/lib/galaxy/model/mapping.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 1910 lines · 1580 code · 266 blank · 64 comment · 5 complexity · 671bc2833c7941cf78847d9c8f1d10bd MD5 · raw file
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- """
- Details of how the data model objects are mapped onto the relational database
- are encapsulated here.
- """
- import logging
- import pkg_resources
- from sqlalchemy import and_, asc, Boolean, Column, DateTime, desc, ForeignKey, Integer, MetaData, not_, Numeric, select, String, Table, TEXT, Unicode, UniqueConstraint
- from sqlalchemy.ext.associationproxy import association_proxy
- from sqlalchemy.ext.orderinglist import ordering_list
- from sqlalchemy.types import BigInteger
- from sqlalchemy.orm import backref, object_session, relation, mapper, class_mapper
- from sqlalchemy.orm.collections import attribute_mapped_collection
- from galaxy import model
- from galaxy.model.orm.engine_factory import build_engine
- from galaxy.model.orm.now import now
- from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
- from galaxy.model.base import ModelMapping
- from galaxy.security import GalaxyRBACAgent
- log = logging.getLogger( __name__ )
- metadata = MetaData()
- model.User.table = Table( "galaxy_user", metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "email", TrimmedString( 255 ), index=True, nullable=False ),
- Column( "username", TrimmedString( 255 ), index=True, unique=True ),
- Column( "password", TrimmedString( 255 ), nullable=False ),
- Column( "external", Boolean, default=False ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "disk_usage", Numeric( 15, 0 ), index=True ) ,
- Column( "active", Boolean, index=True, default=True, nullable=False ),
- Column( "activation_token", TrimmedString( 64 ), nullable=True, index=True ) )
- model.UserAddress.table = Table( "user_address", metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "desc", TrimmedString( 255 )),
- Column( "name", TrimmedString( 255 ), nullable=False),
- Column( "institution", TrimmedString( 255 )),
- Column( "address", TrimmedString( 255 ), nullable=False),
- Column( "city", TrimmedString( 255 ), nullable=False),
- Column( "state", TrimmedString( 255 ), nullable=False),
- Column( "postal_code", TrimmedString( 255 ), nullable=False),
- Column( "country", TrimmedString( 255 ), nullable=False),
- Column( "phone", TrimmedString( 255 )),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ) )
- model.UserOpenID.table = Table( "galaxy_user_openid", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "openid", TEXT, index=True, unique=True ),
- Column( "provider", TrimmedString( 255 ) ),
- )
- model.History.table = Table( "history", metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "name", TrimmedString( 255 ) ),
- Column( "hid_counter", Integer, default=1 ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "importing", Boolean, index=True, default=False ),
- Column( "genome_build", TrimmedString( 40 ) ),
- Column( "importable", Boolean, default=False ),
- Column( "slug", TEXT, index=True ),
- Column( "published", Boolean, index=True, default=False ) )
- model.HistoryUserShareAssociation.table = Table( "history_user_share_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- )
- model.HistoryDatasetAssociation.table = Table( "history_dataset_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "state", TrimmedString( 64 ), index=True, key="_state" ),
- Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
- Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ),
- Column( "hid", Integer ),
- Column( "name", TrimmedString( 255 ) ),
- Column( "info", TrimmedString( 255 ) ),
- Column( "blurb", TrimmedString( 255 ) ),
- Column( "peek" , TEXT ),
- Column( "tool_version" , TEXT ),
- Column( "extension", TrimmedString( 64 ) ),
- Column( "metadata", MetadataType(), key="_metadata" ),
- Column( "parent_id", Integer, ForeignKey( "history_dataset_association.id" ), nullable=True ),
- Column( "designation", TrimmedString( 255 ) ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "visible", Boolean ),
- Column( "extended_metadata_id", Integer,
- ForeignKey( "extended_metadata.id" ), index=True )
- )
- model.Dataset.table = Table( "dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "state", TrimmedString( 64 ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "purgable", Boolean, default=True ),
- Column( "object_store_id", TrimmedString( 255 ), index=True ),
- Column( "external_filename" , TEXT ),
- Column( "_extra_files_path", TEXT ),
- Column( 'file_size', Numeric( 15, 0 ) ),
- Column( 'total_size', Numeric( 15, 0 ) ),
- Column( 'uuid', UUIDType() ) )
- model.HistoryDatasetAssociationDisplayAtAuthorization.table = Table( "history_dataset_association_display_at_authorization", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "site", TrimmedString( 255 ) ) )
- model.HistoryDatasetAssociationSubset.table = Table( "history_dataset_association_subset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "history_dataset_association_subset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "location", Unicode(255), index=True) )
- model.ImplicitlyConvertedDatasetAssociation.table = Table( "implicitly_converted_dataset_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
- Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ),
- Column( "hda_parent_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "ldda_parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "metadata_safe", Boolean, index=True, default=True ),
- Column( "type", TrimmedString( 255 ) ) )
- model.ValidationError.table = Table( "validation_error", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "message", TrimmedString( 255 ) ),
- Column( "err_type", TrimmedString( 64 ) ),
- Column( "attributes", TEXT ) )
- model.Group.table = Table( "galaxy_group", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", String( 255 ), index=True, unique=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.UserGroupAssociation.table = Table( "user_group_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ) )
- model.UserRoleAssociation.table = Table( "user_role_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ) )
- model.GroupRoleAssociation.table = Table( "group_role_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ) )
- model.Role.table = Table( "role", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", String( 255 ), index=True, unique=True ),
- Column( "description", TEXT ),
- Column( "type", String( 40 ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.UserQuotaAssociation.table = Table( "user_quota_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ) )
- model.GroupQuotaAssociation.table = Table( "group_quota_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ),
- Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ) )
- model.Quota.table = Table( "quota", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", String( 255 ), index=True, unique=True ),
- Column( "description", TEXT ),
- Column( "bytes", BigInteger ),
- Column( "operation", String( 8 ) ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.DefaultQuotaAssociation.table = Table( "default_quota_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "type", String( 32 ), index=True, unique=True ),
- Column( "quota_id", Integer, ForeignKey( "quota.id" ), index=True ) )
- model.DatasetPermissions.table = Table( "dataset_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.LibraryPermissions.table = Table( "library_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.LibraryFolderPermissions.table = Table( "library_folder_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.LibraryDatasetPermissions.table = Table( "library_dataset_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.LibraryDatasetDatasetAssociationPermissions.table = Table( "library_dataset_dataset_association_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.DefaultUserPermissions.table = Table( "default_user_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "action", TEXT ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.DefaultHistoryPermissions.table = Table( "default_history_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "action", TEXT ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.LibraryDataset.table = Table( "library_dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected
- Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
- Column( "order_id", Integer ), #not currently being used, but for possible future use
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), key="_name", index=True ), #when not None/null this will supercede display in library (but not when imported into user's history?)
- Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?)
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ) )
- model.LibraryDatasetDatasetAssociation.table = Table( "library_dataset_dataset_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "state", TrimmedString( 64 ), index=True, key="_state" ),
- Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ),
- Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ),
- Column( "name", TrimmedString( 255 ), index=True ),
- Column( "info", TrimmedString( 255 ) ),
- Column( "blurb", TrimmedString( 255 ) ),
- Column( "peek" , TEXT ),
- Column( "tool_version" , TEXT ),
- Column( "extension", TrimmedString( 64 ) ),
- Column( "metadata", MetadataType(), key="_metadata" ),
- Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ),
- Column( "designation", TrimmedString( 255 ) ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "visible", Boolean ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "message", TrimmedString( 255 ) ),
- Column( "extended_metadata_id", Integer,
- ForeignKey( "extended_metadata.id" ), index=True )
- )
- model.ExtendedMetadata.table = Table("extended_metadata", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "data", JSONType ) )
- model.ExtendedMetadataIndex.table = Table("extended_metadata_index", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "extended_metadata_id", Integer, ForeignKey("extended_metadata.id",
- onupdate="CASCADE",
- ondelete="CASCADE" ),
- index=True ),
- Column( "path", String( 255 )),
- Column( "value", TEXT))
- model.Library.table = Table( "library", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "root_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", String( 255 ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "description", TEXT ),
- Column( "synopsis", TEXT ) )
- model.LibraryFolder.table = Table( "library_folder", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TEXT, index=True ),
- Column( "description", TEXT ),
- Column( "order_id", Integer ), #not currently being used, but for possible future use
- Column( "item_count", Integer ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ),
- Column( "genome_build", TrimmedString( 40 ) ) )
- model.LibraryInfoAssociation.table = Table( 'library_info_association', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "inheritable", Boolean, index=True, default=False ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.LibraryFolderInfoAssociation.table = Table( 'library_folder_info_association', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "inheritable", Boolean, index=True, default=False ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.LibraryDatasetDatasetInfoAssociation.table = Table( 'library_dataset_dataset_info_association', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True, index=True ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.Job.table = Table( "job", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
- Column( "tool_id", String( 255 ) ),
- Column( "tool_version", TEXT, default="1.0.0" ),
- Column( "state", String( 64 ), index=True ),
- Column( "info", TrimmedString( 255 ) ),
- Column( "command_line", TEXT ),
- Column( "param_filename", String( 1024 ) ),
- Column( "runner_name", String( 255 ) ),
- Column( "stdout", TEXT ),
- Column( "stderr", TEXT ),
- Column( "exit_code", Integer, nullable=True ),
- Column( "traceback", TEXT ),
- Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
- Column( "job_runner_name", String( 255 ) ),
- Column( "job_runner_external_id", String( 255 ) ),
- Column( "destination_id", String( 255 ), nullable=True ),
- Column( "destination_params", JSONType, nullable=True ),
- Column( "object_store_id", TrimmedString( 255 ), index=True ),
- Column( "imported", Boolean, default=False, index=True ),
- Column( "params", TrimmedString(255), index=True ),
- Column( "handler", TrimmedString( 255 ), index=True ) )
- model.JobParameter.table = Table( "job_parameter", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "name", String(255) ),
- Column( "value", TEXT ) )
- model.JobToInputDatasetAssociation.table = Table( "job_to_input_dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "name", String(255) ) )
- model.JobToOutputDatasetAssociation.table = Table( "job_to_output_dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "name", String(255) ) )
- model.JobToInputLibraryDatasetAssociation.table = Table( "job_to_input_library_dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
- Column( "name", String(255) ) )
- model.JobToOutputLibraryDatasetAssociation.table = Table( "job_to_output_library_dataset", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ),
- Column( "name", String(255) ) )
- model.JobExternalOutputMetadata.table = Table( "job_external_output_metadata", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
- Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ),
- Column( "filename_in", String( 255 ) ),
- Column( "filename_out", String( 255 ) ),
- Column( "filename_results_code", String( 255 ) ),
- Column( "filename_kwds", String( 255 ) ),
- Column( "filename_override_metadata", String( 255 ) ),
- Column( "job_runner_external_pid", String( 255 ) ) )
- model.JobExportHistoryArchive.table = Table( "job_export_history_archive", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "compressed", Boolean, index=True, default=False ),
- Column( "history_attrs_filename", TEXT ),
- Column( "datasets_attrs_filename", TEXT ),
- Column( "jobs_attrs_filename", TEXT )
- )
- model.JobImportHistoryArchive.table = Table( "job_import_history_archive", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "archive_dir", TEXT )
- )
- model.GenomeIndexToolData.table = Table( "genome_index_tool_data", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "deferred_job_id", Integer, ForeignKey( "deferred_job.id" ), index=True ),
- Column( "transfer_job_id", Integer, ForeignKey( "transfer_job.id" ), index=True ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "fasta_path", String( 255 ) ),
- Column( "created_time", DateTime, default=now ),
- Column( "modified_time", DateTime, default=now, onupdate=now ),
- Column( "indexer", String( 64 ) ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- )
- model.Task.table = Table( "task", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "execution_time", DateTime ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "state", String( 64 ), index=True ),
- Column( "command_line", TEXT ),
- Column( "param_filename", String( 1024 ) ),
- Column( "runner_name", String( 255 ) ),
- Column( "stdout", TEXT ),
- Column( "stderr", TEXT ),
- Column( "exit_code", Integer, nullable=True ),
- Column( "info", TrimmedString ( 255 ) ),
- Column( "traceback", TEXT ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False ),
- Column( "working_directory", String(1024)),
- Column( "task_runner_name", String( 255 ) ),
- Column( "task_runner_external_id", String( 255 ) ),
- Column( "prepare_input_files_cmd", TEXT ) )
- model.PostJobAction.table = Table("post_job_action", metadata,
- Column("id", Integer, primary_key=True),
- Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False),
- Column("action_type", String(255), nullable=False),
- Column("output_name", String(255), nullable=True),
- Column("action_arguments", JSONType, nullable=True))
- model.PostJobActionAssociation.table = Table("post_job_action_association", metadata,
- Column("id", Integer, primary_key=True),
- Column("job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=False),
- Column("post_job_action_id", Integer, ForeignKey( "post_job_action.id" ), index=True, nullable=False))
- model.DeferredJob.table = Table( "deferred_job", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "state", String( 64 ), index=True ),
- Column( "plugin", String( 128 ), index=True ),
- Column( "params", JSONType ) )
- model.TransferJob.table = Table( "transfer_job", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "state", String( 64 ), index=True ),
- Column( "path", String( 1024 ) ),
- Column( "info", TEXT ),
- Column( "pid", Integer ),
- Column( "socket", Integer ),
- Column( "params", JSONType ) )
- model.Event.table = Table( "event", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True, nullable=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
- Column( "message", TrimmedString( 1024 ) ),
- Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
- Column( "tool_id", String( 255 ) ) )
- model.GalaxySession.table = Table( "galaxy_session", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
- Column( "remote_host", String( 255 ) ),
- Column( "remote_addr", String( 255 ) ),
- Column( "referer", TEXT ),
- Column( "current_history_id", Integer, ForeignKey( "history.id" ), nullable=True ),
- Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string
- Column( "is_valid", Boolean, default=False ),
- Column( "prev_session_id", Integer ), # saves a reference to the previous session so we have a way to chain them together
- Column( "disk_usage", Numeric( 15, 0 ), index=True ) )
- model.GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) )
- model.StoredWorkflow.table = Table( "stored_workflow", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
- Column( "latest_workflow_id", Integer,
- ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ),
- Column( "name", TEXT ),
- Column( "deleted", Boolean, default=False ),
- Column( "importable", Boolean, default=False ),
- Column( "slug", TEXT, index=True ),
- Column( "published", Boolean, index=True, default=False )
- )
- model.Workflow.table = Table( "workflow", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ),
- Column( "name", TEXT ),
- Column( "has_cycles", Boolean ),
- Column( "has_errors", Boolean )
- )
- model.WorkflowStep.table = Table( "workflow_step", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
- Column( "type", String(64) ),
- Column( "tool_id", TEXT ),
- Column( "tool_version", TEXT ), # Reserved for future
- Column( "tool_inputs", JSONType ),
- Column( "tool_errors", JSONType ),
- Column( "position", JSONType ),
- Column( "config", JSONType ),
- Column( "order_index", Integer ),
- ## Column( "input_connections", JSONType )
- )
- model.WorkflowStepConnection.table = Table( "workflow_step_connection", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
- Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
- Column( "output_name", TEXT ),
- Column( "input_name", TEXT)
- )
- model.WorkflowOutput.table = Table( "workflow_output", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
- Column( "output_name", String(255), nullable=True)
- )
- model.WorkflowInvocation.table = Table( "workflow_invocation", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False )
- )
- model.WorkflowInvocationStep.table = Table( "workflow_invocation_step", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "workflow_invocation_id", Integer, ForeignKey( "workflow_invocation.id" ), index=True, nullable=False ),
- Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True, nullable=True )
- )
- model.StoredWorkflowUserShareAssociation.table = Table( "stored_workflow_user_share_connection", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- )
- model.StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "order_index", Integer ) )
- model.MetadataFile.table = Table( "metadata_file", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "name", TEXT ),
- Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
- Column( "lda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "object_store_id", TrimmedString( 255 ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "purged", Boolean, index=True, default=False ) )
- model.FormDefinitionCurrent.table = Table('form_definition_current', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "latest_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ))
- model.FormDefinition.table = Table('form_definition', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ),
- Column( "form_definition_current_id",
- Integer,
- ForeignKey( "form_definition_current.id", name='for_def_form_def_current_id_fk', use_alter=True ),
- index=True ),
- Column( "fields", JSONType() ),
- Column( "type", TrimmedString( 255 ), index=True ),
- Column( "layout", JSONType() ), )
- model.ExternalService.table = Table( 'external_service', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "description", TEXT ),
- Column( "external_service_type_id", TrimmedString( 255 ), nullable=False ),
- Column( "version", TrimmedString( 255 ) ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.RequestType.table = Table('request_type', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ),
- Column( "request_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "sample_form_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.RequestTypeExternalServiceAssociation.table = Table( "request_type_external_service_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
- Column( "external_service_id", Integer, ForeignKey( "external_service.id" ), index=True ) )
- model.RequestTypePermissions.table = Table( "request_type_permissions", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "action", TEXT ),
- Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), nullable=True, index=True ),
- Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) )
- model.FormValues.table = Table('form_values', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "content", JSONType()) )
- model.Request.table = Table('request', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ),
- Column( "notification", JSONType() ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ) )
- model.RequestEvent.table = Table('request_event', metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
- Column( "state", TrimmedString( 255 ), index=True ),
- Column( "comment", TEXT ) )
- model.Sample.table = Table('sample', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ),
- Column( "bar_code", TrimmedString( 255 ), index=True ),
- Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ),
- Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "workflow", JSONType, nullable=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), nullable=True) )
- model.SampleState.table = Table('sample_state', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "desc", TEXT ),
- Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ) )
- model.SampleEvent.table = Table('sample_event', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ),
- Column( "sample_state_id", Integer, ForeignKey( "sample_state.id" ), index=True ),
- Column( "comment", TEXT ) )
- model.SampleDataset.table = Table('sample_dataset', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ),
- Column( "name", TrimmedString( 255 ), nullable=False ),
- Column( "file_path", TEXT ),
- Column( "status", TrimmedString( 255 ), nullable=False ),
- Column( "error_msg", TEXT ),
- Column( "size", TrimmedString( 255 ) ),
- Column( "external_service_id", Integer, ForeignKey( "external_service.id" ), index=True ) )
- model.Run.table = Table( 'run', metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "form_definition_id", Integer, ForeignKey( "form_definition.id" ), index=True ),
- Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ),
- Column( "deleted", Boolean, index=True, default=False ),
- Column( "subindex", TrimmedString( 255 ), index=True ) )
- model.RequestTypeRunAssociation.table = Table( "request_type_run_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True, nullable=False ),
- Column( "run_id", Integer, ForeignKey( "run.id" ), index=True, nullable=False ) )
- model.SampleRunAssociation.table = Table( "sample_run_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True, nullable=False ),
- Column( "run_id", Integer, ForeignKey( "run.id" ), index=True, nullable=False ) )
- model.Page.table = Table( "page", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
- Column( "latest_revision_id", Integer,
- ForeignKey( "page_revision.id", use_alter=True, name='page_latest_revision_id_fk' ), index=True ),
- Column( "title", TEXT ),
- Column( "slug", TEXT, unique=True, index=True ),
- Column( "importable", Boolean, index=True, default=False ),
- Column( "published", Boolean, index=True, default=False ),
- Column( "deleted", Boolean, index=True, default=False ),
- )
- model.PageRevision.table = Table( "page_revision", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "page_id", Integer, ForeignKey( "page.id" ), index=True, nullable=False ),
- Column( "title", TEXT ),
- Column( "content", TEXT )
- )
- model.PageUserShareAssociation.table = Table( "page_user_share_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- )
- model.Visualization.table = Table( "visualization", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
- Column( "latest_revision_id", Integer,
- ForeignKey( "visualization_revision.id", use_alter=True, name='visualization_latest_revision_id_fk' ), index=True ),
- Column( "title", TEXT ),
- Column( "type", TEXT ),
- Column( "dbkey", TEXT, index=True ),
- Column( "deleted", Boolean, default=False, index=True ),
- Column( "importable", Boolean, default=False, index=True ),
- Column( "slug", TEXT, index=True ),
- Column( "published", Boolean, default=False, index=True )
- )
- model.VisualizationRevision.table = Table( "visualization_revision", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, default=now, onupdate=now ),
- Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True, nullable=False ),
- Column( "title", TEXT ),
- Column( "dbkey", TEXT, index=True ),
- Column( "config", JSONType )
- )
- model.VisualizationUserShareAssociation.table = Table( "visualization_user_share_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "visualization_id", Integer, ForeignKey( "visualization.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- )
- #Data Manager tables
- model.DataManagerHistoryAssociation.table = Table( "data_manager_history_association", metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True )
- )
- model.DataManagerJobAssociation.table = Table( "data_manager_job_association", metadata,
- Column( "id", Integer, primary_key=True),
- Column( "create_time", DateTime, default=now ),
- Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
- Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
- Column( "data_manager_id", TEXT, index=True )
- )
- # Tagging tables.
- model.Tag.table = Table( "tag", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "type", Integer ),
- Column( "parent_id", Integer, ForeignKey( "tag.id" ) ),
- Column( "name", TrimmedString(255) ),
- UniqueConstraint( "name" ) )
- model.HistoryTagAssociation.table = Table( "history_tag_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
- Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "user_tname", TrimmedString(255), index=True),
- Column( "value", TrimmedString(255), index=True),
- Column( "user_value", TrimmedString(255), index=True) )
- model.DatasetTagAssociation.table = Table( "dataset_tag_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
- Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "user_tname", TrimmedString(255), index=True),
- Column( "value", TrimmedString(255), index=True),
- Column( "user_value", TrimmedString(255), index=True) )
- model.HistoryDatasetAssociationTagAssociation.table = Table( "history_dataset_association_tag_association", metadata,
- Column( "id", Integer, primary_key=True ),
- Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ),
- Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ),
- Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
- Column( "user_tname", TrimmedString(255), index=True),
- Column( "value", TrimmedString(255), index=True),
- Column( "user_value", TrimmedString(255), index=True) )…