/main/java/org/caosdb/server/jobs/core/Strict.java
index bb69063c..ccf2b50a 100644
--- a/src/main/java/org/caosdb/server/jobs/core/Strict.java
+++ b/src/main/java/org/caosdb/server/jobs/core/Strict.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.jobs.ContainerJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.jobs.ContainerJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(stage = TransactionStage.POST_CHECK)
public class Strict extends ContainerJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/TestMail.java b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
index 793e6fe2..8a5a3401 100644
--- a/src/main/java/org/caosdb/server/jobs/core/TestMail.java
+++ b/src/main/java/org/caosdb/server/jobs/core/TestMail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
-import org.caosdb.server.utils.mail.Mail;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
+import org.linkahead.server.utils.mail.Mail;
@JobAnnotation(
flag = "testMail",
@@ -38,13 +38,13 @@ import org.caosdb.server.utils.mail.Mail;
public class TestMail extends FlagJob {
private static final String NAME =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_NAME);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_NO_REPLY_NAME);
private static final String EMAIL =
- CaosDBServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_NO_REPLY_EMAIL);
@Override
protected void job(final String recipient) {
- if (CaosDBServer.isDebugMode() && recipient != null) {
+ if (LinkAheadServer.isDebugMode() && recipient != null) {
if (Utils.isRFC822Compliant(recipient)) {
final Mail m = new Mail(NAME, EMAIL, null, recipient, "Test mail", "This is a test mail.");
m.send();
diff --git a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
index 86e6c37e..16617734 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UniqueName.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.exceptions.EntityWasNotUniqueException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.exceptions.EntityWasNotUniqueException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
@JobAnnotation(flag = "uniquename", stage = TransactionStage.PRE_CHECK)
public class UniqueName extends FlagJob {
diff --git a/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java b/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
index 0b71d210..3b97dd40 100644
--- a/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
+++ b/src/main/java/org/caosdb/server/jobs/core/UpdateUnitConverters.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
-import org.caosdb.server.database.backend.transaction.InsertLinCon;
-import org.caosdb.server.jobs.EntityJob;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.unit.Converter;
-import org.caosdb.unit.LinearConverter;
-import org.caosdb.unit.Unit;
+import org.linkahead.server.database.backend.transaction.InsertLinCon;
+import org.linkahead.server.jobs.EntityJob;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.unit.Converter;
+import org.linkahead.unit.LinearConverter;
+import org.linkahead.unit.Unit;
@JobAnnotation(stage = TransactionStage.PRE_TRANSACTION)
public class UpdateUnitConverters extends EntityJob {
diff --git a/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java b/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
index 4f0e57a4..58e8e91b 100644
--- a/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
+++ b/src/main/java/org/caosdb/server/logging/RequestErrorLogMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.logging;
+package org.linkahead.server.logging;
import java.io.IOException;
import java.io.Serializable;
import java.io.UnsupportedEncodingException;
import java.net.URLDecoder;
-import org.caosdb.server.resource.ReReadableRepresentation;
+import org.linkahead.server.resource.ReReadableRepresentation;
import org.restlet.Message;
import org.restlet.Request;
import org.restlet.Response;
diff --git a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
index 4416227f..0db1ad67 100644
--- a/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
+++ b/src/main/java/org/caosdb/server/logging/log4j/CustomConfigurationFactory.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.logging.log4j;
+package org.linkahead.server.logging.log4j;
import java.io.File;
import java.net.URI;
@@ -30,7 +30,7 @@ public class CustomConfigurationFactory extends PropertiesConfigurationFactory {
private List<String> getConfigFiles() {
List<String> configFiles = new ArrayList<>(10);
configFiles.add(core_default.getAbsolutePath());
- if (Boolean.getBoolean("caosdb.debug")) {
+ if (Boolean.getBoolean("linkahead.debug")) {
configFiles.add(core_debug.getAbsolutePath());
}
if (ext_file.exists()) {
diff --git a/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java b/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
index d5d818fd..4705bbc6 100644
--- a/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
+++ b/src/main/java/org/caosdb/server/permissions/AbstractEntityACLFactory.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.ArrayList;
import java.util.Collection;
diff --git a/src/main/java/org/caosdb/server/permissions/CaosPermission.java b/src/main/java/org/caosdb/server/permissions/CaosPermission.java
index 615b4d1a..31746874 100644
--- a/src/main/java/org/caosdb/server/permissions/CaosPermission.java
+++ b/src/main/java/org/caosdb/server/permissions/CaosPermission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.Collection;
import java.util.HashSet;
@@ -28,9 +28,9 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.subject.Subject;
-public class CaosPermission extends HashSet<PermissionRule> implements Permission {
+public class LinkAheadPermission extends HashSet<PermissionRule> implements Permission {
- public CaosPermission(final HashSet<PermissionRule> rules) {
+ public LinkAheadPermission(final HashSet<PermissionRule> rules) {
super(rules);
}
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACI.java b/src/main/java/org/caosdb/server/permissions/EntityACI.java
index 34d713eb..f668b9c1 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACI.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACI.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import java.util.Set;
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACL.java b/src/main/java/org/caosdb/server/permissions/EntityACL.java
index f959ba89..ff94b756 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACL.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,10 +21,10 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
-import static org.caosdb.server.permissions.Role.OTHER_ROLE;
-import static org.caosdb.server.permissions.Role.OWNER_ROLE;
+import static org.linkahead.server.permissions.Role.OTHER_ROLE;
+import static org.linkahead.server.permissions.Role.OWNER_ROLE;
import java.io.File;
import java.io.IOException;
@@ -37,17 +37,17 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.exceptions.TransactionException;
import org.eclipse.jetty.util.ajax.JSON;
import org.jdom2.DataConversionException;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.exceptions.TransactionException;
public class EntityACL {
@@ -68,7 +68,7 @@ public class EntityACL {
SAXBuilder saxBuilder = new SAXBuilder();
File file =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_GLOBAL_ENTITY_PERMISSIONS_FILE)
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_GLOBAL_ENTITY_PERMISSIONS_FILE)
.trim());
try {
@@ -94,7 +94,7 @@ public class EntityACL {
public static final EntityACL getOwnerACLFor(final Subject subject) {
// TODO handle the case where a valid non-guest user (e.g. me@PAM,
- // you@CaosDB) is (just temporarily) authenticated via a
+ // you@LinkAhead) is (just temporarily) authenticated via a
// OneTimeAuthenticationToken
if (AuthenticationUtils.isAnonymous(subject)
|| AuthenticationUtils.isFromOneTimeTokenRealm(subject)) {
diff --git a/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java b/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
index 08e4ae45..bc530193 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityACLFactory.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.Collection;
diff --git a/src/main/java/org/caosdb/server/permissions/EntityPermission.java b/src/main/java/org/caosdb/server/permissions/EntityPermission.java
index 1cfe9901..789d9a76 100644
--- a/src/main/java/org/caosdb/server/permissions/EntityPermission.java
+++ b/src/main/java/org/caosdb/server/permissions/EntityPermission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.ArrayList;
import java.util.HashSet;
@@ -28,16 +28,16 @@ import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.entity.xml.ToElementable;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.entity.xml.ToElementable;
public class EntityPermission extends Permission {
private static final long serialVersionUID = -8935713878537140286L;
private static List<EntityPermission> instances = new ArrayList<>();
private final int bitNumber;
- private final org.caosdb.api.entity.v1.EntityPermission mapping;
+ private final org.linkahead.api.entity.v1.EntityPermission mapping;
public static final Permission EDIT_PRIORITY_ACL =
new Permission(
"ADMIN:ENTITY:EDIT:PRIORITY_ACL",
@@ -66,16 +66,16 @@ public class EntityPermission extends Permission {
final String shortName,
final String description,
final int bitNumber,
- org.caosdb.api.entity.v1.EntityPermission mapping) {
+ org.linkahead.api.entity.v1.EntityPermission mapping) {
super(shortName, description);
this.bitNumber = bitNumber;
this.mapping = mapping;
if (bitNumber > 61) {
- throw new CaosDBException(
+ throw new LinkAheadException(
"This bitNumber is too big. This implementation only handles bitNumbers up to 61.");
}
if (instances.contains(this)) {
- throw new CaosDBException("This EntityPermission is defined already.");
+ throw new LinkAheadException("This EntityPermission is defined already.");
} else {
instances.add(this);
}
@@ -113,7 +113,7 @@ public class EntityPermission extends Permission {
}
public static EntityPermission getEntityPermission(
- final org.caosdb.api.entity.v1.EntityPermission permission) {
+ final org.linkahead.api.entity.v1.EntityPermission permission) {
for (final EntityPermission p : instances) {
if (p.getMapping() == permission) {
return p;
@@ -136,7 +136,7 @@ public class EntityPermission extends Permission {
return ret;
}
- public org.caosdb.api.entity.v1.EntityPermission getMapping() {
+ public org.linkahead.api.entity.v1.EntityPermission getMapping() {
return mapping;
}
@@ -147,144 +147,144 @@ public class EntityPermission extends Permission {
"RETRIEVE:ENTITY",
"Permission to retrieve the full entity (name, description, data type, ...) with all parents and properties (unless prohibited by another rule on the property level).",
4,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
public static final EntityPermission RETRIEVE_ACL =
new EntityPermission(
"RETRIEVE:ACL",
"Permission to retrieve the full and final ACL of this entity.",
5,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
public static final EntityPermission RETRIEVE_HISTORY =
new EntityPermission(
"RETRIEVE:HISTORY",
"Permission to retrieve the history of this entity.",
6,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
public static final EntityPermission RETRIEVE_OWNER =
new EntityPermission(
"RETRIEVE:OWNER",
"Permission to retrieve the owner(s) of this entity.",
9,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
public static final EntityPermission RETRIEVE_FILE =
new EntityPermission(
"RETRIEVE:FILE",
"Permission to download the file belonging to this entity.",
10,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
public static final EntityPermission DELETE =
new EntityPermission(
"DELETE",
"Permission to delete this entity.",
1,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
public static final EntityPermission EDIT_ACL =
new EntityPermission(
"EDIT:ACL",
"Permission to change the user-specified part of this entity's ACL. Roles with this Permission are called 'Owners'.",
0,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
public static final EntityPermission UPDATE_DESCRIPTION =
new EntityPermission(
"UPDATE:DESCRIPTION",
"Permission to change the value of this entity.",
11,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
public static final EntityPermission UPDATE_VALUE =
new EntityPermission(
"UPDATE:VALUE",
"Permission to change the value of this entity.",
12,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
public static final EntityPermission UPDATE_ROLE =
new EntityPermission(
"UPDATE:ROLE",
"Permission to change the role of this entity.",
13,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
public static final EntityPermission UPDATE_REMOVE_PARENT =
new EntityPermission(
"UPDATE:PARENT:REMOVE",
"Permission to remove parents from this entity.",
14,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
public static final EntityPermission UPDATE_ADD_PARENT =
new EntityPermission(
"UPDATE:PARENT:ADD",
"Permission to add a parent to this entity.",
15,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
public static final EntityPermission UPDATE_REMOVE_PROPERTY =
new EntityPermission(
"UPDATE:PROPERTY:REMOVE",
"Permission to remove properties from this entity.",
16,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
public static final EntityPermission UPDATE_ADD_PROPERTY =
new EntityPermission(
"UPDATE:PROPERTY:ADD",
"Permission to add a property to this entity.",
17,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
public static final EntityPermission UPDATE_NAME =
new EntityPermission(
"UPDATE:NAME",
"Permission to change the name of this entity.",
19,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
public static final EntityPermission UPDATE_DATA_TYPE =
new EntityPermission(
"UPDATE:DATA_TYPE",
"Permission to change the data type of this entity.",
20,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
public static final EntityPermission UPDATE_REMOVE_FILE =
new EntityPermission(
"UPDATE:FILE:REMOVE",
"Permission to delete the file of this entity.",
21,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
public static final EntityPermission UPDATE_ADD_FILE =
new EntityPermission(
"UPDATE:FILE:ADD",
"Permission to set a file for this entity.",
22,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
public static final EntityPermission UPDATE_MOVE_FILE =
new EntityPermission(
"UPDATE:FILE:MOVE",
"Permission to move an existing file to a new location.",
23,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
public static final EntityPermission USE_AS_REFERENCE =
new EntityPermission(
"USE:AS_REFERENCE",
"Permission to refer to this entity via a reference property.",
24,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
public static final EntityPermission USE_AS_PROPERTY =
new EntityPermission(
"USE:AS_PROPERTY",
"Permission to implement this entity as a property.",
25,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
public static final EntityPermission USE_AS_PARENT =
new EntityPermission(
"USE:AS_PARENT",
"Permission to use this entity as a super type for other entities.",
26,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
public static final EntityPermission USE_AS_DATA_TYPE =
new EntityPermission(
"USE:AS_DATA_TYPE",
"Permission to use this entity as a data type for reference properties.",
27,
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
public static final EntityPermission UPDATE_QUERY_TEMPLATE_DEFINITION =
new EntityPermission(
"UPDATE:QUERY_TEMPLATE_DEFINITION",
"Permission to update the query template definition of this QueryTemplate",
28,
- org.caosdb.api.entity.v1.EntityPermission
+ org.linkahead.api.entity.v1.EntityPermission
.ENTITY_PERMISSION_UPDATE_QUERY_TEMPLATE_DEFINITION);
}
diff --git a/src/main/java/org/caosdb/server/permissions/Permission.java b/src/main/java/org/caosdb/server/permissions/Permission.java
index e8f33a3a..3721be99 100644
--- a/src/main/java/org/caosdb/server/permissions/Permission.java
+++ b/src/main/java/org/caosdb/server/permissions/Permission.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import org.apache.shiro.authz.permission.WildcardPermission;
diff --git a/src/main/java/org/caosdb/server/permissions/PermissionRule.java b/src/main/java/org/caosdb/server/permissions/PermissionRule.java
index 2e8b6984..815e3c39 100644
--- a/src/main/java/org/caosdb/server/permissions/PermissionRule.java
+++ b/src/main/java/org/caosdb/server/permissions/PermissionRule.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,15 +21,15 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import java.util.Map;
import org.apache.shiro.authz.Permission;
import org.apache.shiro.authz.permission.WildcardPermission;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.Principal;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.Principal;
public class PermissionRule {
diff --git a/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java b/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
index 3f8fd3bb..7b164ebf 100644
--- a/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
+++ b/src/main/java/org/caosdb/server/permissions/ResponsibleAgent.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import org.jdom2.Element;
diff --git a/src/main/java/org/caosdb/server/permissions/Role.java b/src/main/java/org/caosdb/server/permissions/Role.java
index f7f4e55e..ca278daf 100644
--- a/src/main/java/org/caosdb/server/permissions/Role.java
+++ b/src/main/java/org/caosdb/server/permissions/Role.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import java.util.HashMap;
import org.jdom2.Attribute;
diff --git a/src/main/java/org/caosdb/server/query/Backreference.java b/src/main/java/org/caosdb/server/query/Backreference.java
index b801ffaf..3f29ec03 100644
--- a/src/main/java/org/caosdb/server/query/Backreference.java
+++ b/src/main/java/org/caosdb/server/query/Backreference.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -34,11 +34,11 @@ import java.sql.Types;
import java.util.HashMap;
import java.util.Map.Entry;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.Pattern;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.Pattern;
+import org.linkahead.server.query.Query.QueryException;
public class Backreference implements EntityFilterInterface, QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/CQLLexer.g4 b/src/main/java/org/caosdb/server/query/CQLLexer.g4
index be6dcfa9..20dc4438 100644
--- a/src/main/java/org/caosdb/server/query/CQLLexer.g4
+++ b/src/main/java/org/caosdb/server/query/CQLLexer.g4
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/server/query/CQLParser.g4 b/src/main/java/org/caosdb/server/query/CQLParser.g4
index 8615bae3..d042b5bf 100644
--- a/src/main/java/org/caosdb/server/query/CQLParser.g4
+++ b/src/main/java/org/caosdb/server/query/CQLParser.g4
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
diff --git a/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java b/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
index c2b453e5..66b76475 100644
--- a/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
+++ b/src/main/java/org/caosdb/server/query/CQLParsingErrorListener.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.util.ArrayList;
import java.util.BitSet;
diff --git a/src/main/java/org/caosdb/server/query/Conjunction.java b/src/main/java/org/caosdb/server/query/Conjunction.java
index 59dfd57b..f6e199cf 100644
--- a/src/main/java/org/caosdb/server/query/Conjunction.java
+++ b/src/main/java/org/caosdb/server/query/Conjunction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Conjunction extends EntityFilterContainer
implements QueryInterface, EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Disjunction.java b/src/main/java/org/caosdb/server/query/Disjunction.java
index 925ef859..ff4dd8e6 100644
--- a/src/main/java/org/caosdb/server/query/Disjunction.java
+++ b/src/main/java/org/caosdb/server/query/Disjunction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Disjunction extends EntityFilterContainer
implements QueryInterface, EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/EntityFilterContainer.java b/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
index 1b270e9b..7e1ecc95 100644
--- a/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
+++ b/src/main/java/org/caosdb/server/query/EntityFilterContainer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.util.LinkedList;
diff --git a/src/main/java/org/caosdb/server/query/EntityFilterInterface.java b/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
index be8484c2..92c704b3 100644
--- a/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
+++ b/src/main/java/org/caosdb/server/query/EntityFilterInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public interface EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/IDFilter.java b/src/main/java/org/caosdb/server/query/IDFilter.java
index ce01f5f2..663cb6ca 100644
--- a/src/main/java/org/caosdb/server/query/IDFilter.java
+++ b/src/main/java/org/caosdb/server/query/IDFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.CHAR;
import static java.sql.Types.INTEGER;
@@ -29,8 +29,8 @@ import static java.sql.Types.VARCHAR;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.SQLException;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public class IDFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Negation.java b/src/main/java/org/caosdb/server/query/Negation.java
index 431124df..7aad2cae 100644
--- a/src/main/java/org/caosdb/server/query/Negation.java
+++ b/src/main/java/org/caosdb/server/query/Negation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,9 +20,9 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
@@ -30,9 +30,9 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class Negation implements EntityFilterInterface, QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/POV.java b/src/main/java/org/caosdb/server/query/POV.java
index ebc35a16..8374b2d8 100644
--- a/src/main/java/org/caosdb/server/query/POV.java
+++ b/src/main/java/org/caosdb/server/query/POV.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.DOUBLE;
import static java.sql.Types.INTEGER;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import de.timmfitschen.easyunits.parser.ParserException;
import java.sql.CallableStatement;
@@ -39,14 +39,14 @@ import java.util.Map.Entry;
import java.util.Stack;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.DateTimeInterface;
-import org.caosdb.datetime.Interval;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.unit.CaosDBSystemOfUnits;
-import org.caosdb.unit.Unit;
import org.jdom2.Element;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.DateTimeInterface;
+import org.linkahead.datetime.Interval;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.unit.LinkAheadSystemOfUnits;
+import org.linkahead.unit.Unit;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -78,7 +78,7 @@ public class POV implements EntityFilterInterface {
private final Stack<String> prefix = new Stack<>();
private Unit getUnit(final String s) throws ParserException {
- return CaosDBSystemOfUnits.getUnit(s);
+ return LinkAheadSystemOfUnits.getUnit(s);
}
/**
diff --git a/src/main/java/org/caosdb/server/query/Query.java b/src/main/java/org/caosdb/server/query/Query.java
index abaca436..5ed794fc 100644
--- a/src/main/java/org/caosdb/server/query/Query.java
+++ b/src/main/java/org/caosdb/server/query/Query.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,9 +19,9 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.io.Serializable;
import java.sql.CallableStatement;
@@ -46,35 +46,35 @@ import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.apache.commons.jcs.access.behavior.ICacheAccess;
import org.apache.shiro.subject.Subject;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.caching.Cache;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.backend.implementation.MySQL.MySQLHelper;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.misc.DBHelper;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.query.CQLParser.CqContext;
-import org.caosdb.server.query.CQLParsingErrorListener.ParsingError;
-import org.caosdb.server.transaction.TransactionInterface;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.utils.ResultSetIterator;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.caching.Cache;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.backend.implementation.MySQL.MySQLHelper;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.misc.DBHelper;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.query.CQLParser.CqContext;
+import org.linkahead.server.query.CQLParsingErrorListener.ParsingError;
+import org.linkahead.server.transaction.TransactionInterface;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.utils.ResultSetIterator;
import org.slf4j.Logger;
public class Query implements QueryInterface, ToElementable, TransactionInterface {
@@ -259,7 +259,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
}
private final boolean filterEntitiesWithoutRetrievePermisions =
- !CaosDBServer.getServerProperty(
+ !LinkAheadServer.getServerProperty(
ServerProperties.KEY_QUERY_FILTER_ENTITIES_WITHOUT_RETRIEVE_PERMISSIONS)
.equalsIgnoreCase("FALSE");
@@ -602,13 +602,13 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
try {
this.role =
Role.valueOf(
- CaosDBServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
} catch (IllegalArgumentException e) {
addError(
"Unsupportet value of the server property "
+ ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE
+ ": "
- + CaosDBServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_FIND_QUERY_DEFAULT_ROLE));
throw new UnsupportedOperationException(e);
}
}
@@ -645,7 +645,7 @@ public class Query implements QueryInterface, ToElementable, TransactionInterfac
private String generateSelectStatementForResultSet(
final String resultSetTableName, final boolean versioned) {
// TODO remove the entities.role part when
- // https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/issues/245 is resolved
+ // https://gitlab.indiscale.com/caosdb/src/linkahead-server/-/issues/245 is resolved
if (resultSetTableName.equals("entities")) {
final String baseStatement =
"SELECT entities.id, entity_acl.acl FROM entities INNER JOIN entity_acl ON entity_acl.id=entities.acl WHERE entities.role!='DOMAIN'";
diff --git a/src/main/java/org/caosdb/server/query/QueryInterface.java b/src/main/java/org/caosdb/server/query/QueryInterface.java
index 0f2db9a9..bef36cce 100644
--- a/src/main/java/org/caosdb/server/query/QueryInterface.java
+++ b/src/main/java/org/caosdb/server/query/QueryInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.Connection;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
+import org.linkahead.server.database.access.Access;
public interface QueryInterface {
diff --git a/src/main/java/org/caosdb/server/query/RoleFilter.java b/src/main/java/org/caosdb/server/query/RoleFilter.java
index 97d1b1ea..eb73e48f 100644
--- a/src/main/java/org/caosdb/server/query/RoleFilter.java
+++ b/src/main/java/org/caosdb/server/query/RoleFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.SQLException;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.server.query.Query.Role;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.server.query.Query.Role;
public class RoleFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/StoredAt.java b/src/main/java/org/caosdb/server/query/StoredAt.java
index 90adc188..c0731f88 100644
--- a/src/main/java/org/caosdb/server/query/StoredAt.java
+++ b/src/main/java/org/caosdb/server/query/StoredAt.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
@@ -30,8 +30,8 @@ import java.sql.CallableStatement;
import java.sql.SQLException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.query.Query.QueryException;
public class StoredAt implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/SubProperty.java b/src/main/java/org/caosdb/server/query/SubProperty.java
index d5ce9234..00ff7ab4 100644
--- a/src/main/java/org/caosdb/server/query/SubProperty.java
+++ b/src/main/java/org/caosdb/server/query/SubProperty.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,19 +20,19 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static java.sql.Types.VARCHAR;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.query.Query.QueryException;
public class SubProperty implements QueryInterface, EntityFilterInterface {
private final EntityFilterInterface filter;
diff --git a/src/main/java/org/caosdb/server/query/TransactionFilter.java b/src/main/java/org/caosdb/server/query/TransactionFilter.java
index 2099639b..9c4443c6 100644
--- a/src/main/java/org/caosdb/server/query/TransactionFilter.java
+++ b/src/main/java/org/caosdb/server/query/TransactionFilter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.sql.CallableStatement;
import java.sql.Connection;
import java.sql.SQLException;
import java.sql.Types;
-import org.caosdb.datetime.Date;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.datetime.Interval;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.query.Query.QueryException;
import org.jdom2.Element;
+import org.linkahead.datetime.Date;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.datetime.Interval;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.query.Query.QueryException;
public class TransactionFilter implements EntityFilterInterface {
diff --git a/src/main/java/org/caosdb/server/query/Utils.java b/src/main/java/org/caosdb/server/query/Utils.java
index 661cee12..b5180c6b 100644
--- a/src/main/java/org/caosdb/server/query/Utils.java
+++ b/src/main/java/org/caosdb/server/query/Utils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import java.io.PrintStream;
import java.sql.Connection;
diff --git a/src/main/java/org/caosdb/server/query/VersionFilter.java b/src/main/java/org/caosdb/server/query/VersionFilter.java
index aa391778..b6f24038 100644
--- a/src/main/java/org/caosdb/server/query/VersionFilter.java
+++ b/src/main/java/org/caosdb/server/query/VersionFilter.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.query;
+package org.linkahead.server.query;
public class VersionFilter {
diff --git a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
index 44ebfa22..ba20d654 100644
--- a/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
+++ b/src/main/java/org/caosdb/server/resource/AbstractCaosDBServerResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
@@ -41,17 +41,17 @@ import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.WebinterfaceUtils;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Form;
import org.restlet.data.Header;
import org.restlet.data.Parameter;
@@ -69,7 +69,7 @@ import org.restlet.util.Series;
*
* @author Timm Fitschen
*/
-public abstract class AbstractCaosDBServerResource extends ServerResource {
+public abstract class AbstractLinkAheadServerResource extends ServerResource {
private final HashMap<String, String> flags = new HashMap<String, String>();
private Long timestamp = null;
@@ -243,7 +243,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected abstract Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception;
@Post
@@ -277,7 +277,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
@@ -293,7 +293,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
getResponse().setStatus(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
return null;
@@ -314,7 +314,7 @@ public abstract class AbstractCaosDBServerResource extends ServerResource {
}
protected String getXSLScript() {
- return this.utils.getWebinterfaceURI("webcaosdb.xsl");
+ return this.utils.getWebinterfaceURI("weblinkahead.xsl");
}
/** Wrap an element for an "OK" response. */
diff --git a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
index ed60d790..f38a9d66 100644
--- a/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
+++ b/src/main/java/org/caosdb/server/resource/AuthenticationResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -31,28 +31,28 @@ import org.apache.shiro.authc.AccountException;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.authc.CredentialsException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.RealmUsernamePasswordToken;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.RealmUsernamePasswordToken;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Reference;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class AuthenticationResource extends AbstractCaosDBServerResource {
+public class AuthenticationResource extends AbstractLinkAheadServerResource {
/** Returns single "Login" element. XSLT will create a form. */
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
final Element rootElem = generateRootElement();
@@ -66,7 +66,7 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
final Subject user = SecurityUtils.getSubject();
if (user.isAuthenticated()) {
@@ -112,7 +112,7 @@ public class AuthenticationResource extends AbstractCaosDBServerResource {
} catch (final CredentialsException | AccountException e) {
getLogger().log(Level.INFO, "LOGIN_FAILED", e);
} catch (final AuthenticationException e) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getLogger().log(Level.INFO, "LOGIN_FAILED", e);
} else {
getLogger().log(Level.INFO, "LOGIN_FAILED\t" + e.getMessage());
diff --git a/src/main/java/org/caosdb/server/resource/DefaultResource.java b/src/main/java/org/caosdb/server/resource/DefaultResource.java
index 488cd667..5cdad9b8 100644
--- a/src/main/java/org/caosdb/server/resource/DefaultResource.java
+++ b/src/main/java/org/caosdb/server/resource/DefaultResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
import org.restlet.representation.Representation;
-public class DefaultResource extends AbstractCaosDBServerResource {
+public class DefaultResource extends AbstractLinkAheadServerResource {
private Element responseBody = null;
@@ -43,7 +43,7 @@ public class DefaultResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new org.jdom2.Document();
final Element root = generateRootElement();
diff --git a/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java b/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
index 41f92a56..304c8f75 100644
--- a/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
+++ b/src/main/java/org/caosdb/server/resource/EntityOwnerResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,12 +22,12 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.resource.transaction.RetrieveEntityResource;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.resource.transaction.RetrieveEntityResource;
/**
* Resource which returns the entity with the owner information attached to it.
diff --git a/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java b/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
index 1f5ee5f7..144eabe6 100644
--- a/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
+++ b/src/main/java/org/caosdb/server/resource/EntityPermissionsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,11 +22,11 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.resource.transaction.RetrieveEntityResource;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.resource.transaction.RetrieveEntityResource;
/**
* Resource which appends the entity permissions (esp. the global ones) to the normal entity
diff --git a/src/main/java/org/caosdb/server/resource/FileSystemResource.java b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
index 9c0d6158..69653780 100644
--- a/src/main/java/org/caosdb/server/resource/FileSystemResource.java
+++ b/src/main/java/org/caosdb/server/resource/FileSystemResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
-import static org.caosdb.server.FileSystem.getFromFileSystem;
+import static org.linkahead.server.FileSystem.getFromFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.transaction.RetrieveSparseEntityByPath;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Attribute;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.transaction.RetrieveSparseEntityByPath;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
@@ -53,7 +53,7 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen
*/
-public class FileSystemResource extends AbstractCaosDBServerResource {
+public class FileSystemResource extends AbstractLinkAheadServerResource {
public static Message ORPHANED_FILE_WARNING =
new Message(
@@ -61,7 +61,7 @@ public class FileSystemResource extends AbstractCaosDBServerResource {
"Orphaned file. The file is not tracked. This is probably a harmless inconsistency but it might be a sign of other problems.");
/**
- * Download a File from the CaosDBFileSystem. Only one File per Request.
+ * Download a File from the LinkAheadFileSystem. Only one File per Request.
*
* @author Timm Fitschen
* @return InputRepresentation
diff --git a/src/main/java/org/caosdb/server/resource/InfoResource.java b/src/main/java/org/caosdb/server/resource/InfoResource.java
index 452ea795..1d423905 100644
--- a/src/main/java/org/caosdb/server/resource/InfoResource.java
+++ b/src/main/java/org/caosdb/server/resource/InfoResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.util.TimeZone;
-import org.caosdb.datetime.UTCTimeZoneShift;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.utils.FlagInfo;
-import org.caosdb.server.utils.Info;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.datetime.UTCTimeZoneShift;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.utils.FlagInfo;
+import org.linkahead.server.utils.Info;
import org.restlet.representation.Representation;
-/** This class represents the information retrieved by /Info requests (only GET) to CaosDB. */
-public class InfoResource extends AbstractCaosDBServerResource {
+/** This class represents the information retrieved by /Info requests (only GET) to LinkAhead. */
+public class InfoResource extends AbstractLinkAheadServerResource {
/**
* The response to the HTTP GET request is generated here.
diff --git a/src/main/java/org/caosdb/server/resource/JdomRepresentation.java b/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
index 4be6743d..b1a146d9 100644
--- a/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
+++ b/src/main/java/org/caosdb/server/resource/JdomRepresentation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.io.OutputStream;
import java.io.Writer;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.ProcessingInstruction;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.data.MediaType;
import org.restlet.data.Reference;
import org.restlet.representation.WriterRepresentation;
@@ -82,7 +82,7 @@ public class JdomRepresentation extends WriterRepresentation {
public static final String getWebUIRef(final Reference reference) {
return reference.getHostIdentifier()
- + CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT)
+ + LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT)
+ "/webinterface/";
}
diff --git a/src/main/java/org/caosdb/server/resource/LogoutResource.java b/src/main/java/org/caosdb/server/resource/LogoutResource.java
index 1659f751..524d7b29 100644
--- a/src/main/java/org/caosdb/server/resource/LogoutResource.java
+++ b/src/main/java/org/caosdb/server/resource/LogoutResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
import org.restlet.representation.Representation;
public class LogoutResource extends AuthenticationResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
return super.httpDeleteInChildClass();
}
diff --git a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
index 8d2aa172..61b380ac 100644
--- a/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
+++ b/src/main/java/org/caosdb/server/resource/PermissionRulesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,31 +20,31 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
import java.util.HashSet;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.transaction.RetrievePermissionRulesTransaction;
-import org.caosdb.server.transaction.UpdatePermissionRulesTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.transaction.RetrievePermissionRulesTransaction;
+import org.linkahead.server.transaction.UpdatePermissionRulesTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class PermissionRulesResource extends AbstractCaosDBServerResource {
+public class PermissionRulesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final String role = getRequestedItems()[0];
diff --git a/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java b/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
index 3620eef2..f0d16d82 100644
--- a/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
+++ b/src/main/java/org/caosdb/server/resource/ReReadableRepresentation.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import com.google.common.base.Charsets;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/resource/RolesResource.java b/src/main/java/org/caosdb/server/resource/RolesResource.java
index ad1544da..f189e10a 100644
--- a/src/main/java/org/caosdb/server/resource/RolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/RolesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,33 +20,33 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.DeleteRoleTransaction;
-import org.caosdb.server.transaction.InsertRoleTransaction;
-import org.caosdb.server.transaction.RetrieveRoleTransaction;
-import org.caosdb.server.transaction.UpdateRoleTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.DeleteRoleTransaction;
+import org.linkahead.server.transaction.InsertRoleTransaction;
+import org.linkahead.server.transaction.RetrieveRoleTransaction;
+import org.linkahead.server.transaction.UpdateRoleTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class RolesResource extends AbstractCaosDBServerResource {
+public class RolesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Element root = generateRootElement();
final Document document = new Document();
@@ -74,7 +74,7 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
if (getRequestedItems().length > 0) {
final String name = getRequestedItems()[0];
@@ -97,7 +97,7 @@ public class RolesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpPostInChildClass(final Representation entity)
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, xmlNotWellFormedException, JDOMException, Exception {
String name = null;
diff --git a/src/main/java/org/caosdb/server/resource/ScriptingResource.java b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
index 6e7cf721..42a8aeb1 100644
--- a/src/main/java/org/caosdb/server/resource/ScriptingResource.java
+++ b/src/main/java/org/caosdb/server/resource/ScriptingResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import com.ibm.icu.text.Collator;
import java.io.IOException;
@@ -38,19 +38,19 @@ import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.scripting.CallerSerializer;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.scripting.ServerSideScriptingCaller;
-import org.caosdb.server.utils.Serializer;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.scripting.CallerSerializer;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.scripting.ServerSideScriptingCaller;
+import org.linkahead.server.utils.Serializer;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
import org.restlet.data.CharacterSet;
import org.restlet.data.Form;
import org.restlet.data.MediaType;
@@ -60,7 +60,7 @@ import org.restlet.engine.header.ContentType;
import org.restlet.ext.fileupload.RestletFileUpload;
import org.restlet.representation.Representation;
-public class ScriptingResource extends AbstractCaosDBServerResource {
+public class ScriptingResource extends AbstractLinkAheadServerResource {
private ServerSideScriptingCaller caller;
private Collection<FileProperties> deleteFiles = new LinkedList<>();
diff --git a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
index f304f100..bbbd8267 100644
--- a/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
+++ b/src/main/java/org/caosdb/server/resource/ServerLogsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -29,19 +29,19 @@ import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
import java.util.logging.XMLFormatter;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.transaction.RetrieveLogRecordTransaction;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.transaction.RetrieveLogRecordTransaction;
import org.restlet.data.Form;
import org.restlet.data.MediaType;
import org.restlet.representation.Representation;
import org.restlet.representation.StringRepresentation;
-public class ServerLogsResource extends AbstractCaosDBServerResource {
+public class ServerLogsResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
Level level = null;
diff --git a/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java b/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
index 5b4e8316..1d4916cf 100644
--- a/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
+++ b/src/main/java/org/caosdb/server/resource/ServerPropertiesResource.java
@@ -1,14 +1,14 @@
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerPropertiesSerializer;
-import org.caosdb.server.accessControl.ACMPermissions;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerPropertiesSerializer;
+import org.linkahead.server.accessControl.ACMPermissions;
import org.restlet.data.Form;
import org.restlet.data.Parameter;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class ServerPropertiesResource extends AbstractCaosDBServerResource {
+public class ServerPropertiesResource extends AbstractLinkAheadServerResource {
@Override
protected void doInit() {
@@ -22,24 +22,24 @@ public class ServerPropertiesResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpGetInChildClass() {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getUser().checkPermission(ACMPermissions.PERMISSION_ACCESS_SERVER_PROPERTIES);
return super.ok(
- new ServerPropertiesSerializer().serialize(CaosDBServer.getServerProperties()));
+ new ServerPropertiesSerializer().serialize(LinkAheadServer.getServerProperties()));
}
return error(Status.CLIENT_ERROR_NOT_FOUND);
}
@Override
protected Representation httpPostInChildClass(Representation entity) {
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
getUser().checkPermission(ACMPermissions.PERMISSION_ACCESS_SERVER_PROPERTIES);
Form form = new Form(entity);
for (Parameter param : form) {
- CaosDBServer.setProperty(param.getName(), param.getValue());
+ LinkAheadServer.setProperty(param.getName(), param.getValue());
}
return super.ok(
- new ServerPropertiesSerializer().serialize(CaosDBServer.getServerProperties()));
+ new ServerPropertiesSerializer().serialize(LinkAheadServer.getServerProperties()));
}
return error(Status.CLIENT_ERROR_NOT_FOUND);
}
diff --git a/src/main/java/org/caosdb/server/resource/SharedFileResource.java b/src/main/java/org/caosdb/server/resource/SharedFileResource.java
index 971dff69..4bfed91a 100644
--- a/src/main/java/org/caosdb/server/resource/SharedFileResource.java
+++ b/src/main/java/org/caosdb/server/resource/SharedFileResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,17 +22,17 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static java.net.URLDecoder.decode;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.utils.FileUtils;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.JDOMException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.utils.FileUtils;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
@@ -44,7 +44,7 @@ import org.restlet.representation.Representation;
*
* @author Daniel Hornung
*/
-public class SharedFileResource extends AbstractCaosDBServerResource {
+public class SharedFileResource extends AbstractLinkAheadServerResource {
/**
* Download a File from the tempfiles folder. Only one File per Request.
diff --git a/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java b/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
index c74251a1..9396c13f 100644
--- a/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
+++ b/src/main/java/org/caosdb/server/resource/ThumbnailsResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,25 +20,25 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import static org.caosdb.server.FileSystem.getFromFileSystem;
+import static org.linkahead.server.FileSystem.getFromFileSystem;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.JDOMException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Disposition;
import org.restlet.data.MediaType;
import org.restlet.data.Status;
import org.restlet.representation.FileRepresentation;
import org.restlet.representation.Representation;
-public class ThumbnailsResource extends AbstractCaosDBServerResource {
+public class ThumbnailsResource extends AbstractLinkAheadServerResource {
/**
- * Download a File from the CaosDBFileSystem. Only one File per Request.
+ * Download a File from the LinkAheadFileSystem. Only one File per Request.
*
* @author Timm Fitschen
* @return InputRepresentation
diff --git a/src/main/java/org/caosdb/server/resource/UserResource.java b/src/main/java/org/caosdb/server/resource/UserResource.java
index de07331e..b8b0f5e8 100644
--- a/src/main/java/org/caosdb/server/resource/UserResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,27 +20,27 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.DeleteUserTransaction;
-import org.caosdb.server.transaction.InsertUserTransaction;
-import org.caosdb.server.transaction.RetrieveUserTransaction;
-import org.caosdb.server.transaction.UpdateUserTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.DeleteUserTransaction;
+import org.linkahead.server.transaction.InsertUserTransaction;
+import org.linkahead.server.transaction.RetrieveUserTransaction;
+import org.linkahead.server.transaction.UpdateUserTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Form;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
@@ -50,11 +50,11 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen
*/
-public class UserResource extends AbstractCaosDBServerResource {
+public class UserResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
@@ -148,7 +148,8 @@ public class UserResource extends AbstractCaosDBServerResource {
UserStatus.valueOf(
form.getFirstValue(
"status",
- CaosDBServer.getServerProperty(ServerProperties.KEY_NEW_USER_DEFAULT_ACTIVITY))
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_NEW_USER_DEFAULT_ACTIVITY))
.toUpperCase());
Integer userEntity = null;
if (form.getFirst("entity") != null) {
@@ -177,7 +178,7 @@ public class UserResource extends AbstractCaosDBServerResource {
@Override
protected Representation httpDeleteInChildClass()
- throws ConnectionException, SQLException, CaosDBException, IOException,
+ throws ConnectionException, SQLException, LinkAheadException, IOException,
NoSuchAlgorithmException, Exception {
final Document doc = new Document();
diff --git a/src/main/java/org/caosdb/server/resource/UserRolesResource.java b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
index 4eb7f614..8ba20442 100644
--- a/src/main/java/org/caosdb/server/resource/UserRolesResource.java
+++ b/src/main/java/org/caosdb/server/resource/UserRolesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,32 +20,32 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.List;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.RetrieveUserRolesTransaction;
-import org.caosdb.server.transaction.UpdateUserRolesTransaction;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.RetrieveUserRolesTransaction;
+import org.linkahead.server.transaction.UpdateUserRolesTransaction;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.Status;
import org.restlet.representation.Representation;
-public class UserRolesResource extends AbstractCaosDBServerResource {
+public class UserRolesResource extends AbstractLinkAheadServerResource {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final String user = getRequestedItems()[0];
final String realm =
diff --git a/src/main/java/org/caosdb/server/resource/Webinterface.java b/src/main/java/org/caosdb/server/resource/Webinterface.java
index 95901260..bf781217 100644
--- a/src/main/java/org/caosdb/server/resource/Webinterface.java
+++ b/src/main/java/org/caosdb/server/resource/Webinterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.utils.WebinterfaceUtils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.CacheDirective;
import org.restlet.data.Header;
import org.restlet.data.MediaType;
@@ -98,7 +98,8 @@ public class Webinterface extends ServerResource {
cacheDirectives.add(
new CacheDirective(
HeaderConstants.CACHE_MAX_AGE,
- CaosDBServer.getServerProperty(ServerProperties.KEY_WEBUI_HTTP_HEADER_CACHE_MAX_AGE)));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_WEBUI_HTTP_HEADER_CACHE_MAX_AGE)));
getResponse().setCacheDirectives(cacheDirectives);
return ret;
}
diff --git a/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java b/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
index 22f1a46e..428cbe14 100644
--- a/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
+++ b/src/main/java/org/caosdb/server/resource/WebinterfaceBuildNumber.java
@@ -1,5 +1,5 @@
/**
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * ** header v3.0 This file is a part of the LinkAhead Project.
*
* <p>Copyright (c) 2019 IndiScale GmbH Copyright (c) 2019 Daniel Hornung <d.hornung@indiscale.com>
*
@@ -16,9 +16,9 @@
*
* <p>** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
-import org.caosdb.server.utils.WebinterfaceUtils;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Status;
import org.restlet.resource.Get;
import org.restlet.resource.ResourceException;
diff --git a/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java b/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
index 0c66485e..7fd72906 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/EntityNamesResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,9 +22,9 @@
*
* ** end header
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
-import org.caosdb.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.container.RetrieveContainer;
/**
* Resource which returns only the names of entities.
diff --git a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
index 4cd7b2fc..d2a54274 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/EntityResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -28,22 +28,22 @@ import org.apache.commons.fileupload.FileItemIterator;
import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.disk.DiskFileItemFactory;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.transaction.WriteTransaction;
-import org.caosdb.server.transaction.WriteTransactionInterface;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.transaction.WriteTransaction;
+import org.linkahead.server.transaction.WriteTransactionInterface;
+import org.linkahead.server.utils.ServerMessages;
import org.restlet.data.MediaType;
import org.restlet.ext.fileupload.RestletFileUpload;
import org.restlet.representation.Representation;
@@ -130,7 +130,7 @@ public class EntityResource extends RetrieveEntityResource {
*/
private Element parseMultipartEntity(final WritableContainer container)
throws FileUploadException, IOException, Message, xmlNotWellFormedException,
- NoSuchAlgorithmException, CaosDBException {
+ NoSuchAlgorithmException, LinkAheadException {
final DiskFileItemFactory factory = new DiskFileItemFactory();
factory.setSizeThreshold(1000240);
final RestletFileUpload upload = new RestletFileUpload(factory);
diff --git a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
index 6527376d..0a24366a 100644
--- a/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
+++ b/src/main/java/org/caosdb/server/resource/transaction/RetrieveEntityResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,19 +19,19 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.resource.transaction;
+package org.linkahead.server.resource.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.sql.SQLException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.transaction.Retrieve;
import org.jdom2.Document;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.transaction.Retrieve;
import org.restlet.representation.Representation;
/**
@@ -40,7 +40,7 @@ import org.restlet.representation.Representation;
*
* @author Timm Fitschen (t.fitschen@indiscale.com)
*/
-public abstract class RetrieveEntityResource extends AbstractCaosDBServerResource {
+public abstract class RetrieveEntityResource extends AbstractLinkAheadServerResource {
/**
* Parse the segment which specifies the entities which are to be retrieved
@@ -74,7 +74,7 @@ public abstract class RetrieveEntityResource extends AbstractCaosDBServerResourc
/** Handle the GET request. */
@Override
protected final Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
final RetrieveContainer entityContainer =
diff --git a/src/main/java/org/caosdb/server/scripting/CallerSerializer.java b/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
index b133ad5c..710f7860 100644
--- a/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
+++ b/src/main/java/org/caosdb/server/scripting/CallerSerializer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,12 +21,12 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.IOException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.utils.Serializer;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.utils.Serializer;
/**
* Serializes the result of calling a server-side script into XML.
@@ -49,14 +49,14 @@ public class CallerSerializer implements Serializer<ServerSideScriptingCaller, E
try {
stdout.addContent(caller.getStdOut());
} catch (IOException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
Element stderr = new Element("stderr");
try {
stderr.addContent(caller.getStdErr());
} catch (IOException e) {
- throw new CaosDBException(e);
+ throw new LinkAheadException(e);
}
Element tmpdir = new Element("shareddir");
diff --git a/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java b/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
index 0af49e9f..9b09785d 100644
--- a/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
+++ b/src/main/java/org/caosdb/server/scripting/ScriptingPermissions.java
@@ -1,6 +1,6 @@
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
-import org.caosdb.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.ACMPermissions;
public class ScriptingPermissions extends ACMPermissions {
diff --git a/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java b/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
index c9a0b522..5cc3b459 100644
--- a/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
+++ b/src/main/java/org/caosdb/server/scripting/ScriptingUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ConfigurationException;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ConfigurationException;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class ScriptingUtils {
@@ -40,11 +40,11 @@ public class ScriptingUtils {
public ScriptingUtils() {
ArrayList<File> new_bin_dirs = new ArrayList<>();
String bin_dirs_str =
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS);
if (bin_dirs_str == null) {
// fall-back for old server property
bin_dirs_str =
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIR);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIR);
}
// split and process
@@ -75,7 +75,8 @@ public class ScriptingUtils {
this.working =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR));
+ LinkAheadServer.getServerProperty(
+ ServerProperties.KEY_SERVER_SIDE_SCRIPTING_WORKING_DIR));
if (!working.exists()) {
working.mkdirs();
diff --git a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
index edb6b39a..a64378c3 100644
--- a/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
+++ b/src/main/java/org/caosdb/server/scripting/ServerSideScriptingCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.File;
import java.io.FileNotFoundException;
@@ -34,13 +34,13 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
/**
* Calls server-side scripting scripts.
@@ -163,7 +163,7 @@ public class ServerSideScriptingCaller {
}
void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {
+ throws FileNotFoundException, LinkAheadException {
if (files == null) {
return;
}
@@ -174,13 +174,13 @@ public class ServerSideScriptingCaller {
}
for (final FileProperties f : files) {
if (f.getPath() == null || f.getPath().isEmpty()) {
- throw new CaosDBException("The path must not be null or empty!");
+ throw new LinkAheadException("The path must not be null or empty!");
}
File link = getUploadFilesDir().toPath().resolve(f.getPath()).toFile();
if (!link.getParentFile().exists()) {
link.getParentFile().mkdirs();
}
- org.caosdb.server.utils.FileUtils.createSymlink(link, f.getFile());
+ org.linkahead.server.utils.FileUtils.createSymlink(link, f.getFile());
}
}
@@ -196,7 +196,7 @@ public class ServerSideScriptingCaller {
}
/**
- * Create a writable "home like" directory, needed for some Python libs, e.g. caosdb-pylib.
+ * Create a writable "home like" directory, needed for some Python libs, e.g. linkahead-pylib.
*
* <p>The temporary working directory must exist when this method is called.
*/
@@ -212,7 +212,7 @@ public class ServerSideScriptingCaller {
}
File srcDir =
new File(
- CaosDBServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_HOME_DIR));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_SERVER_SIDE_SCRIPTING_HOME_DIR));
FileUtils.copyDirectory(srcDir, this.tmpHome);
}
diff --git a/src/main/java/org/caosdb/server/scripting/TimeoutException.java b/src/main/java/org/caosdb/server/scripting/TimeoutException.java
index 31b9b7e9..bbe0e771 100644
--- a/src/main/java/org/caosdb/server/scripting/TimeoutException.java
+++ b/src/main/java/org/caosdb/server/scripting/TimeoutException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
public class TimeoutException extends Exception {
diff --git a/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java b/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
index c867ca3b..2e1ce29d 100644
--- a/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
+++ b/src/main/java/org/caosdb/server/scripting/TimeoutProcess.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import java.io.InputStream;
diff --git a/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java b/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
index 1cf9f8f7..3dd74264 100644
--- a/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/AccessControlTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.Message;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.Message;
public abstract class AccessControlTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java b/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
index 1f52ca8d..6b742214 100644
--- a/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
+++ b/src/main/java/org/caosdb/server/transaction/ChecksumUpdater.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetUpdateableChecksums;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.database.backend.transaction.SetFileChecksum;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.utils.FileUtils;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetUpdateableChecksums;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.database.backend.transaction.SetFileChecksum;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.utils.FileUtils;
/**
* Retrieves all file without a checksum, calculates one and stores it to the database (method
@@ -108,7 +108,7 @@ public class ChecksumUpdater extends WriteTransaction
private boolean wasChangedInTheMeantime(
final EntityInterface fileEntity, final Access access, final long lastModified)
- throws NoSuchAlgorithmException, IOException, CaosDBException, Message {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException, Message {
final EntityInterface checkEntity =
execute(new RetrieveSparseEntity(fileEntity), access).getEntity();
final FileProperties thatFP = checkEntity.getFileProperties();
@@ -126,7 +126,7 @@ public class ChecksumUpdater extends WriteTransaction
e.printStackTrace();
} catch (final IOException e) {
e.printStackTrace();
- } catch (final CaosDBException e) {
+ } catch (final LinkAheadException e) {
e.printStackTrace();
}
return null;
diff --git a/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
index 2e7e5b2a..532a4afa 100644
--- a/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/DeleteRoleTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,16 +21,16 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.DeleteRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.DeleteRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
index 24aac16b..200277a3 100644
--- a/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/DeleteUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,20 +21,20 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.DeletePassword;
-import org.caosdb.server.database.backend.transaction.DeleteUser;
-import org.caosdb.server.database.backend.transaction.RetrievePasswordValidator;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.DeletePassword;
+import org.linkahead.server.database.backend.transaction.DeleteUser;
+import org.linkahead.server.database.backend.transaction.RetrievePasswordValidator;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class DeleteUserTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
index 59d12c73..54f42f9d 100644
--- a/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
+++ b/src/main/java/org/caosdb/server/transaction/FileStorageConsistencyCheck.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.ArrayList;
import java.util.HashMap;
@@ -28,22 +28,22 @@ import java.util.Iterator;
import java.util.List;
import java.util.Map.Entry;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.FileConsistencyCheck;
-import org.caosdb.server.database.backend.transaction.GetFileIterator;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.backend.transaction.RetrieveAllUncheckedFiles;
-import org.caosdb.server.database.backend.transaction.SetFileCheckedTimestamp;
-import org.caosdb.server.database.exceptions.EntityDoesNotExistException;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.xml.ToElementable;
-import org.caosdb.server.utils.SHA512;
import org.jdom2.Element;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.FileConsistencyCheck;
+import org.linkahead.server.database.backend.transaction.GetFileIterator;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.backend.transaction.RetrieveAllUncheckedFiles;
+import org.linkahead.server.database.backend.transaction.SetFileCheckedTimestamp;
+import org.linkahead.server.database.exceptions.EntityDoesNotExistException;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.xml.ToElementable;
+import org.linkahead.server.utils.SHA512;
public class FileStorageConsistencyCheck extends Thread
implements ToElementable, TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
index 950d9b8d..a7ecbb40 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertLogRecordTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.logging.LogRecord;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.InsertLogRecord;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.InsertLogRecord;
public class InsertLogRecordTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
index 44288af5..173907d8 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertRoleTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.InsertRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.InsertRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class InsertRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
index f3f4c7f5..1ef9e9f7 100644
--- a/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/InsertUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,24 +21,24 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.transaction.SetPassword;
-import org.caosdb.server.database.backend.transaction.UpdateUser;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.transaction.SetPassword;
+import org.linkahead.server.database.backend.transaction.UpdateUser;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
public class InsertUserTransaction extends AccessControlTransaction {
@@ -92,10 +92,10 @@ public class InsertUserTransaction extends AccessControlTransaction {
* Check requirements for user names (length, character set). Default config is POSIX compliant.
*/
private void checkUserName(String name) throws Message {
- String regex = CaosDBServer.getServerProperty(ServerProperties.KEY_USER_NAME_VALID_REGEX);
+ String regex = LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_NAME_VALID_REGEX);
if (!name.matches(regex)) {
throw ServerMessages.INVALID_USER_NAME(
- CaosDBServer.getServerProperty(ServerProperties.KEY_USER_NAME_INVALID_MESSAGE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_USER_NAME_INVALID_MESSAGE));
}
if (UserSources.isUserExisting(new Principal(this.user.realm, this.user.name))) {
diff --git a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
index ed3cd3cc..3abd2dd7 100644
--- a/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListRolesTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,17 +19,17 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.ListRoles;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.ListRoles;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListRolesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
index 2ade4e85..c14051a4 100644
--- a/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/ListUsersTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,15 +19,15 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.ListUsers;
-import org.caosdb.server.database.proto.ProtoUser;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.ListUsers;
+import org.linkahead.server.database.proto.ProtoUser;
public class ListUsersTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java b/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
index dff0d34f..a08bc1f1 100644
--- a/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/LogUserVisitTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,9 +17,9 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.database.backend.transaction.LogUserVisit;
+import org.linkahead.server.database.backend.transaction.LogUserVisit;
public class LogUserVisitTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/Retrieve.java b/src/main/java/org/caosdb/server/transaction/Retrieve.java
index 643c1201..3f11f976 100644
--- a/src/main/java/org/caosdb/server/transaction/Retrieve.java
+++ b/src/main/java/org/caosdb/server/transaction/Retrieve.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,21 +20,21 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.jobs.core.RemoveDuplicates;
-import org.caosdb.server.jobs.core.ResolveNames;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.jobs.core.RemoveDuplicates;
+import org.linkahead.server.jobs.core.ResolveNames;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class Retrieve extends Transaction<RetrieveContainer> {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
index ac0a2896..d905a193 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,19 +19,19 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import com.google.protobuf.ProtocolStringList;
import java.util.UUID;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveEntityACLTransaction;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
+import org.linkahead.server.database.backend.transaction.RetrieveEntityACLTransaction;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
public class RetrieveACL extends Transaction<TransactionContainer> {
@@ -75,7 +75,7 @@ public class RetrieveACL extends Transaction<TransactionContainer> {
&& acl.isPermitted(getTransactor(), EntityPermission.RETRIEVE_ENTITY)) {
throw new AuthorizationException("You are not permitted to update this entity's ACL.");
} else {
- e.addError(org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
+ e.addError(org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
}
}
}
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
index 2f6cafd6..d33d82a2 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveLogRecordTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.LogRecord;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.RetrieveLogRecord;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.RetrieveLogRecord;
public class RetrieveLogRecordTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
index bb1e136b..9d01ecf1 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrievePasswordValidatorTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.database.backend.transaction.RetrievePasswordValidator;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.database.backend.transaction.RetrievePasswordValidator;
+import org.linkahead.server.utils.ServerMessages;
public class RetrievePasswordValidatorTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
index 225d0688..f3fea603 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrievePermissionRulesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
-import org.caosdb.server.database.backend.transaction.RetrievePermissionRules;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.database.backend.transaction.RetrievePermissionRules;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class RetrievePermissionRulesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
index 8e92a347..a60b6bb3 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveRoleTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Iterator;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveRoleTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java b/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
index eca97ce6..902f5f67 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveSparseEntityByPath.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.server.database.backend.transaction.GetFileRecordByPath;
-import org.caosdb.server.database.backend.transaction.RetrieveSparseEntity;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.container.TransactionContainer;
+import org.linkahead.server.database.backend.transaction.GetFileRecordByPath;
+import org.linkahead.server.database.backend.transaction.RetrieveSparseEntity;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.container.TransactionContainer;
public class RetrieveSparseEntityByPath extends Transaction<TransactionContainer> {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
index e26e2983..acc3bdd9 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveUserRolesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,14 +20,14 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveUserRolesTransaction implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
index eb24fb24..41562e0e 100644
--- a/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/RetrieveUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,18 +21,18 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.RetrieveUser;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.RetrieveUser;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveUserTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/Transaction.java b/src/main/java/org/caosdb/server/transaction/Transaction.java
index 5fc06f5e..21ccb9df 100644
--- a/src/main/java/org/caosdb/server/transaction/Transaction.java
+++ b/src/main/java/org/caosdb/server/transaction/Transaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,34 +19,34 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashMap;
import java.util.List;
import org.apache.shiro.subject.Subject;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.InsertTransactionHistory;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.Schedule;
-import org.caosdb.server.jobs.ScheduledJob;
-import org.caosdb.server.jobs.TransactionStage;
-import org.caosdb.server.jobs.core.AccessControl;
-import org.caosdb.server.jobs.core.CheckDatatypePresent;
-import org.caosdb.server.jobs.core.CheckEntityACLRoles;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.jobs.core.PickUp;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.utils.AbstractObservable;
-import org.caosdb.server.utils.Info;
-import org.caosdb.server.utils.Observer;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.InsertTransactionHistory;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.Schedule;
+import org.linkahead.server.jobs.ScheduledJob;
+import org.linkahead.server.jobs.TransactionStage;
+import org.linkahead.server.jobs.core.AccessControl;
+import org.linkahead.server.jobs.core.CheckDatatypePresent;
+import org.linkahead.server.jobs.core.CheckEntityACLRoles;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.jobs.core.PickUp;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.utils.AbstractObservable;
+import org.linkahead.server.utils.Info;
+import org.linkahead.server.utils.Observer;
public abstract class Transaction<C extends TransactionContainer> extends AbstractObservable
implements TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/TransactionInterface.java b/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
index 8e01c7d9..68b0073b 100644
--- a/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
+++ b/src/main/java/org/caosdb/server/transaction/TransactionInterface.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.database.misc.TransactionBenchmark;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.database.misc.TransactionBenchmark;
public interface TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateACL.java b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
index 84c73080..5a8471ac 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateACL.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateACL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -19,22 +19,22 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import static org.caosdb.server.query.Query.clearCache;
+import static org.linkahead.server.query.Query.clearCache;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.UpdateEntityTransaction;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.core.CheckEntityACLRoles;
-import org.caosdb.server.jobs.core.JobFailureSeverity;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.utils.EntityStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.UpdateEntityTransaction;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.core.CheckEntityACLRoles;
+import org.linkahead.server.jobs.core.JobFailureSeverity;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateACL extends Transaction<TransactionContainer>
implements WriteTransactionInterface {
@@ -104,7 +104,7 @@ public class UpdateACL extends Transaction<TransactionContainer>
"You are not permitted to change permission rules of this entity.");
} else {
// we pretend this entity doesn't exist
- result.addError(org.caosdb.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
+ result.addError(org.linkahead.server.utils.ServerMessages.ENTITY_DOES_NOT_EXIST);
}
return result;
});
diff --git a/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
index 4f8c9369..929d8200 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdatePermissionRulesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class UpdatePermissionRulesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
index a62aff5b..02b8ec26 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateRoleTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,19 +21,19 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.backend.transaction.InsertRole;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.SetPermissionRules;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.backend.transaction.InsertRole;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.SetPermissionRules;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.ServerMessages;
public class UpdateRoleTransaction extends AccessControlTransaction {
@@ -58,7 +58,9 @@ public class UpdateRoleTransaction extends AccessControlTransaction {
Set<PermissionRule> oldPermissions = Set.copyOf(oldRole.permission_rules);
Set<PermissionRule> newPermissions = Set.copyOf(role.permission_rules);
if (!oldPermissions.equals(newPermissions)) {
- if (org.caosdb.server.permissions.Role.ADMINISTRATION.toString().equals(this.role.name)) {
+ if (org.linkahead.server.permissions.Role.ADMINISTRATION
+ .toString()
+ .equals(this.role.name)) {
throw ServerMessages.SPECIAL_ROLE_PERMISSIONS_CANNOT_BE_CHANGED();
}
subject.checkPermission(ACMPermissions.PERMISSION_UPDATE_ROLE_PERMISSIONS(this.role.name));
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
index a74d875f..74fa1b54 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateUserRolesTransaction.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.utils.ServerMessages;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.utils.ServerMessages;
public class UpdateUserRolesTransaction extends AccessControlTransaction {
diff --git a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
index 6808968f..0fa8216d 100644
--- a/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/UpdateUserTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,32 +21,32 @@
*
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.util.HashSet;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.accessControl.ACMPermissions;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.accessControl.UserStatus;
-import org.caosdb.server.database.backend.transaction.RetrieveRole;
-import org.caosdb.server.database.backend.transaction.RetrieveUser;
-import org.caosdb.server.database.backend.transaction.SetPassword;
-import org.caosdb.server.database.backend.transaction.UpdateUser;
-import org.caosdb.server.database.backend.transaction.UpdateUserRoles;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
+import org.linkahead.server.accessControl.ACMPermissions;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.accessControl.UserStatus;
+import org.linkahead.server.database.backend.transaction.RetrieveRole;
+import org.linkahead.server.database.backend.transaction.RetrieveUser;
+import org.linkahead.server.database.backend.transaction.SetPassword;
+import org.linkahead.server.database.backend.transaction.UpdateUser;
+import org.linkahead.server.database.backend.transaction.UpdateUserRoles;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
+import org.linkahead.server.utils.Utils;
/**
* This transaction also checks if the current user has sufficient permissions to make the update.
@@ -67,7 +67,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
final String password) {
this.user = new ProtoUser();
this.user.realm =
- realm == null
+ realm == null // If there was no definite realm to be found, use the internal realm's name.
? UserSources.guessRealm(username, UserSources.getInternalRealm().getName())
: realm;
this.user.name = username;
@@ -102,7 +102,7 @@ public class UpdateUserTransaction extends AccessControlTransaction {
+ this.user.realm
+ "' cannot be updated. Only the users from the realm '"
+ UserSources.getInternalRealm().getName()
- + "' can change their passwords from within caosdb.");
+ + "' can change their passwords from within LinkAhead.");
}
SecurityUtils.getSubject()
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
index 47b7a53c..22b8ac0c 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransaction.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
@@ -30,34 +30,34 @@ import java.util.Objects;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authz.AuthorizationException;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.DeleteEntityTransaction;
-import org.caosdb.server.database.backend.transaction.InsertEntityTransaction;
-import org.caosdb.server.database.backend.transaction.RetrieveFullEntityTransaction;
-import org.caosdb.server.database.backend.transaction.UpdateEntityTransaction;
-import org.caosdb.server.database.misc.RollBackHandler;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.container.TransactionContainer;
-import org.caosdb.server.entity.container.WritableContainer;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.Schedule;
-import org.caosdb.server.permissions.EntityACL;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.Permission;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.DeleteEntityTransaction;
+import org.linkahead.server.database.backend.transaction.InsertEntityTransaction;
+import org.linkahead.server.database.backend.transaction.RetrieveFullEntityTransaction;
+import org.linkahead.server.database.backend.transaction.UpdateEntityTransaction;
+import org.linkahead.server.database.misc.RollBackHandler;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.container.TransactionContainer;
+import org.linkahead.server.entity.container.WritableContainer;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.Schedule;
+import org.linkahead.server.permissions.EntityACL;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.Permission;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
/**
* This class is responsible for inserting, updating and deleting entities which are held in the
@@ -362,13 +362,13 @@ public class WriteTransaction extends Transaction<WritableContainer>
*
* @param newEntity
* @param oldEntity
- * @throws CaosDBException
+ * @throws LinkAheadException
* @throws IOException
* @throws NoSuchAlgorithmException
*/
public HashSet<Permission> deriveUpdate(
final EntityInterface newEntity, final EntityInterface oldEntity)
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final HashSet<Permission> needPermissions = new HashSet<>();
boolean updatetable = false;
diff --git a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
index 4e2938e1..44662633 100644
--- a/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
+++ b/src/main/java/org/caosdb/server/transaction/WriteTransactionInterface.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.access.Access;
+import org.linkahead.server.database.access.Access;
public interface WriteTransactionInterface extends TransactionInterface {
diff --git a/src/main/java/org/caosdb/server/utils/AbstractObservable.java b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
index abc7f0a0..996fd0b4 100644
--- a/src/main/java/org/caosdb/server/utils/AbstractObservable.java
+++ b/src/main/java/org/caosdb/server/utils/AbstractObservable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.Iterator;
import org.eclipse.jetty.util.ConcurrentHashSet;
diff --git a/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java b/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
index 47dad864..35524bf2 100644
--- a/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
+++ b/src/main/java/org/caosdb/server/utils/AsynchronousHasher.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@ package org.caosdb.server.utils;
*
* ** end header
*/
-// package org.caosdb.server.utils;
+// package org.linkahead.server.utils;
//
// import java.io.File;
//
diff --git a/src/main/java/org/caosdb/server/utils/ConfigurationException.java b/src/main/java/org/caosdb/server/utils/ConfigurationException.java
index df04ac16..509658fc 100644
--- a/src/main/java/org/caosdb/server/utils/ConfigurationException.java
+++ b/src/main/java/org/caosdb/server/utils/ConfigurationException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class ConfigurationException extends RuntimeException {
diff --git a/src/main/java/org/caosdb/server/utils/CronJob.java b/src/main/java/org/caosdb/server/utils/CronJob.java
index 8110a517..a0ac9703 100644
--- a/src/main/java/org/caosdb/server/utils/CronJob.java
+++ b/src/main/java/org/caosdb/server/utils/CronJob.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,10 +20,10 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.HashMap;
-import org.caosdb.server.CaosDBServer;
+import org.linkahead.server.LinkAheadServer;
public class CronJob {
@@ -44,7 +44,7 @@ public class CronJob {
}
}
if (onShutdown) {
- CaosDBServer.addPreShutdownHook(
+ LinkAheadServer.addPreShutdownHook(
new Runnable() {
@Override
public void run() {
diff --git a/src/main/java/org/caosdb/server/utils/EntityStatus.java b/src/main/java/org/caosdb/server/utils/EntityStatus.java
index d6658ef1..34f917b5 100644
--- a/src/main/java/org/caosdb/server/utils/EntityStatus.java
+++ b/src/main/java/org/caosdb/server/utils/EntityStatus.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,7 +22,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/**
* The order of the EntityStatus values matters, in that everything later than "QUALIFIED" also
diff --git a/src/main/java/org/caosdb/server/utils/FileUtils.java b/src/main/java/org/caosdb/server/utils/FileUtils.java
index eb4270f8..ee29ef7b 100644
--- a/src/main/java/org/caosdb/server/utils/FileUtils.java
+++ b/src/main/java/org/caosdb/server/utils/FileUtils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static java.nio.file.Files.isSameFile;
import static java.nio.file.Files.isSymbolicLink;
@@ -37,13 +37,13 @@ import java.nio.file.LinkOption;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Arrays;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
import org.eclipse.jetty.io.RuntimeIOException;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
public class FileUtils {
@@ -188,12 +188,12 @@ public class FileUtils {
}
public static String chownScript =
- CaosDBServer.getServerProperty(ServerProperties.KEY_CHOWN_SCRIPT);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CHOWN_SCRIPT);
public static void runChownScript(final File file) {
if (chown_enabled) {
try {
- final String sudopw = CaosDBServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
+ final String sudopw = LinkAheadServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
final Process cmd =
Runtime.getRuntime()
.exec(
@@ -208,7 +208,7 @@ public class FileUtils {
+ file.getAbsolutePath()
});
if (cmd.waitFor() != 0) {
- throw new TransactionException("caosdb_chown_dropoffbox failed.");
+ throw new TransactionException("linkahead_chown_dropoffbox failed.");
}
} catch (final InterruptedException e) {
throw new TransactionException(e);
@@ -222,11 +222,12 @@ public class FileUtils {
* @deprecated Soon to be removed.
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Deprecated
- public static void testChownScript() throws IOException, InterruptedException, CaosDBException {
- final String sudopw = CaosDBServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
+ public static void testChownScript()
+ throws IOException, InterruptedException, LinkAheadException {
+ final String sudopw = LinkAheadServer.getServerProperty(ServerProperties.KEY_SUDO_PASSWORD);
final Process cmd =
Runtime.getRuntime()
.exec(
@@ -311,7 +312,7 @@ public class FileUtils {
}
private static void moveReplace(File file, File target)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
if (exists(target)) {
org.apache.commons.io.FileUtils.forceDelete(target);
}
@@ -329,10 +330,10 @@ public class FileUtils {
* @param newlink
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
private static void moveSymlink(File oldlink, File newlink)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
File target = oldlink.toPath().toRealPath().toFile();
createSymlink(newlink, target);
callPosixUnlink(oldlink);
@@ -408,7 +409,7 @@ public class FileUtils {
}
public static Undoable delete(final File file)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
return delete(file, false);
}
@@ -423,10 +424,10 @@ public class FileUtils {
* @return
* @throws IOException
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
public static Undoable delete(final File file, final boolean recursive)
- throws IOException, CaosDBException, InterruptedException {
+ throws IOException, LinkAheadException, InterruptedException {
if (file.exists() && file.isFile()) {
// delete file
final File backup = getTmpFile(file.getName());
@@ -527,7 +528,7 @@ public class FileUtils {
private static void callPosixUnlink(File file) throws IOException, InterruptedException {
final Process cmd = Runtime.getRuntime().exec(new String[] {"unlink", file.getAbsolutePath()});
if (cmd.waitFor() != 0) {
- throw new CaosDBException("could not unlink " + file.getAbsolutePath());
+ throw new LinkAheadException("could not unlink " + file.getAbsolutePath());
}
}
diff --git a/src/main/java/org/caosdb/server/utils/FlagInfo.java b/src/main/java/org/caosdb/server/utils/FlagInfo.java
index 60697cb9..be6a8679 100644
--- a/src/main/java/org/caosdb/server/utils/FlagInfo.java
+++ b/src/main/java/org/caosdb/server/utils/FlagInfo.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,16 +20,16 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.lang.annotation.Annotation;
import java.util.ArrayList;
import java.util.Set;
-import org.caosdb.server.jobs.FlagJob;
-import org.caosdb.server.jobs.Job;
-import org.caosdb.server.jobs.JobAnnotation;
-import org.caosdb.server.transaction.TransactionInterface;
import org.jdom2.Element;
+import org.linkahead.server.jobs.FlagJob;
+import org.linkahead.server.jobs.Job;
+import org.linkahead.server.jobs.JobAnnotation;
+import org.linkahead.server.transaction.TransactionInterface;
import org.reflections.Reflections;
public class FlagInfo {
@@ -38,7 +38,7 @@ public class FlagInfo {
public static ArrayList<JobAnnotation> scan() {
final ArrayList<JobAnnotation> as = new ArrayList<JobAnnotation>();
- final Reflections jobPackage = new Reflections("org.caosdb.server.jobs.core");
+ final Reflections jobPackage = new Reflections("org.linkahead.server.jobs.core");
final Set<Class<? extends FlagJob>> allClassesSet = jobPackage.getSubTypesOf(FlagJob.class);
for (final Class<? extends Job> c : allClassesSet) {
for (final Annotation a : c.getAnnotations()) {
diff --git a/src/main/java/org/caosdb/server/utils/HashAlgorithm.java b/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
index 6bf517fc..1989c2b6 100644
--- a/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
+++ b/src/main/java/org/caosdb/server/utils/HashAlgorithm.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
diff --git a/src/main/java/org/caosdb/server/utils/HashException.java b/src/main/java/org/caosdb/server/utils/HashException.java
index 46c3ecc6..e0ebd41e 100644
--- a/src/main/java/org/caosdb/server/utils/HashException.java
+++ b/src/main/java/org/caosdb/server/utils/HashException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,11 +20,11 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.server.CaosDBException;
+import org.linkahead.server.LinkAheadException;
-public class HashException extends CaosDBException {
+public class HashException extends LinkAheadException {
/** */
private static final long serialVersionUID = 5478908505951882613L;
diff --git a/src/main/java/org/caosdb/server/utils/HashNotReadyException.java b/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
index 7b52a924..264d5084 100644
--- a/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
+++ b/src/main/java/org/caosdb/server/utils/HashNotReadyException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class HashNotReadyException extends HashException {
diff --git a/src/main/java/org/caosdb/server/utils/HashTimeoutException.java b/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
index 4733ae53..b7c3a1af 100644
--- a/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
+++ b/src/main/java/org/caosdb/server/utils/HashTimeoutException.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public class HashTimeoutException extends HashException {
diff --git a/src/main/java/org/caosdb/server/utils/Hasher.java b/src/main/java/org/caosdb/server/utils/Hasher.java
index 9eb009cd..1b36b9db 100644
--- a/src/main/java/org/caosdb/server/utils/Hasher.java
+++ b/src/main/java/org/caosdb/server/utils/Hasher.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/Info.java b/src/main/java/org/caosdb/server/utils/Info.java
index 644239fc..9d31cfff 100644
--- a/src/main/java/org/caosdb/server/utils/Info.java
+++ b/src/main/java/org/caosdb/server/utils/Info.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
@@ -28,18 +28,18 @@ import java.sql.SQLException;
import java.util.LinkedList;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.transaction.GetInfo;
-import org.caosdb.server.database.backend.transaction.SyncStats;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.proto.ProtoInfo;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.transaction.TransactionInterface;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.transaction.GetInfo;
+import org.linkahead.server.database.backend.transaction.SyncStats;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.proto.ProtoInfo;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.transaction.TransactionInterface;
public class Info extends AbstractObservable implements Observer, TransactionInterface {
@@ -184,7 +184,7 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
}
/**
- * Generates an XML element showing the information for the /Info resource in CaosDB.
+ * Generates an XML element showing the information for the /Info resource in LinkAhead.
*
* @return An XML element containing:
* <ul>
@@ -212,7 +212,7 @@ public class Info extends AbstractObservable implements Observer, TransactionInt
counts.setAttribute("files", Integer.toString(filesCount));
counts.setAttribute("fssize", fssize);
counts.setAttribute("tmpfiles", Integer.toString(tmpFilesCount));
- if (CaosDBServer.isDebugMode()) {
+ if (LinkAheadServer.isDebugMode()) {
counts.setAttribute("debug", "true");
}
final Element e = new Element("dropOffBox");
diff --git a/src/main/java/org/caosdb/server/utils/Initialization.java b/src/main/java/org/caosdb/server/utils/Initialization.java
index 4f28f206..2c79499b 100644
--- a/src/main/java/org/caosdb/server/utils/Initialization.java
+++ b/src/main/java/org/caosdb/server/utils/Initialization.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,12 +22,12 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.database.DatabaseAccessManager;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.transaction.TransactionInterface;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.database.DatabaseAccessManager;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.transaction.TransactionInterface;
public final class Initialization implements TransactionInterface, AutoCloseable {
diff --git a/src/main/java/org/caosdb/server/utils/NullPrintStream.java b/src/main/java/org/caosdb/server/utils/NullPrintStream.java
index 9256bdee..c26f386a 100644
--- a/src/main/java/org/caosdb/server/utils/NullPrintStream.java
+++ b/src/main/java/org/caosdb/server/utils/NullPrintStream.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.PrintStream;
import org.apache.commons.io.output.NullOutputStream;
diff --git a/src/main/java/org/caosdb/server/utils/Observable.java b/src/main/java/org/caosdb/server/utils/Observable.java
index a43822eb..4dbeed65 100644
--- a/src/main/java/org/caosdb/server/utils/Observable.java
+++ b/src/main/java/org/caosdb/server/utils/Observable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Observable {
public boolean acceptObserver(Observer o);
diff --git a/src/main/java/org/caosdb/server/utils/ObservableWrapper.java b/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
index 9a1833db..dc2bf92d 100644
--- a/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
+++ b/src/main/java/org/caosdb/server/utils/ObservableWrapper.java
@@ -1,7 +1,7 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@ package org.caosdb.server.utils;
*
* ** end header
*/
-// package org.caosdb.server.utils;
+// package org.linkahead.server.utils;
//
//
// public class ObservableWrapper<T> extends AbstractObservable {
diff --git a/src/main/java/org/caosdb/server/utils/Observer.java b/src/main/java/org/caosdb/server/utils/Observer.java
index b4c8f544..a058db67 100644
--- a/src/main/java/org/caosdb/server/utils/Observer.java
+++ b/src/main/java/org/caosdb/server/utils/Observer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Observer {
diff --git a/src/main/java/org/caosdb/server/utils/Releasable.java b/src/main/java/org/caosdb/server/utils/Releasable.java
index f81a029a..42d49b65 100644
--- a/src/main/java/org/caosdb/server/utils/Releasable.java
+++ b/src/main/java/org/caosdb/server/utils/Releasable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Releasable {
diff --git a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
index 71429f1a..42da71d9 100644
--- a/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
+++ b/src/main/java/org/caosdb/server/utils/ResultSetIterator.java
@@ -1,13 +1,13 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.bytes2UTF8;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Iterator;
import java.util.NoSuchElementException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.Query.IdVersionAclTriplet;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.Query.IdVersionAclTriplet;
/**
* A class for iterating over {@link ResultSet}
diff --git a/src/main/java/org/caosdb/server/utils/SHA512.java b/src/main/java/org/caosdb/server/utils/SHA512.java
index a461d95e..acbab54b 100644
--- a/src/main/java/org/caosdb/server/utils/SHA512.java
+++ b/src/main/java/org/caosdb/server/utils/SHA512.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/Serializer.java b/src/main/java/org/caosdb/server/utils/Serializer.java
index c58ca23e..1ad9f582 100644
--- a/src/main/java/org/caosdb/server/utils/Serializer.java
+++ b/src/main/java/org/caosdb/server/utils/Serializer.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Serializer<T, S> {
diff --git a/src/main/java/org/caosdb/server/utils/ServerMessages.java b/src/main/java/org/caosdb/server/utils/ServerMessages.java
index 9e18ca90..7ed0be5e 100644
--- a/src/main/java/org/caosdb/server/utils/ServerMessages.java
+++ b/src/main/java/org/caosdb/server/utils/ServerMessages.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics, Max-Planck-Institute
* for Dynamics and Self-Organization Göttingen
@@ -21,13 +21,13 @@
*
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
-import org.caosdb.api.entity.v1.MessageCode;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.Message.MessageType;
+import org.linkahead.api.entity.v1.MessageCode;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.Message.MessageType;
public class ServerMessages {
@@ -469,7 +469,7 @@ public class ServerMessages {
public static Message UNKNOWN_ERROR(final String requestID) {
return UNKNOWN_ERROR(
- requestID, CaosDBServer.getServerProperty(ServerProperties.KEY_BUGTRACKER_URI));
+ requestID, LinkAheadServer.getServerProperty(ServerProperties.KEY_BUGTRACKER_URI));
}
public static Message UNKNOWN_ERROR(final String sRID, final String reportTo) {
diff --git a/src/main/java/org/caosdb/server/utils/ServerStat.java b/src/main/java/org/caosdb/server/utils/ServerStat.java
index 8b552633..28f6da2a 100644
--- a/src/main/java/org/caosdb/server/utils/ServerStat.java
+++ b/src/main/java/org/caosdb/server/utils/ServerStat.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.Serializable;
diff --git a/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java b/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
index 368e0908..b38bf21c 100644
--- a/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
+++ b/src/main/java/org/caosdb/server/utils/TransactionLogMessage.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,12 +20,12 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.TimeZone;
-import org.caosdb.datetime.UTCDateTime;
-import org.caosdb.server.entity.EntityInterface;
import org.jdom2.Element;
+import org.linkahead.datetime.UTCDateTime;
+import org.linkahead.server.entity.EntityInterface;
public class TransactionLogMessage {
diff --git a/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java b/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
index 3f70f282..cd39a7a1 100644
--- a/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
+++ b/src/main/java/org/caosdb/server/utils/UncloseableOutputStream.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.IOException;
import java.io.OutputStream;
diff --git a/src/main/java/org/caosdb/server/utils/UndoHandler.java b/src/main/java/org/caosdb/server/utils/UndoHandler.java
index 21027847..68192305 100644
--- a/src/main/java/org/caosdb/server/utils/UndoHandler.java
+++ b/src/main/java/org/caosdb/server/utils/UndoHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.util.ArrayDeque;
import java.util.Deque;
diff --git a/src/main/java/org/caosdb/server/utils/Undoable.java b/src/main/java/org/caosdb/server/utils/Undoable.java
index 2bbbcb17..671df33a 100644
--- a/src/main/java/org/caosdb/server/utils/Undoable.java
+++ b/src/main/java/org/caosdb/server/utils/Undoable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
public interface Undoable {
diff --git a/src/main/java/org/caosdb/server/utils/Utils.java b/src/main/java/org/caosdb/server/utils/Utils.java
index 07a7e961..119f733a 100644
--- a/src/main/java/org/caosdb/server/utils/Utils.java
+++ b/src/main/java/org/caosdb/server/utils/Utils.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static java.net.URLDecoder.decode;
import static java.net.URLEncoder.encode;
@@ -35,13 +35,13 @@ import java.text.DecimalFormat;
import java.util.Scanner;
import java.util.regex.Pattern;
import org.apache.commons.codec.binary.Base32;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.entity.Message;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.output.Format;
import org.jdom2.output.XMLOutputter;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.entity.Message;
/** Utility functions. */
public class Utils {
@@ -306,7 +306,7 @@ public class Utils {
* @param password The password to be checked.
*/
public static void checkPasswordStrength(final String password) throws Message {
- String regex = CaosDBServer.getServerProperty(ServerProperties.KEY_PASSWORD_STRENGTH_REGEX);
+ String regex = LinkAheadServer.getServerProperty(ServerProperties.KEY_PASSWORD_STRENGTH_REGEX);
if (password.equals("correcthorsebatterystaple")) {
throw ServerMessages.PASSWORD_TOO_WEAK("PWNED!");
@@ -314,7 +314,7 @@ public class Utils {
if (!password.matches(regex)) {
throw ServerMessages.PASSWORD_TOO_WEAK(
- CaosDBServer.getServerProperty(ServerProperties.KEY_PASSWORD_WEAK_MESSAGE));
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_PASSWORD_WEAK_MESSAGE));
}
}
}
diff --git a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
index 6c583fcc..1d4c8a18 100644
--- a/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
+++ b/src/main/java/org/caosdb/server/utils/WebinterfaceUtils.java
@@ -1,5 +1,5 @@
/**
- * ** header v3.0 This file is a part of the CaosDB Project.
+ * ** header v3.0 This file is a part of the LinkAhead Project.
*
* <p>Copyright (c) 2019 IndiScale GmbH Copyright (c) 2019 Daniel Hornung <d.hornung@indiscale.com>
*
@@ -16,7 +16,7 @@
*
* <p>** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import java.io.File;
import java.io.IOException;
@@ -29,10 +29,10 @@ import java.util.Map;
import java.util.stream.Stream;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.resource.Webinterface;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.resource.Webinterface;
import org.restlet.Request;
import org.restlet.data.Reference;
@@ -41,15 +41,15 @@ import org.restlet.data.Reference;
* <li>Resolving relative paths of files of the web interface to {@link File} objects.
* <li>Generating URIs to public files of the web interface from relative string paths.
*
- * <p>Especially the {@link AbstractCaosDBServerResource} and the {@link Webinterface} use this
- * class for these tasks.
+ * <p>Especially the {@link AbstractLinkAheadServerResource} and the {@link Webinterface} use
+ * this class for these tasks.
*
* @author Timm Fitschen (t.fitschen@indiscale.com)
*/
public class WebinterfaceUtils {
private Logger logger = LogManager.getLogger(this.getClass());
- public static final String DEFAULT_WEBUI_PUBLIC = "caosdb-webui/public";
+ public static final String DEFAULT_WEBUI_PUBLIC = "linkahead-webui/public";
public static final String DEFAULT_BUILD_NUMBER_FILE = ".build_number";
public static final String DEFAULT_ROUTE = "webinterface";
private final String host;
@@ -162,7 +162,7 @@ public class WebinterfaceUtils {
WebinterfaceUtils(String host) {
this(
host,
- CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT),
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT),
DEFAULT_WEBUI_PUBLIC,
DEFAULT_ROUTE,
DEFAULT_BUILD_NUMBER_FILE);
diff --git a/src/main/java/org/caosdb/server/utils/mail/Mail.java b/src/main/java/org/caosdb/server/utils/mail/Mail.java
index 36588fc1..5004b706 100644
--- a/src/main/java/org/caosdb/server/utils/mail/Mail.java
+++ b/src/main/java/org/caosdb/server/utils/mail/Mail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,18 +20,18 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.util.Date;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class Mail {
private static MailHandler handler = null;
static {
- String clazz = CaosDBServer.getServerProperty(ServerProperties.KEY_MAIL_HANDLER_CLASS);
+ String clazz = LinkAheadServer.getServerProperty(ServerProperties.KEY_MAIL_HANDLER_CLASS);
try {
@SuppressWarnings("unchecked")
Class<? extends MailHandler> mailHandlerClass =
diff --git a/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java b/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
index 2e31724d..52b68e04 100644
--- a/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
+++ b/src/main/java/org/caosdb/server/utils/mail/MailFormatter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface MailFormatter {
diff --git a/src/main/java/org/caosdb/server/utils/mail/MailHandler.java b/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
index ebdf88da..e97d1be4 100644
--- a/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/MailHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface MailHandler {
diff --git a/src/main/java/org/caosdb/server/utils/mail/Mailable.java b/src/main/java/org/caosdb/server/utils/mail/Mailable.java
index fc679aac..4549997c 100644
--- a/src/main/java/org/caosdb/server/utils/mail/Mailable.java
+++ b/src/main/java/org/caosdb/server/utils/mail/Mailable.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
public interface Mailable {
diff --git a/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java b/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
index 88a487c5..d22ef6f4 100644
--- a/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/SendMailHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.BufferedWriter;
import java.io.IOException;
diff --git a/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java b/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
index c1d5ce6b..85c4a47c 100644
--- a/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
+++ b/src/main/java/org/caosdb/server/utils/mail/SimpleMailFormatter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import javax.mail.internet.MailDateFormat;
diff --git a/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java b/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
index 24a6da78..e6af1de2 100644
--- a/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
+++ b/src/main/java/org/caosdb/server/utils/mail/ToFileHandler.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,15 +20,15 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintWriter;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class ToFileHandler implements MailHandler {
@@ -37,7 +37,7 @@ public class ToFileHandler implements MailHandler {
@Override
public void handleMail(final Mail mail) {
final String loc =
- CaosDBServer.getServerProperty(ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC);
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC);
File f = new File(loc);
if ((f.exists() && f.isDirectory()) || !f.exists() && loc.endsWith("/")) {
f = new File(f.getAbsolutePath() + "/OUTBOX");
diff --git a/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java b/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
index ed78c5cf..f9b1ba87 100644
--- a/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
+++ b/src/main/java/org/caosdb/unit/CaosDBSystemOfUnits.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import de.timmfitschen.easyunits.BaseUnit;
import de.timmfitschen.easyunits.DefaultSystemOfUnitsFactory;
@@ -31,7 +31,7 @@ import de.timmfitschen.easyunits.UnknownUnitException;
import de.timmfitschen.easyunits.conversion.Prefix;
import de.timmfitschen.easyunits.parser.ParserException;
-public class CaosDBSystemOfUnits {
+public class LinkAheadSystemOfUnits {
public static Unit getUnit(final String s) throws ParserException {
try {
@@ -43,7 +43,7 @@ public class CaosDBSystemOfUnits {
private static SystemOfUnits system = createSystemOfUnits();
- private CaosDBSystemOfUnits() {}
+ private LinkAheadSystemOfUnits() {}
private static SystemOfUnits createSystemOfUnits() {
final DefaultSystemOfUnitsFactory f = new DefaultSystemOfUnitsFactory();
diff --git a/src/main/java/org/caosdb/unit/Converter.java b/src/main/java/org/caosdb/unit/Converter.java
index dfe63477..290b1023 100644
--- a/src/main/java/org/caosdb/unit/Converter.java
+++ b/src/main/java/org/caosdb/unit/Converter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,6 +20,6 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface Converter {}
diff --git a/src/main/java/org/caosdb/unit/LinearConverter.java b/src/main/java/org/caosdb/unit/LinearConverter.java
index 8eac2d7e..91936e66 100644
--- a/src/main/java/org/caosdb/unit/LinearConverter.java
+++ b/src/main/java/org/caosdb/unit/LinearConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface LinearConverter extends Converter {
diff --git a/src/main/java/org/caosdb/unit/Unit.java b/src/main/java/org/caosdb/unit/Unit.java
index 9e676773..40f7045e 100644
--- a/src/main/java/org/caosdb/unit/Unit.java
+++ b/src/main/java/org/caosdb/unit/Unit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public interface Unit {
diff --git a/src/main/java/org/caosdb/unit/UnknownUnit.java b/src/main/java/org/caosdb/unit/UnknownUnit.java
index 70ad3546..383c0e5f 100644
--- a/src/main/java/org/caosdb/unit/UnknownUnit.java
+++ b/src/main/java/org/caosdb/unit/UnknownUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public class UnknownUnit extends WrappedUnit implements Unit {
diff --git a/src/main/java/org/caosdb/unit/WrappedConverter.java b/src/main/java/org/caosdb/unit/WrappedConverter.java
index f23be039..3f2b727c 100644
--- a/src/main/java/org/caosdb/unit/WrappedConverter.java
+++ b/src/main/java/org/caosdb/unit/WrappedConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
public class WrappedConverter implements Converter {
diff --git a/src/main/java/org/caosdb/unit/WrappedLinearConverter.java b/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
index b90b32cc..b72c65b7 100644
--- a/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
+++ b/src/main/java/org/caosdb/unit/WrappedLinearConverter.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
diff --git a/src/main/java/org/caosdb/unit/WrappedUnit.java b/src/main/java/org/caosdb/unit/WrappedUnit.java
index c29ee5b5..0af35f46 100644
--- a/src/main/java/org/caosdb/unit/WrappedUnit.java
+++ b/src/main/java/org/caosdb/unit/WrappedUnit.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.unit;
+package org.linkahead.unit;
import de.timmfitschen.easyunits.conversion.LinearConverter;
diff --git a/src/test/java/org/caosdb/datetime/DateTimeTest.java b/src/test/java/org/caosdb/datetime/DateTimeTest.java
index 49e883fb..7f7d68d1 100644
--- a/src/test/java/org/caosdb/datetime/DateTimeTest.java
+++ b/src/test/java/org/caosdb/datetime/DateTimeTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -33,22 +33,22 @@ import java.sql.Timestamp;
import java.time.ZoneId;
import java.util.GregorianCalendar;
import java.util.TimeZone;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
public class DateTimeTest {
@BeforeAll
public static void setup() throws InterruptedException, IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initTimeZone();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initTimeZone();
}
@Test
public void testGetTimeZoneFromDate() throws InterruptedException, IOException {
- String tz = CaosDBServer.getTimeZoneFromDate();
+ String tz = LinkAheadServer.getTimeZoneFromDate();
ZoneId of = java.time.ZoneId.of(tz);
assertNotNull(of);
}
diff --git a/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java b/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
index 9cfa98b1..bfb67d4e 100644
--- a/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
+++ b/src/test/java/org/caosdb/datetime/UTCTimeZoneShiftTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.datetime;
+package org.linkahead.datetime;
import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/src/test/java/org/caosdb/server/Misc.java b/src/test/java/org/caosdb/server/Misc.java
index 0b39327e..62aff109 100644
--- a/src/test/java/org/caosdb/server/Misc.java
+++ b/src/test/java/org/caosdb/server/Misc.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server;
+package org.linkahead.server;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -38,18 +38,18 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.jobs.core.CheckFileStorageConsistency;
-import org.caosdb.server.utils.CronJob;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.jvnet.libpam.PAMException;
import org.jvnet.libpam.UnixUser;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.jobs.core.CheckFileStorageConsistency;
+import org.linkahead.server.utils.CronJob;
public class Misc {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
@@ -289,7 +289,7 @@ public class Misc {
@Test
public void testShiro() {
- CaosDBServer.initShiro();
+ LinkAheadServer.initShiro();
final Subject subject = SecurityUtils.getSubject();
diff --git a/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java b/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
index a893b46a..30418c17 100644
--- a/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
+++ b/src/test/java/org/caosdb/server/accessControl/TestDefaultPamScriptCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.accessControl;
+package org.linkahead.server.accessControl;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
diff --git a/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java b/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
index d83651a3..4f4a175d 100644
--- a/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
+++ b/src/test/java/org/caosdb/server/authentication/AuthTokenTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.authentication;
+package org.linkahead.server.authentication;
import static org.junit.jupiter.api.Assertions.assertArrayEquals;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -45,35 +45,35 @@ import org.apache.commons.io.input.CharSequenceInputStream;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.authc.AuthenticationException;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Config;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.SelfValidatingAuthenticationToken;
-import org.caosdb.server.accessControl.SessionToken;
-import org.caosdb.server.accessControl.SessionTokenRealm;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.grpc.AuthInterceptor;
-import org.caosdb.server.resource.TestScriptingResource.RetrievePasswordValidator;
-import org.caosdb.server.resource.TestScriptingResource.RetrievePermissionRules;
-import org.caosdb.server.resource.TestScriptingResource.RetrieveRoleMockup;
-import org.caosdb.server.resource.TestScriptingResource.RetrieveUserMockUp;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Config;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.SelfValidatingAuthenticationToken;
+import org.linkahead.server.accessControl.SessionToken;
+import org.linkahead.server.accessControl.SessionTokenRealm;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.grpc.AuthInterceptor;
+import org.linkahead.server.resource.TestScriptingResource.RetrievePasswordValidator;
+import org.linkahead.server.resource.TestScriptingResource.RetrievePermissionRules;
+import org.linkahead.server.resource.TestScriptingResource.RetrieveRoleMockup;
+import org.linkahead.server.resource.TestScriptingResource.RetrieveUserMockUp;
public class AuthTokenTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@BeforeAll
@@ -84,8 +84,8 @@ public class AuthTokenTest {
BackendTransaction.setImpl(
RetrievePasswordValidatorImpl.class, RetrievePasswordValidator.class);
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
}
@BeforeEach
@@ -284,7 +284,7 @@ public class AuthTokenTest {
assertEquals(
Integer.parseInt(
- CaosDBServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS)),
+ LinkAheadServer.getServerProperty(ServerProperties.KEY_ONE_TIME_TOKEN_EXPIRES_MS)),
config.getExpiresAfter());
assertEquals(1, config.getMaxReplays());
assertNull(config.getPurpose(), "no purpose");
@@ -405,7 +405,7 @@ public class AuthTokenTest {
OneTimeAuthenticationToken.initConfig(new CharSequenceInputStream(testYaml, "utf-8"));
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
OneTimeAuthenticationToken token =
diff --git a/src/test/java/org/caosdb/server/caching/TestCaching.java b/src/test/java/org/caosdb/server/caching/TestCaching.java
index 1aba2ff6..b75bd09e 100644
--- a/src/test/java/org/caosdb/server/caching/TestCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestCaching.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertSame;
@@ -6,17 +6,17 @@ import static org.junit.jupiter.api.Assertions.assertSame;
import java.io.IOException;
import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.CacheAccess;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.accessControl.Pam;
-import org.caosdb.server.database.backend.transaction.RetrieveProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.accessControl.Pam;
+import org.linkahead.server.database.backend.transaction.RetrieveProperties;
public class TestCaching {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/caching/TestNoCaching.java b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
index 4fc73adf..c696531a 100644
--- a/src/test/java/org/caosdb/server/caching/TestNoCaching.java
+++ b/src/test/java/org/caosdb/server/caching/TestNoCaching.java
@@ -1,22 +1,22 @@
-package org.caosdb.server.caching;
+package org.linkahead.server.caching;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import org.apache.commons.jcs.JCS;
import org.apache.commons.jcs.access.CacheAccess;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.backend.transaction.RetrieveProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.backend.transaction.RetrieveProperties;
public class TestNoCaching {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.setProperty(ServerProperties.KEY_CACHE_DISABLE, "TRUE");
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.setProperty(ServerProperties.KEY_CACHE_DISABLE, "TRUE");
JCSCacheHelper.init();
}
diff --git a/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java b/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
index 9d682ce3..29156f79 100644
--- a/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
+++ b/src/test/java/org/caosdb/server/database/DatabaseAccessManagerTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.database;
+package org.linkahead.server.database;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
diff --git a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
index 03bd185c..46324a4c 100644
--- a/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/implementation/MySQL/InsertTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,30 +20,30 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.implementation.MySQL;
+package org.linkahead.server.database.backend.implementation.MySQL;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
-import static org.caosdb.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage1Inserts;
+import static org.linkahead.server.database.backend.implementation.MySQL.DatabaseUtils.deriveStage2Inserts;
import java.util.ArrayDeque;
import java.util.Deque;
import java.util.LinkedList;
import java.util.List;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.SingleValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Property;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.SingleValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Property;
public class InsertTest {
diff --git a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
index 72c84d1f..c538f7fb 100644
--- a/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
+++ b/src/test/java/org/caosdb/server/database/backend/transaction/RetrieveFullEntityTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.database.backend.transaction;
+package org.linkahead.server.database.backend.transaction;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -28,15 +28,15 @@ import static org.junit.jupiter.api.Assertions.assertNull;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategyTest;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategyTest;
+import org.linkahead.server.query.Query.Selection;
public class RetrieveFullEntityTest {
diff --git a/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java b/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
index 90efd310..a3242b96 100644
--- a/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
+++ b/src/test/java/org/caosdb/server/database/backend/transactions/TestGetAllNames.java
@@ -1,20 +1,20 @@
-package org.caosdb.server.database.backend.transactions;
+package org.linkahead.server.database.backend.transactions;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.GetAllNamesImpl;
-import org.caosdb.server.database.backend.transaction.GetAllNames;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.SparseEntity;
-import org.caosdb.server.entity.EntityInterface;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.GetAllNamesImpl;
+import org.linkahead.server.database.backend.transaction.GetAllNames;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.SparseEntity;
+import org.linkahead.server.entity.EntityInterface;
public class TestGetAllNames {
@@ -48,7 +48,7 @@ public class TestGetAllNames {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
BackendTransaction.init();
BackendTransaction.setImpl(GetAllNamesImpl.class, GetAllNamesBackend.class);
}
diff --git a/src/test/java/org/caosdb/server/datatype/testBoolean.java b/src/test/java/org/caosdb/server/datatype/testBoolean.java
index a8b39130..679f3a4e 100644
--- a/src/test/java/org/caosdb/server/datatype/testBoolean.java
+++ b/src/test/java/org/caosdb/server/datatype/testBoolean.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,23 +20,23 @@
*
* ** end header
*/
-package org.caosdb.server.datatype;
+package org.linkahead.server.datatype;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
-import org.caosdb.server.datatype.AbstractDatatype.Table;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.AbstractDatatype.Table;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class testBoolean {
@Test
- public void testCaosEnumCI() {
- CaosEnum ce = new CaosEnum("TRUE", "FALSE", "NEITHER");
+ public void testLinkAheadEnumCI() {
+ LinkAheadEnum ce = new LinkAheadEnum("TRUE", "FALSE", "NEITHER");
assertNotNull(ce.valueOf("TRUE"));
assertNotNull(ce.valueOf("true"));
assertNotNull(ce.valueOf("TRue"));
@@ -56,8 +56,8 @@ public class testBoolean {
}
@Test
- public void testCaosEnumCS() {
- CaosEnum ce = new CaosEnum(true, "TRUE", "FALSE", "NEITHER", "neither");
+ public void testLinkAheadEnumCS() {
+ LinkAheadEnum ce = new LinkAheadEnum(true, "TRUE", "FALSE", "NEITHER", "neither");
assertNotNull(ce.valueOf("TRUE"));
assertNotNull(ce.valueOf("FALSE"));
assertNotNull(ce.valueOf("NEITHER"));
diff --git a/src/test/java/org/caosdb/server/entity/EntityTest.java b/src/test/java/org/caosdb/server/entity/EntityTest.java
index 3a923315..ab5b8248 100644
--- a/src/test/java/org/caosdb/server/entity/EntityTest.java
+++ b/src/test/java/org/caosdb/server/entity/EntityTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -20,13 +20,13 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
-import org.caosdb.server.datatype.IntegerDatatype;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.IntegerDatatype;
public class EntityTest {
diff --git a/src/test/java/org/caosdb/server/entity/SelectionTest.java b/src/test/java/org/caosdb/server/entity/SelectionTest.java
index 87720638..d6da1cbf 100644
--- a/src/test/java/org/caosdb/server/entity/SelectionTest.java
+++ b/src/test/java/org/caosdb/server/entity/SelectionTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -22,25 +22,25 @@
*
* ** end header
*/
-package org.caosdb.server.entity;
+package org.linkahead.server.entity;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
-import org.caosdb.server.query.Query;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
+import org.linkahead.server.query.Query;
+import org.linkahead.server.query.Query.Selection;
public class SelectionTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
index a8ccdbdc..60eed2c3 100644
--- a/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
+++ b/src/test/java/org/caosdb/server/entity/container/PropertyContainerTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.container;
+package org.linkahead.server.entity.container;
import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.PropertyToElementStrategyTest;
-import org.caosdb.server.entity.xml.SerializeFieldStrategy;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.PropertyToElementStrategyTest;
+import org.linkahead.server.entity.xml.SerializeFieldStrategy;
public class PropertyContainerTest {
diff --git a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
index a2c9676b..f11b905a 100644
--- a/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
+++ b/src/test/java/org/caosdb/server/entity/xml/PropertyToElementStrategyTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
* Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
@@ -20,22 +20,22 @@
*
* ** end header
*/
-package org.caosdb.server.entity.xml;
+package org.linkahead.server.entity.xml;
import static org.junit.jupiter.api.Assertions.assertEquals;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.query.Query.Selection;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.query.Query.Selection;
public class PropertyToElementStrategyTest {
diff --git a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
index d46c1873..97fa6671 100644
--- a/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
+++ b/src/test/java/org/caosdb/server/grpc/CaosDBToGrpcConvertersTest.java
@@ -1,34 +1,34 @@
-package org.caosdb.server.grpc;
+package org.linkahead.server.grpc;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.util.TimeZone;
-import org.caosdb.api.entity.v1.Value.Builder;
-import org.caosdb.datetime.DateTimeFactory2;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.datatype.Value;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.wrapper.Parent;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.query.Query.Selection;
import org.junit.jupiter.api.Test;
-
-public class CaosDBToGrpcConvertersTest {
+import org.linkahead.api.entity.v1.Value.Builder;
+import org.linkahead.datetime.DateTimeFactory2;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.datatype.Value;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.wrapper.Parent;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.query.Query.Selection;
+
+public class LinkAheadToGrpcConvertersTest {
@Test
public void testConvertScalarValue_Datetime() {
TimeZone timeZone = TimeZone.getTimeZone("UTC");
DateTimeFactory2 factory = new DateTimeFactory2(timeZone);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(timeZone);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(timeZone);
Value value = null;
assertEquals(
converters.convertScalarValue(value).toString(),
@@ -60,7 +60,7 @@ public class CaosDBToGrpcConvertersTest {
@Test
public void testConvertEntity_FileDescriptor() {
RetrieveEntity entity = new RetrieveEntity();
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
assertEquals(converters.convert(entity).toString(), "entity {\n}\n");
entity.setFileProperties(new FileProperties("checksum1234", "the/path", 1024L));
assertEquals(
@@ -94,7 +94,7 @@ public class CaosDBToGrpcConvertersTest {
p.setValue(new GenericValue("don print"));
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
// first test the normal SerializeFieldStrategy instead
entity.setSerializeFieldStrategy(null);
@@ -115,7 +115,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity entity = new RetrieveEntity();
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
Builder value = converters.getSelectedValue(new Selection("p0"), entity);
assertEquals(
"scalar_value {\n" + " special_value: SPECIAL_VALUE_UNSPECIFIED\n" + "}\n",
@@ -155,7 +155,7 @@ public class CaosDBToGrpcConvertersTest {
RetrieveEntity entity = new RetrieveEntity();
entity.addProperty(p);
- CaosDBToGrpcConverters converters = new CaosDBToGrpcConverters(null);
+ LinkAheadToGrpcConverters converters = new LinkAheadToGrpcConverters(null);
Builder value =
converters.getSelectedValue(
new Selection("Person").setSubSelection(new Selection("full name")), entity);
diff --git a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
index e176c211..333f6cce 100644
--- a/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
+++ b/src/test/java/org/caosdb/server/jobs/JobConfigTest.java
@@ -1,24 +1,24 @@
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.entity.DeleteEntity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.InsertEntity;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.Role;
-import org.caosdb.server.entity.UpdateEntity;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.entity.DeleteEntity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.InsertEntity;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.Role;
+import org.linkahead.server.entity.UpdateEntity;
public class JobConfigTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/jobs/ScheduleTest.java b/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
index 7033ac35..20ca6782 100644
--- a/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
+++ b/src/test/java/org/caosdb/server/jobs/ScheduleTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,20 +20,20 @@
*
* ** end header
*/
-package org.caosdb.server.jobs;
+package org.linkahead.server.jobs;
import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
public class ScheduleTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
/** The problem of ticket #297 was that a CHECK job was executed during the ROLL_BACK stage. */
diff --git a/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java b/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
index a7202be9..144743b7 100644
--- a/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
+++ b/src/test/java/org/caosdb/server/jobs/core/TestInsertFilesInDir.java
@@ -1,18 +1,18 @@
-package org.caosdb.server.jobs.core;
+package org.linkahead.server.jobs.core;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
public class TestInsertFilesInDir {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
diff --git a/src/test/java/org/caosdb/server/logging/TestLogging.java b/src/test/java/org/caosdb/server/logging/TestLogging.java
index 0f67ebea..704a4bde 100644
--- a/src/test/java/org/caosdb/server/logging/TestLogging.java
+++ b/src/test/java/org/caosdb/server/logging/TestLogging.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.logging;
+package org.linkahead.server.logging;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -7,9 +7,9 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.File;
import java.io.IOException;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBServer;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
import org.restlet.Request;
import org.restlet.Response;
import org.slf4j.Logger;
@@ -19,8 +19,8 @@ public class TestLogging {
private Logger logger = LoggerFactory.getLogger(getClass());
private Logger request_errors_logger =
- LoggerFactory.getLogger(CaosDBServer.REQUEST_ERRORS_LOGGER);
- private Logger request_time_logger = LoggerFactory.getLogger(CaosDBServer.REQUEST_TIME_LOGGER);
+ LoggerFactory.getLogger(LinkAheadServer.REQUEST_ERRORS_LOGGER);
+ private Logger request_time_logger = LoggerFactory.getLogger(LinkAheadServer.REQUEST_TIME_LOGGER);
@BeforeAll
public static void setup() throws IOException {
@@ -35,7 +35,7 @@ public class TestLogging {
logger.info("info");
logger.debug("debug");
logger.trace("trace");
- assertEquals(logger.getName(), "org.caosdb.server.logging.TestLogging");
+ assertEquals(logger.getName(), "org.linkahead.server.logging.TestLogging");
assertTrue(logger.isErrorEnabled());
assertTrue(logger.isWarnEnabled());
assertTrue(logger.isInfoEnabled());
@@ -54,7 +54,7 @@ public class TestLogging {
@Test
public void testRequestTimeLogger() {
- assertTrue(CaosDBServer.isDebugMode());
+ assertTrue(LinkAheadServer.isDebugMode());
assertFalse(request_time_logger.isErrorEnabled());
assertFalse(request_time_logger.isTraceEnabled());
}
diff --git a/src/test/java/org/caosdb/server/permissions/EntityACLTest.java b/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
index 5feab38f..aa07da20 100644
--- a/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
+++ b/src/test/java/org/caosdb/server/permissions/EntityACLTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -34,31 +34,31 @@ import java.util.LinkedList;
import java.util.Set;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AuthenticationUtils;
-import org.caosdb.server.accessControl.Config;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.OneTimeAuthenticationToken;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.resource.AbstractCaosDBServerResource;
-import org.caosdb.server.resource.AbstractCaosDBServerResource.XMLParser;
-import org.caosdb.server.utils.Utils;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AuthenticationUtils;
+import org.linkahead.server.accessControl.Config;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.OneTimeAuthenticationToken;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource;
+import org.linkahead.server.resource.AbstractLinkAheadServerResource.XMLParser;
+import org.linkahead.server.utils.Utils;
public class EntityACLTest {
@@ -158,8 +158,8 @@ public class EntityACLTest {
@BeforeAll
public static void init() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
assertNotNull(EntityACL.GLOBAL_PERMISSIONS);
BackendTransaction.setImpl(
@@ -318,7 +318,7 @@ public class EntityACLTest {
return false;
}
- public static AbstractCaosDBServerResource.XMLParser parser = new XMLParser();
+ public static AbstractLinkAheadServerResource.XMLParser parser = new XMLParser();
public Element stringToJdom(final String s) throws JDOMException, IOException {
return parser.parse(Utils.String2InputStream(s)).getRootElement();
@@ -327,7 +327,7 @@ public class EntityACLTest {
@Test
public void testEntityACLForAnonymous() {
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
assertTrue(AuthenticationUtils.isAnonymous(anonymous));
EntityACL acl = EntityACL.getOwnerACLFor(anonymous);
@@ -339,14 +339,16 @@ public class EntityACLTest {
public void testFactory() {
final AbstractEntityACLFactory<EntityACL> f = new EntityACLFactory();
- org.caosdb.server.permissions.Role role1 = org.caosdb.server.permissions.Role.create("role1");
+ org.linkahead.server.permissions.Role role1 =
+ org.linkahead.server.permissions.Role.create("role1");
Config config1 = new Config();
config1.setRoles(new String[] {role1.toString()});
OneTimeAuthenticationToken token1 = OneTimeAuthenticationToken.generate(config1);
Subject user1 = SecurityUtils.getSecurityManager().createSubject(null);
user1.login(token1);
- org.caosdb.server.permissions.Role role2 = org.caosdb.server.permissions.Role.create("role2");
+ org.linkahead.server.permissions.Role role2 =
+ org.linkahead.server.permissions.Role.create("role2");
Config config2 = new Config();
config2.setRoles(new String[] {role2.toString()});
OneTimeAuthenticationToken token2 = OneTimeAuthenticationToken.generate(config2);
@@ -382,41 +384,48 @@ public class EntityACLTest {
@Test
public void testRemove() {
EntityACLFactory f = new EntityACLFactory();
- f.grant(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
f.grant(
- org.caosdb.server.permissions.Role.create("role3"), true, EntityPermission.RETRIEVE_ACL);
+ org.linkahead.server.permissions.Role.create("role3"), true, EntityPermission.RETRIEVE_ACL);
f.deny(
- org.caosdb.server.permissions.Role.create("role4"), true, EntityPermission.RETRIEVE_ENTITY);
+ org.linkahead.server.permissions.Role.create("role4"),
+ true,
+ EntityPermission.RETRIEVE_ENTITY);
EntityACL other = f.create();
- f.grant(org.caosdb.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
f.grant(
- org.caosdb.server.permissions.Role.create("role5"), false, EntityPermission.RETRIEVE_FILE);
+ org.linkahead.server.permissions.Role.create("role2"), false, EntityPermission.EDIT_ACL);
+ f.grant(
+ org.linkahead.server.permissions.Role.create("role5"),
+ false,
+ EntityPermission.RETRIEVE_FILE);
f.remove(other); // normalize and remove "other"
EntityACL tester = f.create();
assertEquals(1, tester.getRules().size()); // Permissions array has been written and read
for (EntityACI aci : tester.getRules()) {
- assertEquals(aci.getResponsibleAgent(), org.caosdb.server.permissions.Role.create("role5"));
+ assertEquals(
+ aci.getResponsibleAgent(), org.linkahead.server.permissions.Role.create("role5"));
}
}
@Test
public void testNormalize() {
EntityACLFactory f = new EntityACLFactory();
- f.grant(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
- f.grant(org.caosdb.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
- f.deny(org.caosdb.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role1"), false, EntityPermission.DELETE);
+ f.grant(org.linkahead.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
+ f.deny(org.linkahead.server.permissions.Role.create("role1"), true, EntityPermission.DELETE);
// priority denail overrides everything else
EntityACL denyDelete = f.create();
assertEquals(1, denyDelete.getRules().size());
for (EntityACI aci : denyDelete.getRules()) {
- assertEquals(org.caosdb.server.permissions.Role.create("role1"), aci.getResponsibleAgent());
+ assertEquals(
+ org.linkahead.server.permissions.Role.create("role1"), aci.getResponsibleAgent());
assertTrue(EntityACL.isDenial(aci.getBitSet()));
assertTrue(EntityACL.isPriorityBitSet(aci.getBitSet()));
}
@@ -426,9 +435,11 @@ public class EntityACLTest {
public void testOwnership() {
EntityACLFactory f = new EntityACLFactory();
f.grant(
- org.caosdb.server.permissions.Role.create("the_owner"), false, EntityPermission.EDIT_ACL);
+ org.linkahead.server.permissions.Role.create("the_owner"),
+ false,
+ EntityPermission.EDIT_ACL);
f.deny(
- org.caosdb.server.permissions.Role.create("someone_else"),
+ org.linkahead.server.permissions.Role.create("someone_else"),
false,
EntityPermission.EDIT_ACL);
EntityACL acl = f.create();
@@ -439,12 +450,12 @@ public class EntityACLTest {
@Test
public void testPermissionsFor() {
EntityACLFactory f = new EntityACLFactory();
- f.deny(org.caosdb.server.permissions.Role.ANONYMOUS_ROLE, false, EntityPermission.EDIT_ACL);
- f.grant(org.caosdb.server.permissions.Role.OWNER_ROLE, false, "*");
+ f.deny(org.linkahead.server.permissions.Role.ANONYMOUS_ROLE, false, EntityPermission.EDIT_ACL);
+ f.grant(org.linkahead.server.permissions.Role.OWNER_ROLE, false, "*");
EntityACL acl = f.create();
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
assertTrue(AuthenticationUtils.isAnonymous(anonymous));
diff --git a/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java b/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
index 8699a431..17bc0e2c 100644
--- a/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
+++ b/src/test/java/org/caosdb/server/permissions/EntityPermissionTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.permissions;
+package org.linkahead.server.permissions;
import static org.junit.jupiter.api.Assertions.*;
@@ -10,83 +10,83 @@ public class EntityPermissionTest {
public void testGRPCMapping() {
assertEquals(
EntityPermission.EDIT_ACL.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_EDIT_ACL);
assertEquals(
EntityPermission.DELETE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_DELETE);
assertEquals(
EntityPermission.USE_AS_DATA_TYPE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_DATA_TYPE);
assertEquals(
EntityPermission.USE_AS_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PARENT);
assertEquals(
EntityPermission.USE_AS_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_PROPERTY);
assertEquals(
EntityPermission.USE_AS_REFERENCE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_USE_AS_REFERENCE);
assertEquals(
EntityPermission.RETRIEVE_ENTITY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ENTITY);
assertEquals(
EntityPermission.RETRIEVE_ACL.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_ACL);
assertEquals(
EntityPermission.RETRIEVE_OWNER.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_OWNER);
assertEquals(
EntityPermission.RETRIEVE_HISTORY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_HISTORY);
assertEquals(
EntityPermission.RETRIEVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_RETRIEVE_FILE);
assertEquals(
EntityPermission.UPDATE_VALUE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_VALUE);
assertEquals(
EntityPermission.UPDATE_DESCRIPTION.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DESCRIPTION);
assertEquals(
EntityPermission.UPDATE_DATA_TYPE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_DATA_TYPE);
assertEquals(
EntityPermission.UPDATE_NAME.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_NAME);
assertEquals(
EntityPermission.UPDATE_QUERY_TEMPLATE_DEFINITION.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission
+ org.linkahead.api.entity.v1.EntityPermission
.ENTITY_PERMISSION_UPDATE_QUERY_TEMPLATE_DEFINITION);
assertEquals(
EntityPermission.UPDATE_ROLE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ROLE);
assertEquals(
EntityPermission.UPDATE_ADD_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PARENT);
assertEquals(
EntityPermission.UPDATE_REMOVE_PARENT.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PARENT);
assertEquals(
EntityPermission.UPDATE_ADD_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_PROPERTY);
assertEquals(
EntityPermission.UPDATE_REMOVE_PROPERTY.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_PROPERTY);
assertEquals(
EntityPermission.UPDATE_ADD_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_ADD_FILE);
assertEquals(
EntityPermission.UPDATE_REMOVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_REMOVE_FILE);
assertEquals(
EntityPermission.UPDATE_MOVE_FILE.getMapping(),
- org.caosdb.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
+ org.linkahead.api.entity.v1.EntityPermission.ENTITY_PERMISSION_UPDATE_MOVE_FILE);
}
}
diff --git a/src/test/java/org/caosdb/server/query/POVTest.java b/src/test/java/org/caosdb/server/query/POVTest.java
index 7212423b..2e9223dc 100644
--- a/src/test/java/org/caosdb/server/query/POVTest.java
+++ b/src/test/java/org/caosdb/server/query/POVTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
diff --git a/src/test/java/org/caosdb/server/query/QueryTest.java b/src/test/java/org/caosdb/server/query/QueryTest.java
index 986122ca..e6a514c8 100644
--- a/src/test/java/org/caosdb/server/query/QueryTest.java
+++ b/src/test/java/org/caosdb/server/query/QueryTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2021 IndiScale GmbH <info@indiscale.com>
* Copyright (C) 2021 Timm Fitschen <t.fitschen@indiscale.com>
@@ -17,7 +17,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
@@ -28,20 +28,20 @@ import static org.junit.jupiter.api.Assertions.fail;
import java.io.IOException;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.database.access.InitAccess;
-import org.caosdb.server.transaction.WriteTransaction;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.database.access.InitAccess;
+import org.linkahead.server.transaction.WriteTransaction;
public class QueryTest {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
}
String getCacheKey(String query) {
@@ -52,7 +52,7 @@ public class QueryTest {
String getCacheKeyWithUser(String query) {
Subject anonymous = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
anonymous.login(AnonymousAuthenticationToken.getInstance());
Query q = new Query(query, anonymous);
q.parse();
diff --git a/src/test/java/org/caosdb/server/query/TestCQL.java b/src/test/java/org/caosdb/server/query/TestCQL.java
index 8d7a7e8f..f8c3fadc 100644
--- a/src/test/java/org/caosdb/server/query/TestCQL.java
+++ b/src/test/java/org/caosdb/server/query/TestCQL.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,7 +19,7 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.query;
+package org.linkahead.server.query;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -37,24 +37,24 @@ import org.antlr.v4.runtime.CharStreams;
import org.antlr.v4.runtime.CommonTokenStream;
import org.antlr.v4.runtime.Token;
import org.antlr.v4.runtime.tree.ParseTree;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.query.CQLParser.CqContext;
-import org.caosdb.server.query.Query.Pattern;
-import org.caosdb.server.query.Query.QueryException;
-import org.caosdb.server.utils.Initialization;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.query.CQLParser.CqContext;
+import org.linkahead.server.query.Query.Pattern;
+import org.linkahead.server.query.Query.QueryException;
+import org.linkahead.server.utils.Initialization;
public class TestCQL {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
static Access access = Initialization.setUp().getAccess();
@@ -268,7 +268,7 @@ public class TestCQL {
String queryMR56 = "FIND ENTITY WITH ((p0 = v0 OR p1=v1) AND p2=v2)";
String versionedQuery1 = "FIND ANY VERSION OF ENTITY e1";
- // https://gitlab.com/caosdb/caosdb-server/-/issues/131
+ // https://gitlab.com/linkahead/linkahead-server/-/issues/131
String issue131a = "FIND ename WITH pname1.x AND pname2";
String issue131b = "FIND ename WITH (pname1.x < 10) AND (pname1.x)";
String issue131c = "FIND ename WITH pname2 AND pname1.x ";
@@ -277,7 +277,7 @@ public class TestCQL {
String issue131f = "FIND ename WITH (pname1.pname2 > 30) AND pname1.pname2 < 40";
String issue144 = "FIND ename WITH pname = ";
- // https://gitlab.com/caosdb/caosdb-server/-/issues/130
+ // https://gitlab.com/linkahead/linkahead-server/-/issues/130
String issue130a =
"SELECT 'name with spaces.and dot', 'name with spaces'.name, name with spaces.name, name with\\,comma and\\.dot and \\'single_quote.sub FROM ENTITY";
String issue130b = "SELECT 'Wrapper' FROM RECORD TestRT";
@@ -7074,7 +7074,7 @@ public class TestCQL {
/**
* Test that brackets around 'has pname' do not cause filter to become subproperty filter.
*
- * <p>https://gitlab.com/caosdb/caosdb-server/-/issues/203
+ * <p>https://gitlab.com/linkahead/linkahead-server/-/issues/203
*/
@Test
public void testIssue203() {
diff --git a/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java b/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
index 63c10c1f..936bd542 100644
--- a/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
+++ b/src/test/java/org/caosdb/server/resource/FileSystemResourceTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertThrows;
diff --git a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
index ca4fbb09..a8fc04cc 100644
--- a/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestAbstractCaosDBServerResource.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -14,29 +14,29 @@ import java.util.HashSet;
import org.apache.shiro.mgt.DefaultSecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.subject.support.DelegatingSubject;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.MySQL.ConnectionException;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.utils.WebinterfaceUtils;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.MySQL.ConnectionException;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.utils.WebinterfaceUtils;
import org.restlet.data.Reference;
import org.restlet.representation.Representation;
-public class TestAbstractCaosDBServerResource {
+public class TestAbstractLinkAheadServerResource {
/** a no-op mock-up which resolved all rules to an empty set of permissions. */
public static class RetrievePermissionRulesMockup implements RetrievePermissionRulesImpl {
@@ -78,7 +78,7 @@ public class TestAbstractCaosDBServerResource {
@BeforeAll
public static void initServerProperties() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
BackendTransaction.setImpl(
RetrievePermissionRulesImpl.class, RetrievePermissionRulesMockup.class);
@@ -88,14 +88,14 @@ public class TestAbstractCaosDBServerResource {
@Test
public void testReponseRootElement(@TempDir Path tmpDir) throws IOException {
final Subject user = new DelegatingSubject(new DefaultSecurityManager(new AnonymousRealm()));
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
- AbstractCaosDBServerResource s =
- new AbstractCaosDBServerResource() {
+ AbstractLinkAheadServerResource s =
+ new AbstractLinkAheadServerResource() {
@Override
protected Representation httpGetInChildClass()
- throws ConnectionException, IOException, SQLException, CaosDBException,
+ throws ConnectionException, IOException, SQLException, LinkAheadException,
NoSuchAlgorithmException, Exception {
// TODO Auto-generated method stub
return null;
@@ -158,7 +158,7 @@ public class TestAbstractCaosDBServerResource {
+ "defaultRealm = PAM\n"
+ "\n"
+ "[PAM]\n"
- + "class = org.caosdb.server.accessControl.Pam\n"
+ + "class = org.linkahead.server.accessControl.Pam\n"
+ "default_status = ACTIVE\n"
+ "include.user = admin\n"
+ ";include.group = [uncomment and put your groups here]\n"
@@ -169,6 +169,6 @@ public class TestAbstractCaosDBServerResource {
+ "user.admin.roles = administration";
Files.write(Paths.get(usersourcesFileName), usersourcesContent.getBytes());
- CaosDBServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
+ LinkAheadServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
}
}
diff --git a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
index 31d4a384..88b66c5f 100644
--- a/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestScriptingResource.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -21,7 +21,7 @@
*
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -31,29 +31,29 @@ import java.util.HashSet;
import java.util.List;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.CredentialsValidator;
-import org.caosdb.server.accessControl.Principal;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.accessControl.UserSources;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
-import org.caosdb.server.database.backend.interfaces.RetrievePermissionRulesImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.backend.interfaces.RetrieveUserImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.database.proto.ProtoUser;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.permissions.PermissionRule;
-import org.caosdb.server.scripting.ScriptingPermissions;
-import org.caosdb.server.scripting.ServerSideScriptingCaller;
import org.jdom2.Element;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.CredentialsValidator;
+import org.linkahead.server.accessControl.Principal;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.accessControl.UserSources;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrievePasswordValidatorImpl;
+import org.linkahead.server.database.backend.interfaces.RetrievePermissionRulesImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.backend.interfaces.RetrieveUserImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.database.proto.ProtoUser;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.permissions.PermissionRule;
+import org.linkahead.server.scripting.ScriptingPermissions;
+import org.linkahead.server.scripting.ServerSideScriptingCaller;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.data.Form;
@@ -153,8 +153,8 @@ public class TestScriptingResource {
@BeforeAll
public static void setupShiro() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.initShiro();
BackendTransaction.setImpl(RetrieveRoleImpl.class, RetrieveRoleMockup.class);
BackendTransaction.setImpl(RetrievePermissionRulesImpl.class, RetrievePermissionRules.class);
@@ -171,7 +171,7 @@ public class TestScriptingResource {
public int callScript(
java.util.List<String> invokation,
Integer timeout_ms,
- java.util.List<org.caosdb.server.entity.FileProperties> files,
+ java.util.List<org.linkahead.server.entity.FileProperties> files,
Object authToken)
throws Message {
if (invokation.get(0).equals("anonymous_ok")) {
@@ -206,7 +206,7 @@ public class TestScriptingResource {
@Test
public void testAnonymousWithOutPermission() {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_no_permission");
Representation entity = form.getWebRepresentation();
@@ -224,7 +224,7 @@ public class TestScriptingResource {
@Test
public void testAnonymousWithPermission() {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_ok");
Representation entity = form.getWebRepresentation();
@@ -257,7 +257,7 @@ public class TestScriptingResource {
@Test
public void testHandleForm() throws Message, IOException {
Subject user = SecurityUtils.getSubject();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
Form form = new Form("call=anonymous_ok");
assertEquals(0, resource.handleForm(form));
diff --git a/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java b/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
index 6b9fab19..988ba24d 100644
--- a/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
+++ b/src/test/java/org/caosdb/server/resource/TestSharedFileResource.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 IndiScale GmbH
*
@@ -20,7 +20,7 @@
* ** end header
*/
-package org.caosdb.server.resource;
+package org.linkahead.server.resource;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -38,14 +38,14 @@ import net.jcip.annotations.NotThreadSafe;
import org.apache.shiro.mgt.DefaultSecurityManager;
import org.apache.shiro.subject.Subject;
import org.apache.shiro.subject.support.DelegatingSubject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.AnonymousRealm;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.AnonymousRealm;
import org.restlet.Request;
import org.restlet.Response;
import org.restlet.data.Disposition;
@@ -75,7 +75,7 @@ public class TestSharedFileResource {
@BeforeAll
public static void setup() throws Exception {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
String tmpStr = FileSystem.getTmp();
illegalTopLevelFile = new File(tmpStr, illegalTopLevelString);
@@ -109,7 +109,7 @@ public class TestSharedFileResource {
provideUserSourcesFile(tmpDir);
final Subject user = new DelegatingSubject(new DefaultSecurityManager(new AnonymousRealm()));
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "true");
user.login(AnonymousAuthenticationToken.getInstance());
SharedFileResource resource =
new SharedFileResource() {
@@ -176,7 +176,7 @@ public class TestSharedFileResource {
+ "defaultRealm = PAM\n"
+ "\n"
+ "[PAM]\n"
- + "class = org.caosdb.server.accessControl.Pam\n"
+ + "class = org.linkahead.server.accessControl.Pam\n"
+ "default_status = ACTIVE\n"
+ "include.user = admin\n"
+ ";include.group = [uncomment and put your groups here]\n"
@@ -187,6 +187,6 @@ public class TestSharedFileResource {
+ "user.admin.roles = administration";
Files.write(Paths.get(usersourcesFileName), usersourcesContent.getBytes());
- CaosDBServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
+ LinkAheadServer.setProperty(ServerProperties.KEY_USER_SOURCES_INI_FILE, usersourcesFileName);
}
}
diff --git a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
index 0d379282..22773355 100644
--- a/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
+++ b/src/test/java/org/caosdb/server/scripting/TestServerSideScriptingCaller.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.scripting;
+package org.linkahead.server.scripting;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -39,19 +39,19 @@ import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.FileProperties;
-import org.caosdb.server.entity.Message;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.Timeout;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.FileProperties;
+import org.linkahead.server.entity.Message;
+import org.linkahead.server.utils.ServerMessages;
public class TestServerSideScriptingCaller {
@@ -63,8 +63,8 @@ public class TestServerSideScriptingCaller {
@BeforeAll
public static void setupTestFolder() throws IOException {
testFolder = Files.createTempDirectory(".TestDir_ServerSideScripting").toFile();
- CaosDBServer.initServerProperties();
- CaosDBServer.getServerProperties()
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.getServerProperties()
.setProperty(
ServerProperties.KEY_SERVER_SIDE_SCRIPTING_BIN_DIRS, testFolder.getAbsolutePath());
@@ -163,10 +163,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link FileNotFoundException} because PWD does not exist.
*
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test()
- public void testPutFilesInWorkingDirFailure1() throws IOException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure1() throws IOException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -177,13 +177,13 @@ public class TestServerSideScriptingCaller {
}
/**
- * Throw {@link CaosDBException} because tmpIdentifier is null or empty.
+ * Throw {@link LinkAheadException} because tmpIdentifier is null or empty.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure2() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure2() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -200,10 +200,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link NullPointerException} because file is null.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure3() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure3() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -223,10 +223,10 @@ public class TestServerSideScriptingCaller {
* Throw {@link TransactionException} because file does not exist.
*
* @throws FileNotFoundException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test
- public void testPutFilesInWorkingDirFailure4() throws FileNotFoundException, CaosDBException {
+ public void testPutFilesInWorkingDirFailure4() throws FileNotFoundException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -247,10 +247,10 @@ public class TestServerSideScriptingCaller {
* putFilesInWorkingDir returns silently because files is null.
*
* @throws IOException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@Test()
- public void testPutFilesInWorkingDirReturnSilently() throws IOException, CaosDBException {
+ public void testPutFilesInWorkingDirReturnSilently() throws IOException, LinkAheadException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -259,7 +259,7 @@ public class TestServerSideScriptingCaller {
}
@Test
- public void testPutFilesInWorkingDirOk() throws CaosDBException, IOException {
+ public void testPutFilesInWorkingDirOk() throws LinkAheadException, IOException {
final ServerSideScriptingCaller caller =
new ServerSideScriptingCaller(
null, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
@@ -405,7 +405,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public int callScript(
@@ -431,8 +431,8 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {
- throw new CaosDBException("");
+ throws FileNotFoundException, LinkAheadException {
+ throw new LinkAheadException("");
}
@Override
@@ -460,7 +460,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public void createTmpHomeDir() throws Exception {}
@@ -490,7 +490,7 @@ public class TestServerSideScriptingCaller {
@Override
public void putFilesInWorkingDir(final Collection<FileProperties> files)
- throws FileNotFoundException, CaosDBException {}
+ throws FileNotFoundException, LinkAheadException {}
@Override
public int callScript(
@@ -614,9 +614,9 @@ public class TestServerSideScriptingCaller {
cmd, -1, null, null, emptyEnv, new ScriptingUtils(), this.pwd);
caller.createWorkingDir();
// Create source folder in working directory
- String scriptingHomeDir = CaosDBServer.getServerProperty("SERVER_SIDE_SCRIPTING_HOME_DIR");
+ String scriptingHomeDir = LinkAheadServer.getServerProperty("SERVER_SIDE_SCRIPTING_HOME_DIR");
File tempHomeDirSrc = new File(caller.getTmpWorkingDir(), "home_source");
- CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", tempHomeDirSrc.toString());
+ LinkAheadServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", tempHomeDirSrc.toString());
tempHomeDirSrc.mkdir();
String testFileName = "testfile.txt";
String testContent = "sloikdfgu89w4t78930tvgyum9q238456t27ht2";
@@ -631,6 +631,6 @@ public class TestServerSideScriptingCaller {
String expectedFileContent = FileUtils.readFileToString(expectedFile, "UTF-8");
assertEquals(expectedFileContent, testContent);
caller.cleanup();
- CaosDBServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", scriptingHomeDir);
+ LinkAheadServer.setProperty("SERVER_SIDE_SCRIPTING_HOME_DIR", scriptingHomeDir);
}
}
diff --git a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
index a3ac40e1..c8ae9417 100644
--- a/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
+++ b/src/test/java/org/caosdb/server/transaction/RetrieveTest.java
@@ -1,4 +1,4 @@
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -7,34 +7,34 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import org.apache.shiro.SecurityUtils;
import org.apache.shiro.subject.Subject;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.accessControl.AnonymousAuthenticationToken;
-import org.caosdb.server.accessControl.Role;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.interfaces.RetrieveRoleImpl;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.database.misc.TransactionBenchmark;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.container.RetrieveContainer;
-import org.caosdb.server.entity.xml.IdAndServerMessagesOnlyStrategy;
-import org.caosdb.server.permissions.EntityACLFactory;
-import org.caosdb.server.utils.EntityStatus;
-import org.caosdb.server.utils.ServerMessages;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.accessControl.AnonymousAuthenticationToken;
+import org.linkahead.server.accessControl.Role;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.interfaces.RetrieveRoleImpl;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.database.misc.TransactionBenchmark;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.container.RetrieveContainer;
+import org.linkahead.server.entity.xml.IdAndServerMessagesOnlyStrategy;
+import org.linkahead.server.permissions.EntityACLFactory;
+import org.linkahead.server.utils.EntityStatus;
+import org.linkahead.server.utils.ServerMessages;
public class RetrieveTest {
// @review Florian Spreckelsen 2022-03-22
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
- CaosDBServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "TRUE");
- CaosDBServer.initShiro();
+ LinkAheadServer.initServerProperties();
+ LinkAheadServer.setProperty(ServerProperties.KEY_AUTH_OPTIONAL, "TRUE");
+ LinkAheadServer.initShiro();
BackendTransaction.setImpl(RetrieveRoleImpl.class, RetrieveRoleMockup.class);
}
diff --git a/src/test/java/org/caosdb/server/transaction/UpdateTest.java b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
index a0891a3e..ace94c5a 100644
--- a/src/test/java/org/caosdb/server/transaction/UpdateTest.java
+++ b/src/test/java/org/caosdb/server/transaction/UpdateTest.java
@@ -1,5 +1,5 @@
/*
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -19,44 +19,44 @@
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <https://www.gnu.org/licenses/>.
*/
-package org.caosdb.server.transaction;
+package org.linkahead.server.transaction;
-import static org.caosdb.server.utils.EntityStatus.QUALIFIED;
-import static org.caosdb.server.utils.EntityStatus.VALID;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.linkahead.server.utils.EntityStatus.QUALIFIED;
+import static org.linkahead.server.utils.EntityStatus.VALID;
import java.io.IOException;
import java.security.NoSuchAlgorithmException;
import java.util.HashSet;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.datatype.CollectionValue;
-import org.caosdb.server.datatype.GenericValue;
-import org.caosdb.server.datatype.ReferenceValue;
-import org.caosdb.server.entity.Entity;
-import org.caosdb.server.entity.EntityID;
-import org.caosdb.server.entity.EntityInterface;
-import org.caosdb.server.entity.RetrieveEntity;
-import org.caosdb.server.entity.StatementStatus;
-import org.caosdb.server.entity.UpdateEntity;
-import org.caosdb.server.entity.wrapper.Property;
-import org.caosdb.server.permissions.EntityPermission;
-import org.caosdb.server.permissions.Permission;
-import org.caosdb.server.utils.EntityStatus;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.datatype.CollectionValue;
+import org.linkahead.server.datatype.GenericValue;
+import org.linkahead.server.datatype.ReferenceValue;
+import org.linkahead.server.entity.Entity;
+import org.linkahead.server.entity.EntityID;
+import org.linkahead.server.entity.EntityInterface;
+import org.linkahead.server.entity.RetrieveEntity;
+import org.linkahead.server.entity.StatementStatus;
+import org.linkahead.server.entity.UpdateEntity;
+import org.linkahead.server.entity.wrapper.Property;
+import org.linkahead.server.permissions.EntityPermission;
+import org.linkahead.server.permissions.Permission;
+import org.linkahead.server.utils.EntityStatus;
public class UpdateTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
public void testDeriveUpdate_SameName()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity("Name");
final Entity oldEntity = new RetrieveEntity("Name");
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -65,7 +65,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_DifferentName()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity("NewName");
final Entity oldEntity = new RetrieveEntity("OldName");
new WriteTransaction(null).deriveUpdate(newEntity, oldEntity);
@@ -74,7 +74,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameProperty()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity(new EntityID(1234));
final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
newEntity.addProperty(newProperty);
@@ -88,7 +88,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_AnotherProperty()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final Entity newEntity = new RetrieveEntity(new EntityID(1234));
final Property newProperty = new Property(new RetrieveEntity(new EntityID(1)));
final Property newProperty2 = new Property(new RetrieveEntity(new EntityID(2)));
@@ -106,7 +106,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_SameUnit()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
magicUnit.setName("Unit");
magicUnit.setId(new EntityID(24));
@@ -148,7 +148,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_DifferentUnit()
- throws NoSuchAlgorithmException, IOException, CaosDBException {
+ throws NoSuchAlgorithmException, IOException, LinkAheadException {
final EntityInterface magicUnit = new RetrieveEntity(new EntityID(1234));
magicUnit.setName("Unit");
magicUnit.setId(new EntityID(24));
@@ -189,7 +189,7 @@ public class UpdateTest {
@Test
public void testDeriveUpdate_Collections()
- throws NoSuchAlgorithmException, CaosDBException, IOException {
+ throws NoSuchAlgorithmException, LinkAheadException, IOException {
final Entity newEntity = new UpdateEntity();
final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
@@ -264,7 +264,7 @@ public class UpdateTest {
/** For issue #217: Server gets list property datatype wrong if description is updated. */
@Test
public void testDeriveUpdate_UpdateList()
- throws NoSuchAlgorithmException, CaosDBException, IOException {
+ throws NoSuchAlgorithmException, LinkAheadException, IOException {
// @review Florian Spreckelsen 2022-03-15
final Property oldProperty = new Property(new UpdateEntity(new EntityID(1)));
final Property newProperty = new Property(new UpdateEntity(new EntityID(1)));
diff --git a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
index e05a3c7f..8079a2c4 100644
--- a/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/FileUtilsTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
@@ -38,34 +38,34 @@ import java.security.NoSuchAlgorithmException;
import java.util.Iterator;
import java.util.regex.Pattern;
import net.jcip.annotations.NotThreadSafe;
-import org.caosdb.server.CaosDBException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.FileSystem;
-import org.caosdb.server.ServerProperties;
-import org.caosdb.server.database.BackendTransaction;
-import org.caosdb.server.database.access.Access;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator.FileNameIterator;
-import org.caosdb.server.database.backend.implementation.UnixFileSystem.UnixFileSystemHelper;
-import org.caosdb.server.database.backend.interfaces.FileCheckHash;
-import org.caosdb.server.database.backend.interfaces.FileCheckSize;
-import org.caosdb.server.database.backend.interfaces.FileExists;
-import org.caosdb.server.database.backend.interfaces.FileWasModifiedAfter;
-import org.caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
-import org.caosdb.server.database.backend.transaction.FileConsistencyCheck;
-import org.caosdb.server.database.backend.transaction.GetFileIterator;
-import org.caosdb.server.database.exceptions.TransactionException;
-import org.caosdb.server.entity.Message;
import org.eclipse.jetty.io.RuntimeIOException;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.FileSystem;
+import org.linkahead.server.LinkAheadException;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
+import org.linkahead.server.database.BackendTransaction;
+import org.linkahead.server.database.access.Access;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckHash;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemCheckSize;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileExists;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemFileWasModifiedAfter;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemGetFileIterator.FileNameIterator;
+import org.linkahead.server.database.backend.implementation.UnixFileSystem.UnixFileSystemHelper;
+import org.linkahead.server.database.backend.interfaces.FileCheckHash;
+import org.linkahead.server.database.backend.interfaces.FileCheckSize;
+import org.linkahead.server.database.backend.interfaces.FileExists;
+import org.linkahead.server.database.backend.interfaces.FileWasModifiedAfter;
+import org.linkahead.server.database.backend.interfaces.GetFileIteratorImpl;
+import org.linkahead.server.database.backend.transaction.FileConsistencyCheck;
+import org.linkahead.server.database.backend.transaction.GetFileIterator;
+import org.linkahead.server.database.exceptions.TransactionException;
+import org.linkahead.server.entity.Message;
@NotThreadSafe
public class FileUtilsTest {
@@ -76,7 +76,7 @@ public class FileUtilsTest {
public static File someFile;
public static File someDir_someFile;
public static File linkToSomeFile;
- public static File tmpFolderCaosDB;
+ public static File tmpFolderLinkAhead;
private static File newFolder(String name) throws IOException {
Path ret = Files.createTempDirectory(tempDirectory, name);
@@ -84,8 +84,8 @@ public class FileUtilsTest {
}
@BeforeAll
- public static void setup() throws Message, IOException, CaosDBException, InterruptedException {
- CaosDBServer.initServerProperties();
+ public static void setup() throws Message, IOException, LinkAheadException, InterruptedException {
+ LinkAheadServer.initServerProperties();
BackendTransaction.setImpl(FileExists.class, UnixFileSystemFileExists.class);
BackendTransaction.setImpl(GetFileIteratorImpl.class, UnixFileSystemGetFileIterator.class);
BackendTransaction.setImpl(
@@ -95,7 +95,7 @@ public class FileUtilsTest {
tempDirectory = Files.createTempDirectory(null);
testRoot = newFolder("fileutils_testfolder");
- File basePath = newFolder("caosdbRoot");
+ File basePath = newFolder("linkaheadRoot");
File dropOffBox = newFolder("dropOffBox");
someDir = testRoot.toPath().resolve("some_dir").toFile();
linkToSomeDir = testRoot.toPath().resolve("link_to_some_dir").toFile();
@@ -103,10 +103,10 @@ public class FileUtilsTest {
someDir_someFile = someDir.toPath().resolve("someFile").toFile();
linkToSomeFile = testRoot.toPath().resolve("link_to_some_file").toFile();
- tmpFolderCaosDB = newFolder("tmpFolderCaosDB");
- CaosDBServer.setProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT, basePath.toString());
- CaosDBServer.setProperty(ServerProperties.KEY_DROP_OFF_BOX, dropOffBox.toString());
- CaosDBServer.setProperty(ServerProperties.KEY_TMP_FILES, tmpFolderCaosDB.toString());
+ tmpFolderLinkAhead = newFolder("tmpFolderLinkAhead");
+ LinkAheadServer.setProperty(ServerProperties.KEY_FILE_SYSTEM_ROOT, basePath.toString());
+ LinkAheadServer.setProperty(ServerProperties.KEY_DROP_OFF_BOX, dropOffBox.toString());
+ LinkAheadServer.setProperty(ServerProperties.KEY_TMP_FILES, tmpFolderLinkAhead.toString());
FileSystem.init();
basePath = new File(FileSystem.getBasepath());
@@ -130,7 +130,7 @@ public class FileUtilsTest {
}
@AfterAll
- public static void teardown() throws IOException, CaosDBException, InterruptedException {
+ public static void teardown() throws IOException, LinkAheadException, InterruptedException {
FileUtils.delete(testRoot, true);
deleteTmp();
assertFalse(testRoot.exists());
@@ -141,10 +141,10 @@ public class FileUtilsTest {
/**
* @throws InterruptedException
- * @throws CaosDBException
+ * @throws LinkAheadException
*/
@BeforeEach
- public void testTmpEmpty() throws IOException, CaosDBException, InterruptedException {
+ public void testTmpEmpty() throws IOException, LinkAheadException, InterruptedException {
if (new File(FileSystem.getTmp()).exists()) {
if (0 != new File(FileSystem.getTmp()).list().length) {
System.err.println("TMP not empty, aborting test!");
@@ -159,7 +159,7 @@ public class FileUtilsTest {
}
}
- public static void deleteTmp() throws IOException, CaosDBException, InterruptedException {
+ public static void deleteTmp() throws IOException, LinkAheadException, InterruptedException {
File tmpDir = new File(FileSystem.getTmp());
if (tmpDir.exists())
for (File f : tmpDir.listFiles()) {
@@ -169,7 +169,7 @@ public class FileUtilsTest {
}
@AfterEach
- public void callDeleteTmp() throws IOException, CaosDBException, InterruptedException {
+ public void callDeleteTmp() throws IOException, LinkAheadException, InterruptedException {
deleteTmp();
}
@@ -196,7 +196,8 @@ public class FileUtilsTest {
}
@Test
- public void testGetMimeTypeSymlink() throws IOException, InterruptedException, CaosDBException {
+ public void testGetMimeTypeSymlink()
+ throws IOException, InterruptedException, LinkAheadException {
final File symlink = testRoot.toPath().resolve("simlink").toFile();
try {
@@ -241,7 +242,7 @@ public class FileUtilsTest {
}
@Test
- public void testSymlinkRoot() throws IOException, InterruptedException, CaosDBException {
+ public void testSymlinkRoot() throws IOException, InterruptedException, LinkAheadException {
final File symlink_root = linkToSomeDir;
assertTrue(symlink_root.exists());
assertTrue(symlink_root.isDirectory());
@@ -283,7 +284,7 @@ public class FileUtilsTest {
}
@Test
- public void TestChownScript() throws IOException, InterruptedException, CaosDBException {
+ public void TestChownScript() throws IOException, InterruptedException, LinkAheadException {
FileUtils.testChownScript();
final File f = new File(FileSystem.getDropOffBox() + "chown_test_file");
@@ -465,7 +466,7 @@ public class FileUtilsTest {
}
@Test
- public void testSymlinkBehavior() throws IOException, InterruptedException, CaosDBException {
+ public void testSymlinkBehavior() throws IOException, InterruptedException, LinkAheadException {
// root dir for this test
final String rootPath = "./testSymlinkBehavior/";
@@ -721,11 +722,11 @@ public class FileUtilsTest {
String existingDirStr = "existingDir";
String existingFileStr = "existingFile";
String newDirStr = "newDir/";
- File existingDir = new File(tmpFolderCaosDB, existingDirStr);
+ File existingDir = new File(tmpFolderLinkAhead, existingDirStr);
existingDir.mkdir();
- File existingFile = new File(tmpFolderCaosDB, existingFileStr);
+ File existingFile = new File(tmpFolderLinkAhead, existingFileStr);
existingFile.createNewFile();
- File newDir = new File(tmpFolderCaosDB, newDirStr);
+ File newDir = new File(tmpFolderLinkAhead, newDirStr);
// Existing directory
assertEquals(existingDir.toString(), FileSystem.assertDir(existingDirStr));
diff --git a/src/test/java/org/caosdb/server/utils/UtilsTest.java b/src/test/java/org/caosdb/server/utils/UtilsTest.java
index 562d5927..6f5c71ef 100644
--- a/src/test/java/org/caosdb/server/utils/UtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/UtilsTest.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2019 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,7 +20,7 @@
*
* ** end header
*/
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
diff --git a/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java b/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
index c607afd0..f812287e 100644
--- a/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
+++ b/src/test/java/org/caosdb/server/utils/WebinterfaceUtilsTest.java
@@ -1,21 +1,21 @@
-package org.caosdb.server.utils;
+package org.linkahead.server.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import java.io.IOException;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
import org.restlet.data.Reference;
public class WebinterfaceUtilsTest {
@BeforeAll
public static void setup() throws IOException {
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
}
@Test
@@ -23,7 +23,7 @@ public class WebinterfaceUtilsTest {
WebinterfaceUtils utils = new WebinterfaceUtils(new Reference("https://host:2345/some_path"));
String buildNumber = utils.getBuildNumber();
String ref = utils.getWebinterfaceURI("sub");
- String contextRoot = CaosDBServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT);
+ String contextRoot = LinkAheadServer.getServerProperty(ServerProperties.KEY_CONTEXT_ROOT);
contextRoot =
contextRoot != null && contextRoot.length() > 0
? "/" + contextRoot.replaceFirst("^/", "").replaceFirst("/$", "")
diff --git a/src/test/java/org/caosdb/server/utils/mail/TestMail.java b/src/test/java/org/caosdb/server/utils/mail/TestMail.java
index 05cf5bf5..415ee72d 100644
--- a/src/test/java/org/caosdb/server/utils/mail/TestMail.java
+++ b/src/test/java/org/caosdb/server/utils/mail/TestMail.java
@@ -1,6 +1,6 @@
/*
* ** header v3.0
- * This file is a part of the CaosDB Project.
+ * This file is a part of the LinkAhead Project.
*
* Copyright (C) 2018 Research Group Biomedical Physics,
* Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -20,17 +20,17 @@
*
* ** end header
*/
-package org.caosdb.server.utils.mail;
+package org.linkahead.server.utils.mail;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import org.apache.commons.io.FileUtils;
-import org.caosdb.server.CaosDBServer;
-import org.caosdb.server.ServerProperties;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
+import org.linkahead.server.LinkAheadServer;
+import org.linkahead.server.ServerProperties;
public class TestMail {
@@ -40,9 +40,9 @@ public class TestMail {
public static void setupUp() throws IOException {
testDir = Files.createTempDirectory(".TestDir_Mail").toFile();
- CaosDBServer.initServerProperties();
+ LinkAheadServer.initServerProperties();
// output mails to the test dir
- CaosDBServer.setProperty(
+ LinkAheadServer.setProperty(
ServerProperties.KEY_MAIL_TO_FILE_HANDLER_LOC, testDir.getAbsolutePath());
}
--
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