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Source code for galaxy.model.mapping
"""
Details of how the data model objects are mapped onto the relational database
are encapsulated here.
"""
import logging
from threading import local
from typing import Optional, Type
from sqlalchemy import (
and_,
asc,
Boolean,
Column,
DateTime,
desc,
false,
ForeignKey,
func,
Index,
Integer,
MetaData,
not_,
Numeric,
PrimaryKeyConstraint,
select,
String, Table,
TEXT,
Text,
true,
Unicode,
UniqueConstraint,
VARCHAR
)
from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.ext.orderinglist import ordering_list
from sqlalchemy.orm import backref, class_mapper, column_property, deferred, mapper, object_session, relation
from sqlalchemy.orm.collections import attribute_mapped_collection
from sqlalchemy.sql import exists
from sqlalchemy.types import BigInteger
from galaxy import model
from galaxy.model.base import SharedModelMapping
from galaxy.model.custom_types import (
JSONType,
MetadataType,
MutableJSONType,
TrimmedString,
UUIDType,
)
from galaxy.model.migrate.triggers.update_audit_table import install as install_timestamp_triggers
from galaxy.model.orm.engine_factory import build_engine
from galaxy.model.orm.now import now
from galaxy.model.security import GalaxyRBACAgent
from galaxy.model.view import HistoryDatasetCollectionJobStateSummary
from galaxy.model.view.utils import install_views
log = logging.getLogger(__name__)
metadata = MetaData()
model.WorkerProcess.table = Table(
'worker_process',
metadata,
Column("id", Integer, primary_key=True),
Column("server_name", String(255), index=True),
Column("hostname", String(255)),
Column("pid", Integer),
Column("update_time", DateTime, default=now, onupdate=now),
UniqueConstraint('server_name', 'hostname'),
)
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("last_password_change", DateTime, default=now),
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("person_metadata", JSONType), # TODO: add persistent, configurable metadata rep for workflow creator
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.PSAAssociation.table = Table(
"psa_association", metadata,
Column('id', Integer, primary_key=True),
Column('server_url', VARCHAR(255)),
Column('handle', VARCHAR(255)),
Column('secret', VARCHAR(255)),
Column('issued', Integer),
Column('lifetime', Integer),
Column('assoc_type', VARCHAR(64)))
model.PSACode.table = Table(
"psa_code", metadata,
Column('id', Integer, primary_key=True),
Column('email', VARCHAR(200)),
Column('code', VARCHAR(32)))
model.PSANonce.table = Table(
"psa_nonce", metadata,
Column('id', Integer, primary_key=True),
Column('server_url', VARCHAR(255)),
Column('timestamp', Integer),
Column('salt', VARCHAR(40)))
model.PSAPartial.table = Table(
"psa_partial", metadata,
Column('id', Integer, primary_key=True),
Column('token', VARCHAR(32)),
Column('data', TEXT),
Column('next_step', Integer),
Column('backend', VARCHAR(32)))
model.UserAuthnzToken.table = Table(
"oidc_user_authnz_tokens", metadata,
Column('id', Integer, primary_key=True),
Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True),
Column('uid', VARCHAR(255)),
Column('provider', VARCHAR(32)),
Column('extra_data', MutableJSONType, nullable=True),
Column('lifetime', Integer),
Column('assoc_type', VARCHAR(64)))
model.CustosAuthnzToken.table = Table(
"custos_authnz_token", metadata,
Column('id', Integer, primary_key=True),
Column('user_id', Integer, ForeignKey("galaxy_user.id")),
Column('external_user_id', String(64)),
Column('provider', String(255)),
Column('access_token', Text),
Column('id_token', Text),
Column('refresh_token', Text),
Column("expiration_time", DateTime),
Column("refresh_expiration_time", DateTime),
UniqueConstraint("user_id", "external_user_id", "provider"),
UniqueConstraint("external_user_id", "provider"),
)
model.CloudAuthz.table = Table(
"cloudauthz", metadata,
Column('id', Integer, primary_key=True),
Column('user_id', Integer, ForeignKey("galaxy_user.id"), index=True),
Column('provider', String(255)),
Column('config', MutableJSONType),
Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True),
Column('tokens', MutableJSONType),
Column('last_update', DateTime),
Column('last_activity', DateTime),
Column('description', TEXT),
Column('create_time', DateTime, default=now))
model.PasswordResetToken.table = Table(
"password_reset_token", metadata,
Column("token", String(32), primary_key=True, unique=True, index=True),
Column("expiration_time", DateTime),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))
model.DynamicTool.table = Table(
"dynamic_tool", metadata,
Column("id", Integer, primary_key=True),
Column("uuid", UUIDType()),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, index=True, default=now, onupdate=now),
Column("tool_id", Unicode(255)),
Column("tool_version", Unicode(255)),
Column("tool_format", Unicode(255)),
Column("tool_path", Unicode(255)),
Column("tool_directory", Unicode(255)),
Column("hidden", Boolean, default=True),
Column("active", Boolean, default=True),
Column("value", MutableJSONType),
)
model.History.table = Table(
"history", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, key="_update_time", 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),
Column("published", Boolean, index=True, default=False),
Index('ix_history_slug', 'slug', mysql_length=200),
)
model.HistoryAudit.table = Table(
"history_audit", metadata,
Column("history_id", Integer, ForeignKey("history.id"), primary_key=True, nullable=False),
Column("update_time", DateTime, default=now, primary_key=True, nullable=False),
PrimaryKeyConstraint(sqlite_on_conflict='IGNORE')
)
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, index=True),
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("name", TrimmedString(255)),
Column("info", TrimmedString(255)),
Column("blurb", TrimmedString(255)),
Column("peek", TEXT, key="_peek"),
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("visible", Boolean),
Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
Column("version", Integer, default=1, nullable=True, index=True),
Column("hid", Integer),
Column("purged", Boolean, index=True, default=False),
Column("validated_state", TrimmedString(64), default='unvalidated', nullable=False),
Column("validated_state_message", TEXT),
Column("hidden_beneath_collection_instance_id",
ForeignKey("history_dataset_collection_association.id"), nullable=True))
model.HistoryDatasetAssociationHistory.table = Table(
"history_dataset_association_history", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
Column("update_time", DateTime, default=now),
Column("version", Integer),
Column("name", TrimmedString(255)),
Column("extension", TrimmedString(64)),
Column("metadata", MetadataType, key="_metadata"),
Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
)
model.Dataset.table = Table(
"dataset", metadata,
Column("id", Integer, primary_key=True),
Column('job_id', Integer, ForeignKey('job.id'), index=True, nullable=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("created_from_basename", TEXT),
Column('file_size', Numeric(15, 0)),
Column('total_size', Numeric(15, 0)),
Column('uuid', UUIDType()))
model.DatasetSource.table = Table(
"dataset_source", metadata,
Column("id", Integer, primary_key=True),
Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
Column("source_uri", TEXT),
Column("extra_files_path", TEXT),
Column("transform", MutableJSONType)
)
model.DatasetHash.table = Table(
"dataset_hash", metadata,
Column("id", Integer, primary_key=True),
Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
Column("hash_function", TEXT),
Column("hash_value", TEXT),
Column("extra_files_path", TEXT),
)
model.DatasetSourceHash.table = Table(
"dataset_source_hash", metadata,
Column("id", Integer, primary_key=True),
Column("dataset_source_id", Integer, ForeignKey("dataset_source.id"), index=True),
Column("hash_function", TEXT),
Column("hash_value", TEXT)
)
# hda read access permission given by a user to a specific site (gen. for external display applications)
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.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),
# current version of dataset, if null, there is not a current version selected
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),
Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True),
# not currently being used, but for possible future use
Column("order_id", Integer),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
# when not None/null this will supercede display in library (but not when imported into user's history?)
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"),
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, index=True),
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, key="_peek"),
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("validated_state", TrimmedString(64), default='unvalidated', nullable=False),
Column("validated_state_message", TEXT),
Column("visible", Boolean),
Column("extended_metadata_id", Integer, ForeignKey("extended_metadata.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("message", TrimmedString(255)))
model.ExtendedMetadata.table = Table(
"extended_metadata", metadata,
Column("id", Integer, primary_key=True),
Column("data", MutableJSONType))
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),
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)),
Index('ix_library_folder_name', 'name', mysql_length=200),
)
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, index=True),
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("galaxy_version", String(64), default=None),
Column("dynamic_tool_id", Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True),
Column("state", String(64), index=True),
Column("info", TrimmedString(255)),
Column("copied_from_job_id", Integer, nullable=True),
Column("command_line", TEXT),
Column("dependencies", MutableJSONType, nullable=True),
Column("job_messages", MutableJSONType, nullable=True),
Column("param_filename", String(1024)),
Column("runner_name", String(255)),
Column("job_stdout", TEXT),
Column("job_stderr", TEXT),
Column("tool_stdout", TEXT),
Column("tool_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), index=True),
Column("destination_id", String(255), nullable=True),
Column("destination_params", MutableJSONType, 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.JobStateHistory.table = Table(
"job_state_history", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("state", String(64), index=True),
Column("info", TrimmedString(255)))
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("dataset_version", Integer),
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.JobToInputDatasetCollectionAssociation.table = Table(
"job_to_input_dataset_collection", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
Column("name", Unicode(255)))
model.JobToInputDatasetCollectionElementAssociation.table = Table(
"job_to_input_dataset_collection_element", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("dataset_collection_element_id", Integer, ForeignKey("dataset_collection_element.id"), index=True),
Column("name", Unicode(255)))
model.JobToImplicitOutputDatasetCollectionAssociation.table = Table(
"job_to_implicit_output_dataset_collection", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
Column("name", Unicode(255)))
model.JobToOutputDatasetCollectionAssociation.table = Table(
"job_to_output_dataset_collection", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True),
Column("name", Unicode(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.ImplicitlyCreatedDatasetCollectionInput.table = Table(
"implicitly_created_dataset_collection_inputs", metadata,
Column("id", Integer, primary_key=True),
Column("dataset_collection_id", Integer,
ForeignKey("history_dataset_collection_association.id"), index=True),
Column("input_dataset_collection_id", Integer,
ForeignKey("history_dataset_collection_association.id"), index=True),
Column("name", Unicode(255)))
model.ImplicitCollectionJobs.table = Table(
"implicit_collection_jobs", metadata,
Column("id", Integer, primary_key=True),
Column("populated_state", TrimmedString(64), default='new', nullable=False),
)
model.ImplicitCollectionJobsJobAssociation.table = Table(
"implicit_collection_jobs_job_association", metadata,
Column("id", Integer, primary_key=True),
Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True), # Consider making this nullable...
Column("order_index", Integer, nullable=False),
)
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("is_valid", Boolean, default=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))
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.JobMetricText.table = Table(
"job_metric_text", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("plugin", Unicode(255)),
Column("metric_name", Unicode(255)),
Column("metric_value", Unicode(model.JOB_METRIC_MAX_LENGTH)))
model.TaskMetricText.table = Table(
"task_metric_text", metadata,
Column("id", Integer, primary_key=True),
Column("task_id", Integer, ForeignKey("task.id"), index=True),
Column("plugin", Unicode(255)),
Column("metric_name", Unicode(255)),
Column("metric_value", Unicode(model.JOB_METRIC_MAX_LENGTH)))
model.JobMetricNumeric.table = Table(
"job_metric_numeric", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("plugin", Unicode(255)),
Column("metric_name", Unicode(255)),
Column("metric_value", Numeric(model.JOB_METRIC_PRECISION, model.JOB_METRIC_SCALE)))
model.TaskMetricNumeric.table = Table(
"task_metric_numeric", metadata,
Column("id", Integer, primary_key=True),
Column("task_id", Integer, ForeignKey("task.id"), index=True),
Column("plugin", Unicode(255)),
Column("metric_name", Unicode(255)),
Column("metric_value", Numeric(model.JOB_METRIC_PRECISION, model.JOB_METRIC_SCALE)))
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.InteractiveToolEntryPoint.table = Table(
"interactivetool_entry_point", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("name", TEXT),
Column("token", TEXT),
Column("tool_port", Integer),
Column("host", TEXT),
Column("port", Integer),
Column("protocol", TEXT),
Column("entry_url", TEXT),
Column("requires_domain", Boolean, default=True),
Column("info", MutableJSONType, nullable=True),
Column("configured", Boolean, default=False),
Column("deleted", Boolean, default=False),
Column("created_time", DateTime, default=now),
Column("modified_time", DateTime, default=now, onupdate=now))
model.JobContainerAssociation.table = Table(
"job_container_association", metadata,
Column("id", Integer, primary_key=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True),
Column("container_type", TEXT),
Column("container_name", TEXT),
Column("container_info", MutableJSONType, nullable=True),
Column("created_time", DateTime, default=now),
Column("modified_time", DateTime, default=now, onupdate=now))
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("job_stdout", TEXT), # job_stdout makes sense here because it is short for job script standard out.
Column("job_stderr", TEXT),
Column("tool_stdout", TEXT),
Column("tool_stderr", TEXT),
Column("exit_code", Integer, nullable=True),
Column("job_messages", MutableJSONType, 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=True),
Column("action_type", String(255), nullable=False),
Column("output_name", String(255), nullable=True),
Column("action_arguments", MutableJSONType, 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", MutableJSONType))
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", MutableJSONType))
model.DatasetCollection.table = Table(
"dataset_collection", metadata,
Column("id", Integer, primary_key=True),
Column("collection_type", Unicode(255), nullable=False),
Column("populated_state", TrimmedString(64), default='ok', nullable=False),
Column("populated_state_message", TEXT),
Column("element_count", Integer, nullable=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now))
model.HistoryDatasetCollectionAssociation.table = Table(
"history_dataset_collection_association", metadata,
Column("id", Integer, primary_key=True),
Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
Column("history_id", Integer, ForeignKey("history.id"), index=True),
Column("name", TrimmedString(255)),
Column("hid", Integer),
Column("visible", Boolean),
Column("deleted", Boolean, default=False),
Column("copied_from_history_dataset_collection_association_id", Integer,
ForeignKey("history_dataset_collection_association.id"), nullable=True),
Column("implicit_output_name", Unicode(255), nullable=True),
Column("job_id", ForeignKey("job.id"), index=True, nullable=True),
Column("implicit_collection_jobs_id", ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
Column("create_time", DateTime, default=now),
Column("update_time", DateTime, default=now, onupdate=now, index=True))
model.LibraryDatasetCollectionAssociation.table = Table(
"library_dataset_collection_association", metadata,
Column("id", Integer, primary_key=True),
Column("collection_id", Integer, ForeignKey("dataset_collection.id"), index=True),
Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True),
Column("name", TrimmedString(255)),
Column("deleted", Boolean, default=False))
model.DatasetCollectionElement.table = Table(
"dataset_collection_element", metadata,
Column("id", Integer, primary_key=True),
# Parent collection id describing what collection this element belongs to.
Column("dataset_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=False),
# Child defined by this association - HDA, LDDA, or another dataset association...
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("child_collection_id", Integer, ForeignKey("dataset_collection.id"), index=True, nullable=True),
# Element index and identifier to define this parent-child relationship.
Column("element_index", Integer),
Column("element_identifier", Unicode(255), ))
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),
# unique 128 bit random number coerced to a string
Column("session_key", TrimmedString(255), index=True, unique=True),
Column("is_valid", Boolean, default=False),
# saves a reference to the previous session so we have a way to chain them together
Column("prev_session_id", Integer),
Column("disk_usage", Numeric(15, 0), index=True),
Column("last_action", DateTime))
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, index=True),
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("hidden", Boolean, default=False),
Column("importable", Boolean, default=False),
Column("slug", TEXT),
Column("from_path", TEXT),
Column("published", Boolean, index=True, default=False),
Index('ix_stored_workflow_slug', 'slug', mysql_length=200),
)
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),
# workflows will belong to either a stored workflow or a parent/nesting workflow.
Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.id"), index=True, nullable=True),
Column("parent_workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=True),
Column("name", TEXT),
Column("has_cycles", Boolean),
Column("has_errors", Boolean),
Column("reports_config", MutableJSONType),
Column("creator_metadata", MutableJSONType),
Column("license", TEXT),
Column("uuid", UUIDType, nullable=True))
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("subworkflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=True),
Column("dynamic_tool_id", Integer, ForeignKey("dynamic_tool.id"), index=True, nullable=True),
Column("type", String(64)),
Column("tool_id", TEXT),
Column("tool_version", TEXT),
Column("tool_inputs", JSONType),
Column("tool_errors", JSONType),
Column("position", MutableJSONType),
Column("config", JSONType),
Column("order_index", Integer),
Column("uuid", UUIDType),
# Column( "input_connections", JSONType ),
Column("label", Unicode(255)))
model.WorkflowStepInput.table = Table(
"workflow_step_input", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("name", TEXT),
Column("merge_type", TEXT),
Column("scatter_type", TEXT),
Column("value_from", MutableJSONType),
Column("value_from_type", TEXT),
Column("default_value", MutableJSONType),
Column("default_value_set", Boolean, default=False),
Column("runtime_value", Boolean, default=False),
Index('ix_workflow_step_input_workflow_step_id_name_unique', "workflow_step_id", "name", unique=True, mysql_length={'name': 200}),
)
model.WorkflowRequestStepState.table = Table(
"workflow_request_step_states", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer,
ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
Column("value", MutableJSONType))
model.WorkflowRequestInputParameter.table = Table(
"workflow_request_input_parameters", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer,
ForeignKey("workflow_invocation.id", onupdate="CASCADE", ondelete="CASCADE")),
Column("name", Unicode(255)),
Column("value", TEXT),
Column("type", Unicode(255)))
model.WorkflowRequestInputStepParameter.table = Table(
"workflow_request_input_step_parameter", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
Column("parameter_value", MutableJSONType),
)
model.WorkflowRequestToInputDatasetAssociation.table = Table(
"workflow_request_to_input_dataset", metadata,
Column("id", Integer, primary_key=True),
Column("name", String(255)),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True))
model.WorkflowRequestToInputDatasetCollectionAssociation.table = Table(
"workflow_request_to_input_collection_dataset", metadata,
Column("id", Integer, primary_key=True),
Column("name", String(255)),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id"), index=True))
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_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True),
Column("output_name", TEXT),
Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
)
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),
Column("label", Unicode(255)),
Column("uuid", UUIDType),
)
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, index=True),
Column("workflow_id", Integer, ForeignKey("workflow.id"), index=True, nullable=False),
Column("state", TrimmedString(64), index=True),
Column("scheduler", TrimmedString(255), index=True),
Column("handler", TrimmedString(255), index=True),
Column('uuid', UUIDType()),
Column("history_id", Integer, ForeignKey("history.id"), index=True))
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("state", TrimmedString(64), index=True),
Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=True),
Column("implicit_collection_jobs_id", Integer, ForeignKey("implicit_collection_jobs.id"), index=True, nullable=True),
Column("action", MutableJSONType, nullable=True))
model.WorkflowInvocationOutputDatasetAssociation.table = Table(
"workflow_invocation_output_dataset_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
)
model.WorkflowInvocationOutputDatasetCollectionAssociation.table = Table(
"workflow_invocation_output_dataset_collection_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name='fk_wiodca_wii'), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wiodca_wsi'), index=True),
Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wiodca_dci'), index=True),
Column("workflow_output_id", Integer, ForeignKey("workflow_output.id", name='fk_wiodca_woi'), index=True),
)
model.WorkflowInvocationOutputValue.table = Table(
"workflow_invocation_output_value", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id"), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id")),
Column("workflow_output_id", Integer, ForeignKey("workflow_output.id"), index=True),
Column("value", MutableJSONType),
)
model.WorkflowInvocationStepOutputDatasetAssociation.table = Table(
"workflow_invocation_step_output_dataset_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id"), index=True),
Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
Column("output_name", String(255), nullable=True),
)
model.WorkflowInvocationStepOutputDatasetCollectionAssociation.table = Table(
"workflow_invocation_step_output_dataset_collection_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_step_id", Integer, ForeignKey("workflow_invocation_step.id", name='fk_wisodca_wisi'), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wisodca_wsi'), index=True),
Column("dataset_collection_id", Integer, ForeignKey("history_dataset_collection_association.id", name='fk_wisodca_dci'), index=True),
Column("output_name", String(255), nullable=True),
)
model.WorkflowInvocationToSubworkflowInvocationAssociation.table = Table(
"workflow_invocation_to_subworkflow_invocation_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name='fk_wfi_swi_wfi'), index=True),
Column("subworkflow_invocation_id", Integer, ForeignKey("workflow_invocation.id", name='fk_wfi_swi_swi'), index=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id", name='fk_wfi_swi_ws')),
)
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("uuid", UUIDType(), 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", use_alter=True), index=True, nullable=False),
Column("fields", MutableJSONType),
Column("type", TrimmedString(255), index=True),
Column("layout", MutableJSONType))
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", MutableJSONType))
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("deleted", Boolean, index=True, default=False),
Column("importable", Boolean, index=True, default=False),
Column("slug", TEXT),
Column("published", Boolean, index=True, default=False),
Index('ix_page_slug', 'slug', mysql_length=200),
)
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),
Column("content_format", TrimmedString(32)))
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),
Column("deleted", Boolean, default=False, index=True),
Column("importable", Boolean, default=False, index=True),
Column("slug", TEXT),
Column("published", Boolean, default=False, index=True),
Index('ix_visualization_dbkey', 'dbkey', mysql_length=200),
Index('ix_visualization_slug', 'slug', mysql_length=200),
)
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),
Column("config", MutableJSONType),
Index('ix_visualization_revision_dbkey', 'dbkey', mysql_length=200),
)
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('ix_data_manager_job_association_data_manager_id', 'data_manager_id', mysql_length=200),
)
# 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.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))
model.LibraryDatasetDatasetAssociationTagAssociation.table = Table(
"library_dataset_dataset_association_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_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))
model.StoredWorkflowTagAssociation.table = Table(
"stored_workflow_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("stored_workflow_id", Integer, ForeignKey("stored_workflow.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", Unicode(255), index=True),
Column("value", Unicode(255), index=True),
Column("user_value", Unicode(255), index=True))
model.PageTagAssociation.table = Table(
"page_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("page_id", Integer, ForeignKey("page.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.WorkflowStepTagAssociation.table = Table(
"workflow_step_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.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", Unicode(255), index=True),
Column("value", Unicode(255), index=True),
Column("user_value", Unicode(255), index=True))
model.VisualizationTagAssociation.table = Table(
"visualization_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("visualization_id", Integer, ForeignKey("visualization.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.HistoryDatasetCollectionTagAssociation.table = Table(
"history_dataset_collection_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_collection_id", Integer,
ForeignKey("history_dataset_collection_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))
model.LibraryDatasetCollectionTagAssociation.table = Table(
"library_dataset_collection_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("library_dataset_collection_id", Integer,
ForeignKey("library_dataset_collection_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))
model.ToolTagAssociation.table = Table(
"tool_tag_association", metadata,
Column("id", Integer, primary_key=True),
Column("tool_id", TrimmedString(255), 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))
# Annotation tables.
model.HistoryAnnotationAssociation.table = Table(
"history_annotation_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),
Column("annotation", TEXT),
Index('ix_history_anno_assoc_annotation', 'annotation', mysql_length=200),
)
model.HistoryDatasetAssociationAnnotationAssociation.table = Table(
"history_dataset_association_annotation_association", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_association_id", Integer,
ForeignKey("history_dataset_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("annotation", TEXT),
Index('ix_history_dataset_anno_assoc_annotation', 'annotation', mysql_length=200),
)
model.StoredWorkflowAnnotationAssociation.table = Table(
"stored_workflow_annotation_association", 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("annotation", TEXT),
Index('ix_stored_workflow_ann_assoc_annotation', 'annotation', mysql_length=200),
)
model.WorkflowStepAnnotationAssociation.table = Table(
"workflow_step_annotation_association", metadata,
Column("id", Integer, primary_key=True),
Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("annotation", TEXT),
Index('ix_workflow_step_ann_assoc_annotation', 'annotation', mysql_length=200),
)
model.PageAnnotationAssociation.table = Table(
"page_annotation_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),
Column("annotation", TEXT),
Index('ix_page_annotation_association_annotation', 'annotation', mysql_length=200),
)
model.VisualizationAnnotationAssociation.table = Table(
"visualization_annotation_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),
Column("annotation", TEXT),
Index('ix_visualization_annotation_association_annotation', 'annotation', mysql_length=200),
)
model.HistoryDatasetCollectionAssociationAnnotationAssociation.table = Table(
"history_dataset_collection_annotation_association", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_collection_id", Integer,
ForeignKey("history_dataset_collection_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("annotation", TEXT),
)
model.LibraryDatasetCollectionAnnotationAssociation.table = Table(
"library_dataset_collection_annotation_association", metadata,
Column("id", Integer, primary_key=True),
Column("library_dataset_collection_id", Integer,
ForeignKey("library_dataset_collection_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("annotation", TEXT),
)
# Ratings tables.
model.HistoryRatingAssociation.table = Table("history_rating_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),
Column("rating", Integer, index=True))
model.HistoryDatasetAssociationRatingAssociation.table = Table(
"history_dataset_association_rating_association", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_association_id", Integer,
ForeignKey("history_dataset_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("rating", Integer, index=True))
model.StoredWorkflowRatingAssociation.table = Table(
"stored_workflow_rating_association", 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("rating", Integer, index=True))
model.PageRatingAssociation.table = Table(
"page_rating_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),
Column("rating", Integer, index=True))
model.VisualizationRatingAssociation.table = Table(
"visualization_rating_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),
Column("rating", Integer, index=True))
model.HistoryDatasetCollectionRatingAssociation.table = Table(
"history_dataset_collection_rating_association", metadata,
Column("id", Integer, primary_key=True),
Column("history_dataset_collection_id", Integer,
ForeignKey("history_dataset_collection_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("rating", Integer, index=True))
model.LibraryDatasetCollectionRatingAssociation.table = Table(
"library_dataset_collection_rating_association", metadata,
Column("id", Integer, primary_key=True),
Column("library_dataset_collection_id", Integer,
ForeignKey("library_dataset_collection_association.id"), index=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("rating", Integer, index=True))
# User tables.
model.UserPreference.table = Table(
"user_preference", metadata,
Column("id", Integer, primary_key=True),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("name", Unicode(255), index=True),
Column("value", Text))
model.UserAction.table = Table(
"user_action", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("session_id", Integer, ForeignKey("galaxy_session.id"), index=True),
Column("action", Unicode(255)),
Column("context", Unicode(512)),
Column("params", Unicode(1024)))
model.APIKeys.table = Table(
"api_keys", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
Column("key", TrimmedString(32), index=True, unique=True))
CleanupEvent_table = Table("cleanup_event", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("message", TrimmedString(1024)))
CleanupEventDatasetAssociation_table = Table("cleanup_event_dataset_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True))
CleanupEventMetadataFileAssociation_table = Table("cleanup_event_metadata_file_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("metadata_file_id", Integer, ForeignKey("metadata_file.id"), index=True))
CleanupEventHistoryAssociation_table = Table("cleanup_event_history_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("history_id", Integer, ForeignKey("history.id"), index=True))
CleanupEventHistoryDatasetAssociationAssociation_table = Table("cleanup_event_hda_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("hda_id", Integer, ForeignKey("history_dataset_association.id"), index=True))
CleanupEventLibraryAssociation_table = Table("cleanup_event_library_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("library_id", Integer, ForeignKey("library.id"), index=True))
CleanupEventLibraryFolderAssociation_table = Table("cleanup_event_library_folder_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("library_folder_id", Integer, ForeignKey("library_folder.id"), index=True))
CleanupEventLibraryDatasetAssociation_table = Table("cleanup_event_library_dataset_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True))
CleanupEventLibraryDatasetDatasetAssociationAssociation_table = Table("cleanup_event_ldda_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("ldda_id", Integer, ForeignKey("library_dataset_dataset_association.id"), index=True))
CleanupEventImplicitlyConvertedDatasetAssociationAssociation_table = Table("cleanup_event_icda_association", metadata,
Column("id", Integer, primary_key=True),
Column("create_time", DateTime, default=now),
Column("cleanup_event_id", Integer, ForeignKey("cleanup_event.id"), index=True, nullable=True),
Column("icda_id", Integer, ForeignKey("implicitly_converted_dataset_association.id"), index=True))
# With the tables defined we can define the mappers and setup the
# relationships between the model objects.
simple_mapping(model.WorkerProcess)
# User tables.
mapper(model.UserPreference, model.UserPreference.table, properties={})
mapper(model.UserAction, model.UserAction.table, properties=dict(
# user=relation( model.User.mapper )
user=relation(model.User)
))
mapper(model.APIKeys, model.APIKeys.table, properties={})
mapper(model.FormValues, model.FormValues.table, properties=dict(
form_definition=relation(model.FormDefinition,
primaryjoin=(model.FormValues.table.c.form_definition_id == model.FormDefinition.table.c.id))
))
mapper(model.FormDefinition, model.FormDefinition.table, properties=dict(
current=relation(model.FormDefinitionCurrent,
primaryjoin=(model.FormDefinition.table.c.form_definition_current_id == model.FormDefinitionCurrent.table.c.id))
))
mapper(model.FormDefinitionCurrent, model.FormDefinitionCurrent.table, properties=dict(
forms=relation(model.FormDefinition,
backref='form_definition_current',
cascade="all, delete-orphan",
primaryjoin=(model.FormDefinitionCurrent.table.c.id == model.FormDefinition.table.c.form_definition_current_id)),
latest_form=relation(model.FormDefinition,
post_update=True,
primaryjoin=(model.FormDefinitionCurrent.table.c.latest_form_id == model.FormDefinition.table.c.id))
))
mapper(model.UserAddress, model.UserAddress.table, properties=dict(
user=relation(model.User,
primaryjoin=(model.UserAddress.table.c.user_id == model.User.table.c.id),
backref='addresses',
order_by=desc(model.UserAddress.table.c.update_time)),
))
mapper(model.PSAAssociation, model.PSAAssociation.table, properties=None)
mapper(model.PSACode, model.PSACode.table, properties=None)
mapper(model.PSANonce, model.PSANonce.table, properties=None)
mapper(model.PSAPartial, model.PSAPartial.table, properties=None)
mapper(model.UserAuthnzToken, model.UserAuthnzToken.table, properties=dict(
user=relation(model.User,
primaryjoin=(model.UserAuthnzToken.table.c.user_id == model.User.table.c.id),
backref='social_auth')
))
mapper(model.CustosAuthnzToken, model.CustosAuthnzToken.table, properties=dict(
user=relation(model.User,
primaryjoin=(model.CustosAuthnzToken.table.c.user_id == model.User.table.c.id),
backref='custos_auth')
))
mapper(model.CloudAuthz, model.CloudAuthz.table, properties=dict(
user=relation(model.User,
primaryjoin=(model.CloudAuthz.table.c.user_id == model.User.table.c.id),
backref='cloudauthz'),
authn=relation(model.UserAuthnzToken,
primaryjoin=(model.CloudAuthz.table.c.authn_id == model.UserAuthnzToken.table.c.id),
backref='cloudauthz')
))
simple_mapping(model.DynamicTool)
simple_mapping(model.HistoryDatasetAssociation,
dataset=relation(model.Dataset,
primaryjoin=(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id), lazy=False),
# .history defined in History mapper
copied_from_history_dataset_association=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
== model.HistoryDatasetAssociation.table.c.id),
remote_side=[model.HistoryDatasetAssociation.table.c.id],
uselist=False),
copied_to_history_dataset_associations=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id
== model.HistoryDatasetAssociation.table.c.id)),
copied_from_library_dataset_dataset_association=relation(
model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id),
uselist=False),
copied_to_library_dataset_dataset_associations=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id)),
implicitly_converted_datasets=relation(model.ImplicitlyConvertedDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id
== model.HistoryDatasetAssociation.table.c.id)),
tags=relation(model.HistoryDatasetAssociationTagAssociation,
order_by=model.HistoryDatasetAssociationTagAssociation.table.c.id,
backref='history_tag_associations'),
annotations=relation(model.HistoryDatasetAssociationAnnotationAssociation,
order_by=model.HistoryDatasetAssociationAnnotationAssociation.table.c.id,
backref="hdas"),
ratings=relation(model.HistoryDatasetAssociationRatingAssociation,
order_by=model.HistoryDatasetAssociationRatingAssociation.table.c.id,
backref="hdas"),
extended_metadata=relation(model.ExtendedMetadata,
primaryjoin=(model.HistoryDatasetAssociation.table.c.extended_metadata_id
== model.ExtendedMetadata.table.c.id)),
hidden_beneath_collection_instance=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.hidden_beneath_collection_instance_id
== model.HistoryDatasetCollectionAssociation.table.c.id),
uselist=False,
backref="hidden_dataset_instances"),
_metadata=deferred(model.HistoryDatasetAssociation.table.c._metadata)
)
simple_mapping(model.Dataset,
job=relation(model.Job, primaryjoin=(model.Dataset.table.c.job_id == model.Job.table.c.id)),
history_associations=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)),
active_history_associations=relation(model.HistoryDatasetAssociation,
primaryjoin=(
(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)
& (model.HistoryDatasetAssociation.table.c.deleted == false())
& (model.HistoryDatasetAssociation.table.c.purged == false()))),
purged_history_associations=relation(model.HistoryDatasetAssociation,
primaryjoin=(
(model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id)
& (model.HistoryDatasetAssociation.table.c.purged == true()))),
library_associations=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id)),
active_library_associations=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(
(model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id)
& (model.LibraryDatasetDatasetAssociation.table.c.deleted == false()))),
)
mapper(model.DatasetHash, model.DatasetHash.table, properties=dict(
dataset=relation(model.Dataset, backref='hashes')
))
mapper(model.DatasetSource, model.DatasetSource.table, properties=dict(
dataset=relation(model.Dataset, backref='sources')
))
mapper(model.DatasetSourceHash, model.DatasetSourceHash.table, properties=dict(
source=relation(model.DatasetSource, backref='hashes')
))
mapper(model.HistoryDatasetAssociationHistory, model.HistoryDatasetAssociationHistory.table)
mapper(model.HistoryDatasetAssociationDisplayAtAuthorization, model.HistoryDatasetAssociationDisplayAtAuthorization.table, properties=dict(
history_dataset_association=relation(model.HistoryDatasetAssociation),
user=relation(model.User)
))
mapper(model.HistoryDatasetAssociationSubset, model.HistoryDatasetAssociationSubset.table, properties=dict(
hda=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_id
== model.HistoryDatasetAssociation.table.c.id)),
subset=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociationSubset.table.c.history_dataset_association_subset_id
== model.HistoryDatasetAssociation.table.c.id))
))
mapper(model.ImplicitlyConvertedDatasetAssociation, model.ImplicitlyConvertedDatasetAssociation.table, properties=dict(
parent_hda=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id
== model.HistoryDatasetAssociation.table.c.id)),
parent_ldda=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id
== model.LibraryDatasetDatasetAssociation.table.c.id)),
dataset_ldda=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_id
== model.LibraryDatasetDatasetAssociation.table.c.id),
backref="implicitly_converted_parent_datasets"),
dataset=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.hda_id
== model.HistoryDatasetAssociation.table.c.id),
backref="implicitly_converted_parent_datasets")
))
mapper(model.History, model.History.table, properties=dict(
galaxy_sessions=relation(model.GalaxySessionToHistoryAssociation),
datasets=relation(model.HistoryDatasetAssociation,
backref="history",
order_by=asc(model.HistoryDatasetAssociation.table.c.hid)),
exports=relation(model.JobExportHistoryArchive,
primaryjoin=(model.JobExportHistoryArchive.table.c.history_id == model.History.table.c.id),
order_by=desc(model.JobExportHistoryArchive.table.c.id)),
active_datasets=relation(model.HistoryDatasetAssociation,
primaryjoin=(
(model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id)
& not_(model.HistoryDatasetAssociation.table.c.deleted)
),
order_by=asc(model.HistoryDatasetAssociation.table.c.hid),
viewonly=True),
active_dataset_collections=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(
(model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id)
& not_(model.HistoryDatasetCollectionAssociation.table.c.deleted)
),
order_by=asc(model.HistoryDatasetCollectionAssociation.table.c.hid),
viewonly=True),
visible_datasets=relation(model.HistoryDatasetAssociation,
primaryjoin=(
(model.HistoryDatasetAssociation.table.c.history_id == model.History.table.c.id)
& not_(model.HistoryDatasetAssociation.table.c.deleted)
& model.HistoryDatasetAssociation.table.c.visible
),
order_by=asc(model.HistoryDatasetAssociation.table.c.hid),
viewonly=True),
visible_dataset_collections=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(
(model.HistoryDatasetCollectionAssociation.table.c.history_id == model.History.table.c.id)
& not_(model.HistoryDatasetCollectionAssociation.table.c.deleted)
& model.HistoryDatasetCollectionAssociation.table.c.visible
),
order_by=asc(model.HistoryDatasetCollectionAssociation.table.c.hid),
viewonly=True),
tags=relation(model.HistoryTagAssociation,
order_by=model.HistoryTagAssociation.table.c.id,
backref="histories"),
annotations=relation(model.HistoryAnnotationAssociation,
order_by=model.HistoryAnnotationAssociation.table.c.id,
backref="histories"),
ratings=relation(model.HistoryRatingAssociation,
order_by=model.HistoryRatingAssociation.table.c.id,
backref="histories"),
average_rating=column_property(
select([func.avg(model.HistoryRatingAssociation.table.c.rating)]).where(model.HistoryRatingAssociation.table.c.history_id == model.History.table.c.id),
deferred=True
),
users_shared_with_count=column_property(
select([func.count(model.HistoryUserShareAssociation.table.c.id)]).where(model.History.table.c.id == model.HistoryUserShareAssociation.table.c.history_id),
deferred=True
),
update_time=column_property(
select([func.max(model.HistoryAudit.table.c.update_time)]).where(model.HistoryAudit.table.c.history_id == model.History.table.c.id),
),
))
# Set up proxy so that
# History.users_shared_with
# returns a list of users that history is shared with.
model.History.users_shared_with_dot_users = association_proxy('users_shared_with', 'user') # type: ignore
mapper(model.HistoryUserShareAssociation, model.HistoryUserShareAssociation.table, properties=dict(
user=relation(model.User, backref='histories_shared_by_others'),
history=relation(model.History, backref='users_shared_with')
))
mapper(model.User, model.User.table, properties=dict(
histories=relation(model.History,
backref="user",
order_by=desc(model.History.update_time)),
active_histories=relation(model.History,
primaryjoin=(
(model.History.table.c.user_id == model.User.table.c.id)
& (not_(model.History.table.c.deleted))
),
order_by=desc(model.History.update_time)),
galaxy_sessions=relation(model.GalaxySession,
order_by=desc(model.GalaxySession.table.c.update_time)),
stored_workflow_menu_entries=relation(model.StoredWorkflowMenuEntry,
primaryjoin=(
(model.StoredWorkflowMenuEntry.table.c.user_id == model.User.table.c.id)
& (model.StoredWorkflowMenuEntry.table.c.stored_workflow_id == model.StoredWorkflow.table.c.id)
& not_(model.StoredWorkflow.table.c.deleted)
),
backref="user",
cascade="all, delete-orphan",
collection_class=ordering_list('order_index')),
_preferences=relation(model.UserPreference,
backref="user",
collection_class=attribute_mapped_collection('name')),
# addresses=relation( UserAddress,
# primaryjoin=( User.table.c.id == UserAddress.table.c.user_id ) ),
values=relation(model.FormValues,
primaryjoin=(model.User.table.c.form_values_id == model.FormValues.table.c.id)),
api_keys=relation(model.APIKeys,
backref="user",
order_by=desc(model.APIKeys.table.c.create_time)),
cloudauthzs=relation(model.CloudAuthz,
primaryjoin=model.CloudAuthz.table.c.user_id == model.User.table.c.id),
))
mapper(model.PasswordResetToken, model.PasswordResetToken.table,
properties=dict(user=relation(model.User, backref="reset_tokens")))
# Set up proxy so that this syntax is possible:
# <user_obj>.preferences[pref_name] = pref_value
model.User.preferences = association_proxy('_preferences', 'value', creator=model.UserPreference) # type: ignore
mapper(model.Group, model.Group.table, properties=dict(
users=relation(model.UserGroupAssociation)
))
mapper(model.UserGroupAssociation, model.UserGroupAssociation.table, properties=dict(
user=relation(model.User, backref="groups"),
group=relation(model.Group, backref="members")
))
mapper(model.DefaultUserPermissions, model.DefaultUserPermissions.table, properties=dict(
user=relation(model.User, backref="default_permissions"),
role=relation(model.Role)
))
mapper(model.DefaultHistoryPermissions, model.DefaultHistoryPermissions.table, properties=dict(
history=relation(model.History, backref="default_permissions"),
role=relation(model.Role)
))
mapper(model.Role, model.Role.table, properties=dict(
users=relation(model.UserRoleAssociation),
groups=relation(model.GroupRoleAssociation)
))
mapper(model.UserRoleAssociation, model.UserRoleAssociation.table, properties=dict(
user=relation(model.User, backref="roles"),
non_private_roles=relation(
model.User,
backref="non_private_roles",
primaryjoin=(
(model.User.table.c.id == model.UserRoleAssociation.table.c.user_id)
& (model.UserRoleAssociation.table.c.role_id == model.Role.table.c.id)
& not_(model.Role.table.c.name == model.User.table.c.email))
),
role=relation(model.Role)
))
mapper(model.GroupRoleAssociation, model.GroupRoleAssociation.table, properties=dict(
group=relation(model.Group, backref="roles"),
role=relation(model.Role)
))
mapper(model.Quota, model.Quota.table, properties=dict(
users=relation(model.UserQuotaAssociation),
groups=relation(model.GroupQuotaAssociation)
))
mapper(model.UserQuotaAssociation, model.UserQuotaAssociation.table, properties=dict(
user=relation(model.User, backref="quotas"),
quota=relation(model.Quota)
))
mapper(model.GroupQuotaAssociation, model.GroupQuotaAssociation.table, properties=dict(
group=relation(model.Group, backref="quotas"),
quota=relation(model.Quota)
))
mapper(model.DefaultQuotaAssociation, model.DefaultQuotaAssociation.table, properties=dict(
quota=relation(model.Quota, backref="default")
))
mapper(model.DatasetPermissions, model.DatasetPermissions.table, properties=dict(
dataset=relation(model.Dataset, backref="actions"),
role=relation(model.Role, backref="dataset_actions")
))
mapper(model.LibraryPermissions, model.LibraryPermissions.table, properties=dict(
library=relation(model.Library, backref="actions"),
role=relation(model.Role, backref="library_actions")
))
mapper(model.LibraryFolderPermissions, model.LibraryFolderPermissions.table, properties=dict(
folder=relation(model.LibraryFolder, backref="actions"),
role=relation(model.Role, backref="library_folder_actions")
))
mapper(model.LibraryDatasetPermissions, model.LibraryDatasetPermissions.table, properties=dict(
library_dataset=relation(model.LibraryDataset, backref="actions"),
role=relation(model.Role, backref="library_dataset_actions")
))
mapper(model.LibraryDatasetDatasetAssociationPermissions, model.LibraryDatasetDatasetAssociationPermissions.table, properties=dict(
library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation, backref="actions"),
role=relation(model.Role, backref="library_dataset_dataset_actions")
))
mapper(model.Library, model.Library.table, properties=dict(
root_folder=relation(model.LibraryFolder, backref=backref("library_root"))
))
mapper(model.ExtendedMetadata, model.ExtendedMetadata.table, properties=dict(
children=relation(model.ExtendedMetadataIndex,
primaryjoin=(model.ExtendedMetadataIndex.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id),
backref=backref("parent",
primaryjoin=(model.ExtendedMetadataIndex.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id)))
))
mapper(model.ExtendedMetadataIndex, model.ExtendedMetadataIndex.table, properties=dict(
extended_metadata=relation(model.ExtendedMetadata,
primaryjoin=(model.ExtendedMetadataIndex.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id))
))
mapper(model.LibraryInfoAssociation, model.LibraryInfoAssociation.table, properties=dict(
library=relation(model.Library,
primaryjoin=(
(model.LibraryInfoAssociation.table.c.library_id == model.Library.table.c.id)
& (not_(model.LibraryInfoAssociation.table.c.deleted))
),
backref="info_association"),
template=relation(model.FormDefinition,
primaryjoin=(model.LibraryInfoAssociation.table.c.form_definition_id == model.FormDefinition.table.c.id)),
info=relation(model.FormValues,
primaryjoin=(model.LibraryInfoAssociation.table.c.form_values_id == model.FormValues.table.c.id))
))
mapper(model.LibraryFolder, model.LibraryFolder.table, properties=dict(
folders=relation(model.LibraryFolder,
primaryjoin=(model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id),
order_by=asc(model.LibraryFolder.table.c.name),
backref=backref("parent",
primaryjoin=(model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id),
remote_side=[model.LibraryFolder.table.c.id])),
active_folders=relation(model.LibraryFolder,
primaryjoin=(
(model.LibraryFolder.table.c.parent_id == model.LibraryFolder.table.c.id)
& (not_(model.LibraryFolder.table.c.deleted))
),
order_by=asc(model.LibraryFolder.table.c.name),
# """sqlalchemy.exc.ArgumentError: Error creating eager relationship 'active_folders'
# on parent class '<class 'galaxy.model.LibraryFolder'>' to child class '<class 'galaxy.model.LibraryFolder'>':
# Cant use eager loading on a self referential relationship."""
lazy=True,
viewonly=True),
datasets=relation(model.LibraryDataset,
primaryjoin=(
(model.LibraryDataset.table.c.folder_id == model.LibraryFolder.table.c.id)
& model.LibraryDataset.table.c.library_dataset_dataset_association_id.isnot(None)),
order_by=asc(model.LibraryDataset.table.c._name),
lazy=True,
viewonly=True),
active_datasets=relation(model.LibraryDataset,
primaryjoin=(
(model.LibraryDataset.table.c.folder_id == model.LibraryFolder.table.c.id)
& (not_(model.LibraryDataset.table.c.deleted)
& model.LibraryDataset.table.c.library_dataset_dataset_association_id.isnot(None))
),
order_by=asc(model.LibraryDataset.table.c._name),
lazy=True,
viewonly=True)
))
mapper(model.LibraryFolderInfoAssociation, model.LibraryFolderInfoAssociation.table, properties=dict(
folder=relation(model.LibraryFolder,
primaryjoin=(
(model.LibraryFolderInfoAssociation.table.c.library_folder_id == model.LibraryFolder.table.c.id)
& (not_(model.LibraryFolderInfoAssociation.table.c.deleted))
),
backref="info_association"),
template=relation(model.FormDefinition,
primaryjoin=(model.LibraryFolderInfoAssociation.table.c.form_definition_id == model.FormDefinition.table.c.id)),
info=relation(model.FormValues,
primaryjoin=(model.LibraryFolderInfoAssociation.table.c.form_values_id == model.FormValues.table.c.id))
))
mapper(model.LibraryDataset, model.LibraryDataset.table, properties=dict(
folder=relation(model.LibraryFolder),
library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation,
foreign_keys=model.LibraryDataset.table.c.library_dataset_dataset_association_id,
post_update=True),
expired_datasets=relation(model.LibraryDatasetDatasetAssociation,
foreign_keys=[model.LibraryDataset.table.c.id, model.LibraryDataset.table.c.library_dataset_dataset_association_id],
primaryjoin=(
(model.LibraryDataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.library_dataset_id)
& (not_(model.LibraryDataset.table.c.library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id))
),
viewonly=True,
uselist=True)
))
mapper(model.LibraryDatasetDatasetAssociation, model.LibraryDatasetDatasetAssociation.table, properties=dict(
dataset=relation(model.Dataset),
library_dataset=relation(model.LibraryDataset,
foreign_keys=model.LibraryDatasetDatasetAssociation.table.c.library_dataset_id),
# user=relation( model.User.mapper ),
user=relation(model.User),
copied_from_library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id),
remote_side=[model.LibraryDatasetDatasetAssociation.table.c.id],
uselist=False),
copied_to_library_dataset_dataset_associations=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id)),
copied_from_history_dataset_association=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id
== model.HistoryDatasetAssociation.table.c.id),
uselist=False),
copied_to_history_dataset_associations=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id)),
implicitly_converted_datasets=relation(model.ImplicitlyConvertedDatasetAssociation,
primaryjoin=(model.ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id
== model.LibraryDatasetDatasetAssociation.table.c.id)),
tags=relation(model.LibraryDatasetDatasetAssociationTagAssociation,
order_by=model.LibraryDatasetDatasetAssociationTagAssociation.table.c.id,
backref='history_tag_associations'),
extended_metadata=relation(model.ExtendedMetadata,
primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.extended_metadata_id == model.ExtendedMetadata.table.c.id)
),
_metadata=deferred(model.LibraryDatasetDatasetAssociation.table.c._metadata)
))
mapper(model.LibraryDatasetDatasetInfoAssociation, model.LibraryDatasetDatasetInfoAssociation.table, properties=dict(
library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(
(model.LibraryDatasetDatasetInfoAssociation.table.c.library_dataset_dataset_association_id
== model.LibraryDatasetDatasetAssociation.table.c.id)
& (not_(model.LibraryDatasetDatasetInfoAssociation.table.c.deleted))
),
backref="info_association"),
template=relation(model.FormDefinition,
primaryjoin=(model.LibraryDatasetDatasetInfoAssociation.table.c.form_definition_id == model.FormDefinition.table.c.id)),
info=relation(model.FormValues,
primaryjoin=(model.LibraryDatasetDatasetInfoAssociation.table.c.form_values_id == model.FormValues.table.c.id))
))
mapper(model.JobToInputDatasetAssociation, model.JobToInputDatasetAssociation.table, properties=dict(
job=relation(model.Job),
dataset=relation(model.HistoryDatasetAssociation,
lazy=False,
backref="dependent_jobs")
))
mapper(model.JobToOutputDatasetAssociation, model.JobToOutputDatasetAssociation.table, properties=dict(
job=relation(model.Job),
dataset=relation(model.HistoryDatasetAssociation,
lazy=False)
))
mapper(model.JobToInputDatasetCollectionAssociation, model.JobToInputDatasetCollectionAssociation.table, properties=dict(
job=relation(model.Job),
dataset_collection=relation(model.HistoryDatasetCollectionAssociation,
lazy=False)
))
mapper(model.JobToInputDatasetCollectionElementAssociation, model.JobToInputDatasetCollectionElementAssociation.table, properties=dict(
job=relation(model.Job),
dataset_collection_element=relation(model.DatasetCollectionElement,
lazy=False)
))
mapper(model.JobToOutputDatasetCollectionAssociation, model.JobToOutputDatasetCollectionAssociation.table, properties=dict(
job=relation(model.Job),
dataset_collection_instance=relation(model.HistoryDatasetCollectionAssociation,
lazy=False,
backref="output_dataset_collection_instances")
))
mapper(model.JobToImplicitOutputDatasetCollectionAssociation, model.JobToImplicitOutputDatasetCollectionAssociation.table, properties=dict(
job=relation(model.Job),
dataset_collection=relation(model.DatasetCollection,
backref="output_dataset_collections")
))
mapper(model.JobToInputLibraryDatasetAssociation, model.JobToInputLibraryDatasetAssociation.table, properties=dict(
job=relation(model.Job),
dataset=relation(model.LibraryDatasetDatasetAssociation,
lazy=False,
backref="dependent_jobs")
))
mapper(model.JobToOutputLibraryDatasetAssociation, model.JobToOutputLibraryDatasetAssociation.table, properties=dict(
job=relation(model.Job),
dataset=relation(model.LibraryDatasetDatasetAssociation,
lazy=False)
))
simple_mapping(model.JobStateHistory,
job=relation(model.Job, backref="state_history"))
simple_mapping(model.JobMetricText,
job=relation(model.Job, backref="text_metrics"))
simple_mapping(model.TaskMetricText,
task=relation(model.Task, backref="text_metrics"))
simple_mapping(model.JobMetricNumeric,
job=relation(model.Job, backref="numeric_metrics"))
simple_mapping(model.TaskMetricNumeric,
task=relation(model.Task, backref="numeric_metrics"))
simple_mapping(model.ImplicitlyCreatedDatasetCollectionInput,
input_dataset_collection=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id
== model.ImplicitlyCreatedDatasetCollectionInput.table.c.input_dataset_collection_id),
# backref="implicitly_created_dataset_collections",
),
)
simple_mapping(model.ImplicitCollectionJobs)
# simple_mapping(
# model.ImplicitCollectionJobsHistoryDatasetCollectionAssociation,
# history_dataset_collection_associations=relation(
# model.HistoryDatasetCollectionAssociation,
# backref=backref("implicit_collection_jobs_association", uselist=False),
# uselist=True,
# ),
# )
simple_mapping(
model.ImplicitCollectionJobsJobAssociation,
implicit_collection_jobs=relation(
model.ImplicitCollectionJobs,
backref=backref("jobs", uselist=True),
uselist=False,
),
job=relation(
model.Job,
backref=backref("implicit_collection_jobs_association", uselist=False),
uselist=False,
),
)
mapper(model.JobParameter, model.JobParameter.table)
mapper(model.JobExternalOutputMetadata, model.JobExternalOutputMetadata.table, properties=dict(
job=relation(model.Job),
history_dataset_association=relation(model.HistoryDatasetAssociation, lazy=False),
library_dataset_dataset_association=relation(model.LibraryDatasetDatasetAssociation, lazy=False)
))
mapper(model.JobExportHistoryArchive, model.JobExportHistoryArchive.table, properties=dict(
job=relation(model.Job),
history=relation(model.History),
dataset=relation(model.Dataset, backref='job_export_history_archive')
))
mapper(model.JobImportHistoryArchive, model.JobImportHistoryArchive.table, properties=dict(
job=relation(model.Job),
history=relation(model.History)
))
mapper(model.GenomeIndexToolData, model.GenomeIndexToolData.table, properties=dict(
job=relation(model.Job, backref='job'),
dataset=relation(model.Dataset, backref='genome_index_tool_data'),
user=relation(model.User),
deferred=relation(model.DeferredJob, backref='deferred_job'),
transfer=relation(model.TransferJob, backref='transfer_job')
))
mapper(model.InteractiveToolEntryPoint, model.InteractiveToolEntryPoint.table, properties=dict(
job=relation(model.Job, backref=backref('interactivetool_entry_points', uselist=True), uselist=False)
))
mapper(model.JobContainerAssociation, model.JobContainerAssociation.table, properties=dict(
job=relation(model.Job, backref=backref('container', uselist=False), uselist=False)
))
mapper(model.PostJobAction, model.PostJobAction.table, properties=dict(
workflow_step=relation(model.WorkflowStep,
backref='post_job_actions',
primaryjoin=(model.WorkflowStep.table.c.id == model.PostJobAction.table.c.workflow_step_id))
))
mapper(model.PostJobActionAssociation, model.PostJobActionAssociation.table, properties=dict(
job=relation(model.Job),
post_job_action=relation(model.PostJobAction)
))
mapper(model.Task, model.Task.table, properties=dict(
job=relation(model.Job)
))
mapper(model.DeferredJob, model.DeferredJob.table, properties={})
mapper(model.TransferJob, model.TransferJob.table, properties={})
simple_mapping(model.DatasetCollection,
elements=relation(model.DatasetCollectionElement,
primaryjoin=(model.DatasetCollection.table.c.id == model.DatasetCollectionElement.table.c.dataset_collection_id),
remote_side=[model.DatasetCollectionElement.table.c.dataset_collection_id],
backref="collection",
order_by=model.DatasetCollectionElement.table.c.element_index)
)
simple_mapping(model.HistoryDatasetCollectionAssociation,
collection=relation(model.DatasetCollection),
history=relation(model.History,
backref='dataset_collections'),
copied_from_history_dataset_collection_association=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id
== model.HistoryDatasetCollectionAssociation.table.c.id),
remote_side=[model.HistoryDatasetCollectionAssociation.table.c.id],
uselist=False),
copied_to_history_dataset_collection_associations=relation(model.HistoryDatasetCollectionAssociation,
primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.copied_from_history_dataset_collection_association_id
== model.HistoryDatasetCollectionAssociation.table.c.id)),
implicit_input_collections=relation(model.ImplicitlyCreatedDatasetCollectionInput,
primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id
== model.ImplicitlyCreatedDatasetCollectionInput.table.c.dataset_collection_id),
backref="dataset_collection",
),
implicit_collection_jobs=relation(
model.ImplicitCollectionJobs,
backref=backref("history_dataset_collection_associations", uselist=True),
uselist=False,
),
job=relation(
model.Job,
backref=backref("history_dataset_collection_associations", uselist=True),
uselist=False,
),
job_state_summary=relation(HistoryDatasetCollectionJobStateSummary,
primaryjoin=(model.HistoryDatasetCollectionAssociation.table.c.id == HistoryDatasetCollectionJobStateSummary.__table__.c.hdca_id),
foreign_keys=HistoryDatasetCollectionJobStateSummary.__table__.c.hdca_id,
uselist=False
),
tags=relation(model.HistoryDatasetCollectionTagAssociation,
order_by=model.HistoryDatasetCollectionTagAssociation.table.c.id,
backref='dataset_collections'),
annotations=relation(model.HistoryDatasetCollectionAssociationAnnotationAssociation,
order_by=model.HistoryDatasetCollectionAssociationAnnotationAssociation.table.c.id,
backref="dataset_collections"),
ratings=relation(model.HistoryDatasetCollectionRatingAssociation,
order_by=model.HistoryDatasetCollectionRatingAssociation.table.c.id,
backref="dataset_collections")
)
simple_mapping(model.LibraryDatasetCollectionAssociation,
collection=relation(model.DatasetCollection),
folder=relation(model.LibraryFolder,
backref='dataset_collections'),
tags=relation(model.LibraryDatasetCollectionTagAssociation,
order_by=model.LibraryDatasetCollectionTagAssociation.table.c.id,
backref='dataset_collections'),
annotations=relation(model.LibraryDatasetCollectionAnnotationAssociation,
order_by=model.LibraryDatasetCollectionAnnotationAssociation.table.c.id,
backref="dataset_collections"),
ratings=relation(model.LibraryDatasetCollectionRatingAssociation,
order_by=model.LibraryDatasetCollectionRatingAssociation.table.c.id,
backref="dataset_collections"))
simple_mapping(model.DatasetCollectionElement,
hda=relation(model.HistoryDatasetAssociation,
primaryjoin=(model.DatasetCollectionElement.table.c.hda_id == model.HistoryDatasetAssociation.table.c.id)),
ldda=relation(model.LibraryDatasetDatasetAssociation,
primaryjoin=(model.DatasetCollectionElement.table.c.ldda_id == model.LibraryDatasetDatasetAssociation.table.c.id)),
child_collection=relation(model.DatasetCollection,
primaryjoin=(model.DatasetCollectionElement.table.c.child_collection_id == model.DatasetCollection.table.c.id)))
mapper(model.Event, model.Event.table, properties=dict(
history=relation(model.History),
galaxy_session=relation(model.GalaxySession),
# user=relation( model.User.mapper ) ) )
user=relation(model.User)
))
mapper(model.GalaxySession, model.GalaxySession.table, properties=dict(
histories=relation(model.GalaxySessionToHistoryAssociation),
current_history=relation(model.History),
# user=relation( model.User.mapper ) ) )
user=relation(model.User)
))
mapper(model.GalaxySessionToHistoryAssociation, model.GalaxySessionToHistoryAssociation.table, properties=dict(
galaxy_session=relation(model.GalaxySession),
history=relation(model.History)
))
mapper(model.Workflow, model.Workflow.table, properties=dict(
steps=relation(model.WorkflowStep,
backref='workflow',
primaryjoin=(model.Workflow.table.c.id == model.WorkflowStep.table.c.workflow_id),
order_by=asc(model.WorkflowStep.table.c.order_index),
cascade="all, delete-orphan",
lazy=False),
step_count=column_property(
select([func.count(model.WorkflowStep.table.c.id)]).where(model.Workflow.table.c.id == model.WorkflowStep.table.c.workflow_id),
deferred=True
)
))
mapper(model.WorkflowStep, model.WorkflowStep.table, properties=dict(
subworkflow=relation(model.Workflow,
primaryjoin=(model.Workflow.table.c.id == model.WorkflowStep.table.c.subworkflow_id),
backref="parent_workflow_steps"),
dynamic_tool=relation(model.DynamicTool,
primaryjoin=(model.DynamicTool.table.c.id == model.WorkflowStep.table.c.dynamic_tool_id),
backref="workflow_steps"),
tags=relation(model.WorkflowStepTagAssociation,
order_by=model.WorkflowStepTagAssociation.table.c.id,
backref="workflow_steps"),
annotations=relation(model.WorkflowStepAnnotationAssociation,
order_by=model.WorkflowStepAnnotationAssociation.table.c.id,
backref="workflow_steps")
))
mapper(model.WorkflowStepInput, model.WorkflowStepInput.table, properties=dict(
workflow_step=relation(model.WorkflowStep,
backref=backref("inputs", uselist=True),
cascade="all",
primaryjoin=(model.WorkflowStepInput.table.c.workflow_step_id == model.WorkflowStep.table.c.id))
))
mapper(model.WorkflowOutput, model.WorkflowOutput.table, properties=dict(
workflow_step=relation(model.WorkflowStep,
backref='workflow_outputs',
primaryjoin=(model.WorkflowStep.table.c.id == model.WorkflowOutput.table.c.workflow_step_id))
))
mapper(model.WorkflowStepConnection, model.WorkflowStepConnection.table, properties=dict(
input_step_input=relation(model.WorkflowStepInput,
backref="connections",
cascade="all",
primaryjoin=(model.WorkflowStepConnection.table.c.input_step_input_id == model.WorkflowStepInput.table.c.id)),
input_subworkflow_step=relation(model.WorkflowStep,
backref=backref("parent_workflow_input_connections", uselist=True),
primaryjoin=(model.WorkflowStepConnection.table.c.input_subworkflow_step_id == model.WorkflowStep.table.c.id),
),
output_step=relation(model.WorkflowStep,
backref="output_connections",
cascade="all",
primaryjoin=(model.WorkflowStepConnection.table.c.output_step_id == model.WorkflowStep.table.c.id)),
))
mapper(model.StoredWorkflow, model.StoredWorkflow.table, properties=dict(
user=relation(model.User,
primaryjoin=(model.User.table.c.id == model.StoredWorkflow.table.c.user_id),
backref='stored_workflows'),
workflows=relation(model.Workflow,
backref='stored_workflow',
cascade="all, delete-orphan",
primaryjoin=(model.StoredWorkflow.table.c.id == model.Workflow.table.c.stored_workflow_id),
order_by=-model.Workflow.id),
latest_workflow=relation(model.Workflow,
post_update=True,
primaryjoin=(model.StoredWorkflow.table.c.latest_workflow_id == model.Workflow.table.c.id),
lazy=False),
tags=relation(model.StoredWorkflowTagAssociation,
order_by=model.StoredWorkflowTagAssociation.table.c.id,
backref="stored_workflows"),
owner_tags=relation(model.StoredWorkflowTagAssociation,
primaryjoin=(
and_(model.StoredWorkflow.table.c.id == model.StoredWorkflowTagAssociation.table.c.stored_workflow_id,
model.StoredWorkflow.table.c.user_id == model.StoredWorkflowTagAssociation.table.c.user_id)
),
order_by=model.StoredWorkflowTagAssociation.table.c.id),
annotations=relation(model.StoredWorkflowAnnotationAssociation,
order_by=model.StoredWorkflowAnnotationAssociation.table.c.id,
backref="stored_workflows"),
ratings=relation(model.StoredWorkflowRatingAssociation,
order_by=model.StoredWorkflowRatingAssociation.table.c.id,
backref="stored_workflows"),
average_rating=column_property(
select([func.avg(model.StoredWorkflowRatingAssociation.table.c.rating)]).where(model.StoredWorkflowRatingAssociation.table.c.stored_workflow_id == model.StoredWorkflow.table.c.id),
deferred=True
)
))
# Set up proxy so that
# StoredWorkflow.users_shared_with
# returns a list of users that workflow is shared with.
model.StoredWorkflow.users_shared_with_dot_users = association_proxy('users_shared_with', 'user') # type: ignore
mapper(model.StoredWorkflowUserShareAssociation, model.StoredWorkflowUserShareAssociation.table, properties=dict(
user=relation(model.User,
backref='workflows_shared_by_others'),
stored_workflow=relation(model.StoredWorkflow,
backref='users_shared_with')
))
mapper(model.StoredWorkflowMenuEntry, model.StoredWorkflowMenuEntry.table, properties=dict(
stored_workflow=relation(model.StoredWorkflow)
))
mapper(model.WorkflowInvocation, model.WorkflowInvocation.table, properties=dict(
history=relation(model.History, backref=backref('workflow_invocations', uselist=True)),
input_parameters=relation(model.WorkflowRequestInputParameter),
step_states=relation(model.WorkflowRequestStepState),
input_step_parameters=relation(model.WorkflowRequestInputStepParameter),
input_datasets=relation(model.WorkflowRequestToInputDatasetAssociation),
input_dataset_collections=relation(model.WorkflowRequestToInputDatasetCollectionAssociation),
subworkflow_invocations=relation(model.WorkflowInvocationToSubworkflowInvocationAssociation,
primaryjoin=(model.WorkflowInvocationToSubworkflowInvocationAssociation.table.c.workflow_invocation_id == model.WorkflowInvocation.table.c.id),
backref=backref("parent_workflow_invocation", uselist=False),
uselist=True,
),
steps=relation(model.WorkflowInvocationStep,
backref="workflow_invocation"),
workflow=relation(model.Workflow)
))
mapper(model.WorkflowInvocationToSubworkflowInvocationAssociation, model.WorkflowInvocationToSubworkflowInvocationAssociation.table, properties=dict(
subworkflow_invocation=relation(model.WorkflowInvocation,
primaryjoin=(model.WorkflowInvocationToSubworkflowInvocationAssociation.table.c.subworkflow_invocation_id == model.WorkflowInvocation.table.c.id),
backref="parent_workflow_invocation_association",
uselist=False,
),
workflow_step=relation(model.WorkflowStep),
))
simple_mapping(model.WorkflowInvocationStep,
workflow_step=relation(model.WorkflowStep),
job=relation(model.Job, backref=backref('workflow_invocation_step', uselist=False), uselist=False),
implicit_collection_jobs=relation(model.ImplicitCollectionJobs, backref=backref('workflow_invocation_step', uselist=False), uselist=False),
subworkflow_invocation_id=column_property(
select([(model.WorkflowInvocationToSubworkflowInvocationAssociation.table.c.subworkflow_invocation_id)]).where(and_(
model.WorkflowInvocationToSubworkflowInvocationAssociation.table.c.workflow_invocation_id == model.WorkflowInvocationStep.table.c.workflow_invocation_id,
model.WorkflowInvocationToSubworkflowInvocationAssociation.table.c.workflow_step_id == model.WorkflowInvocationStep.table.c.workflow_step_id,
)),
),
)
simple_mapping(model.WorkflowRequestInputParameter,
workflow_invocation=relation(model.WorkflowInvocation))
simple_mapping(model.WorkflowRequestStepState,
workflow_invocation=relation(model.WorkflowInvocation),
workflow_step=relation(model.WorkflowStep))
simple_mapping(model.WorkflowRequestInputStepParameter,
workflow_invocation=relation(model.WorkflowInvocation),
workflow_step=relation(model.WorkflowStep))
simple_mapping(model.WorkflowRequestToInputDatasetAssociation,
workflow_invocation=relation(model.WorkflowInvocation),
workflow_step=relation(model.WorkflowStep),
dataset=relation(model.HistoryDatasetAssociation))
simple_mapping(model.WorkflowRequestToInputDatasetCollectionAssociation,
workflow_invocation=relation(model.WorkflowInvocation),
workflow_step=relation(model.WorkflowStep),
dataset_collection=relation(model.HistoryDatasetCollectionAssociation))
mapper(model.MetadataFile, model.MetadataFile.table, properties=dict(
history_dataset=relation(model.HistoryDatasetAssociation),
library_dataset=relation(model.LibraryDatasetDatasetAssociation)
))
simple_mapping(
model.WorkflowInvocationOutputDatasetAssociation,
workflow_invocation=relation(model.WorkflowInvocation, backref="output_datasets"),
workflow_step=relation(model.WorkflowStep),
dataset=relation(model.HistoryDatasetAssociation),
workflow_output=relation(model.WorkflowOutput),
)
simple_mapping(
model.WorkflowInvocationOutputDatasetCollectionAssociation,
workflow_invocation=relation(model.WorkflowInvocation, backref="output_dataset_collections"),
workflow_step=relation(model.WorkflowStep),
dataset_collection=relation(model.HistoryDatasetCollectionAssociation),
workflow_output=relation(model.WorkflowOutput),
)
simple_mapping(
model.WorkflowInvocationOutputValue,
workflow_invocation=relation(model.WorkflowInvocation, backref="output_values"),
workflow_invocation_step=relation(model.WorkflowInvocationStep,
foreign_keys=[model.WorkflowInvocationStep.table.c.workflow_invocation_id, model.WorkflowInvocationStep.table.c.workflow_step_id],
primaryjoin=and_(
model.WorkflowInvocationStep.table.c.workflow_invocation_id == model.WorkflowInvocationOutputValue.table.c.workflow_invocation_id,
model.WorkflowInvocationStep.table.c.workflow_step_id == model.WorkflowInvocationOutputValue.table.c.workflow_step_id,
),
backref='output_value'
),
workflow_step=relation(model.WorkflowStep),
workflow_output=relation(model.WorkflowOutput),
)
simple_mapping(
model.WorkflowInvocationStepOutputDatasetAssociation,
workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="output_datasets"),
dataset=relation(model.HistoryDatasetAssociation),
)
simple_mapping(
model.WorkflowInvocationStepOutputDatasetCollectionAssociation,
workflow_invocation_step=relation(model.WorkflowInvocationStep, backref="output_dataset_collections"),
dataset_collection=relation(model.HistoryDatasetCollectionAssociation),
)
mapper(model.PageRevision, model.PageRevision.table)
mapper(model.Page, model.Page.table, properties=dict(
user=relation(model.User),
revisions=relation(model.PageRevision,
backref='page',
cascade="all, delete-orphan",
primaryjoin=(model.Page.table.c.id == model.PageRevision.table.c.page_id)),
latest_revision=relation(model.PageRevision,
post_update=True,
primaryjoin=(model.Page.table.c.latest_revision_id == model.PageRevision.table.c.id),
lazy=False),
tags=relation(model.PageTagAssociation,
order_by=model.PageTagAssociation.table.c.id,
backref="pages"),
annotations=relation(model.PageAnnotationAssociation,
order_by=model.PageAnnotationAssociation.table.c.id,
backref="pages"),
ratings=relation(model.PageRatingAssociation,
order_by=model.PageRatingAssociation.table.c.id,
backref="pages"),
average_rating=column_property(
select([func.avg(model.PageRatingAssociation.table.c.rating)]).where(model.PageRatingAssociation.table.c.page_id == model.Page.table.c.id),
deferred=True
)
))
# Set up proxy so that
# Page.users_shared_with
# returns a list of users that page is shared with.
model.Page.users_shared_with_dot_users = association_proxy('users_shared_with', 'user') # type: ignore
mapper(model.PageUserShareAssociation, model.PageUserShareAssociation.table,
properties=dict(user=relation(model.User, backref='pages_shared_by_others'),
page=relation(model.Page, backref='users_shared_with')))
mapper(model.VisualizationRevision, model.VisualizationRevision.table)
mapper(model.Visualization, model.Visualization.table, properties=dict(
user=relation(model.User),
revisions=relation(model.VisualizationRevision,
backref='visualization',
cascade="all, delete-orphan",
primaryjoin=(model.Visualization.table.c.id == model.VisualizationRevision.table.c.visualization_id)),
latest_revision=relation(model.VisualizationRevision,
post_update=True,
primaryjoin=(model.Visualization.table.c.latest_revision_id == model.VisualizationRevision.table.c.id),
lazy=False),
tags=relation(model.VisualizationTagAssociation,
order_by=model.VisualizationTagAssociation.table.c.id,
backref="visualizations"),
annotations=relation(model.VisualizationAnnotationAssociation,
order_by=model.VisualizationAnnotationAssociation.table.c.id,
backref="visualizations"),
ratings=relation(model.VisualizationRatingAssociation,
order_by=model.VisualizationRatingAssociation.table.c.id,
backref="visualizations"),
average_rating=column_property(
select([func.avg(model.VisualizationRatingAssociation.table.c.rating)]).where(model.VisualizationRatingAssociation.table.c.visualization_id == model.Visualization.table.c.id),
deferred=True
)
))
# Set up proxy so that
# Visualization.users_shared_with
# returns a list of users that visualization is shared with.
model.Visualization.users_shared_with_dot_users = association_proxy('users_shared_with', 'user') # type: ignore
mapper(model.VisualizationUserShareAssociation, model.VisualizationUserShareAssociation.table, properties=dict(
user=relation(model.User,
backref='visualizations_shared_by_others'),
visualization=relation(model.Visualization,
backref='users_shared_with')
))
# Tag tables.
simple_mapping(model.Tag,
children=relation(model.Tag, backref=backref('parent', remote_side=[model.Tag.table.c.id])))
[docs]def tag_mapping(tag_association_class, backref_name):
simple_mapping(tag_association_class, tag=relation(model.Tag, backref=backref_name), user=relation(model.User))
tag_mapping(model.HistoryTagAssociation, "tagged_histories")
tag_mapping(model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations")
tag_mapping(model.LibraryDatasetDatasetAssociationTagAssociation, "tagged_library_dataset_dataset_associations")
tag_mapping(model.PageTagAssociation, "tagged_pages")
tag_mapping(model.StoredWorkflowTagAssociation, "tagged_workflows")
tag_mapping(model.WorkflowStepTagAssociation, "tagged_workflow_steps")
tag_mapping(model.VisualizationTagAssociation, "tagged_visualizations")
tag_mapping(model.HistoryDatasetCollectionTagAssociation, "tagged_history_dataset_collections")
tag_mapping(model.LibraryDatasetCollectionTagAssociation, "tagged_library_dataset_collections")
tag_mapping(model.ToolTagAssociation, "tagged_tools")
# Annotation tables.
[docs]def annotation_mapping(annotation_class, **kwds):
kwds = {key: relation(value) for key, value in kwds.items()}
simple_mapping(annotation_class, **dict(user=relation(model.User), **kwds))
annotation_mapping(model.HistoryAnnotationAssociation, history=model.History)
annotation_mapping(model.HistoryDatasetAssociationAnnotationAssociation, hda=model.HistoryDatasetAssociation)
annotation_mapping(model.StoredWorkflowAnnotationAssociation, stored_workflow=model.StoredWorkflow)
annotation_mapping(model.WorkflowStepAnnotationAssociation, workflow_step=model.WorkflowStep)
annotation_mapping(model.PageAnnotationAssociation, page=model.Page)
annotation_mapping(model.VisualizationAnnotationAssociation, visualization=model.Visualization)
annotation_mapping(model.HistoryDatasetCollectionAssociationAnnotationAssociation,
history_dataset_collection=model.HistoryDatasetCollectionAssociation)
annotation_mapping(model.LibraryDatasetCollectionAnnotationAssociation,
library_dataset_collection=model.LibraryDatasetCollectionAssociation)
# Rating tables.
[docs]def rating_mapping(rating_class, **kwds):
kwds = {key: relation(value) for key, value in kwds.items()}
simple_mapping(rating_class, **dict(user=relation(model.User), **kwds))
rating_mapping(model.HistoryRatingAssociation, history=model.History)
rating_mapping(model.HistoryDatasetAssociationRatingAssociation, hda=model.HistoryDatasetAssociation)
rating_mapping(model.StoredWorkflowRatingAssociation, stored_workflow=model.StoredWorkflow)
rating_mapping(model.PageRatingAssociation, page=model.Page)
rating_mapping(model.VisualizationRatingAssociation, visualizaiton=model.Visualization)
rating_mapping(model.HistoryDatasetCollectionRatingAssociation,
history_dataset_collection=model.HistoryDatasetCollectionAssociation)
rating_mapping(model.LibraryDatasetCollectionRatingAssociation,
libary_dataset_collection=model.LibraryDatasetCollectionAssociation)
mapper(model.Job, model.Job.table, properties=dict(
# user=relation( model.User.mapper ),
user=relation(model.User),
galaxy_session=relation(model.GalaxySession),
history=relation(model.History, backref="jobs"),
library_folder=relation(model.LibraryFolder, lazy=True),
parameters=relation(model.JobParameter, lazy=True),
input_datasets=relation(model.JobToInputDatasetAssociation),
input_dataset_collections=relation(model.JobToInputDatasetCollectionAssociation, lazy=True),
input_dataset_collection_elements=relation(model.JobToInputDatasetCollectionElementAssociation, lazy=True),
output_datasets=relation(model.JobToOutputDatasetAssociation, lazy=True),
output_dataset_collection_instances=relation(model.JobToOutputDatasetCollectionAssociation, lazy=True),
output_dataset_collections=relation(model.JobToImplicitOutputDatasetCollectionAssociation, lazy=True),
post_job_actions=relation(model.PostJobActionAssociation, lazy=False),
input_library_datasets=relation(model.JobToInputLibraryDatasetAssociation),
output_library_datasets=relation(model.JobToOutputLibraryDatasetAssociation, lazy=True),
external_output_metadata=relation(model.JobExternalOutputMetadata, lazy=True),
tasks=relation(model.Task)
))
model.Job.any_output_dataset_deleted = column_property( # type: ignore
exists([model.HistoryDatasetAssociation],
and_(model.Job.table.c.id == model.JobToOutputDatasetAssociation.table.c.job_id,
model.HistoryDatasetAssociation.table.c.id == model.JobToOutputDatasetAssociation.table.c.dataset_id,
model.HistoryDatasetAssociation.table.c.deleted == true())
)
)
model.Job.any_output_dataset_collection_instances_deleted = column_property( # type: ignore
exists([model.HistoryDatasetCollectionAssociation.table.c.id],
and_(model.Job.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.job_id,
model.HistoryDatasetCollectionAssociation.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.dataset_collection_id,
model.HistoryDatasetCollectionAssociation.table.c.deleted == true())
)
)
# Data Manager tables
mapper(model.DataManagerHistoryAssociation, model.DataManagerHistoryAssociation.table, properties=dict(
history=relation(model.History),
user=relation(model.User,
backref='data_manager_histories')
))
mapper(model.DataManagerJobAssociation, model.DataManagerJobAssociation.table, properties=dict(
job=relation(model.Job,
backref=backref('data_manager_association', uselist=False),
uselist=False)
))
# model.HistoryDatasetAssociation.mapper.add_property( "creating_job_associations",
# relation( model.JobToOutputDatasetAssociation ) )
# model.LibraryDatasetDatasetAssociation.mapper.add_property( "creating_job_associations",
# relation( model.JobToOutputLibraryDatasetAssociation ) )
class_mapper(model.HistoryDatasetAssociation).add_property(
"creating_job_associations", relation(model.JobToOutputDatasetAssociation))
class_mapper(model.LibraryDatasetDatasetAssociation).add_property(
"creating_job_associations", relation(model.JobToOutputLibraryDatasetAssociation))
class_mapper(model.HistoryDatasetCollectionAssociation).add_property(
"creating_job_associations", relation(model.JobToOutputDatasetCollectionAssociation))
# Helper methods.
[docs]def db_next_hid(self, n=1):
"""
db_next_hid( self )
Override __next_hid to generate from the database in a concurrency safe way.
Loads the next history ID from the DB and returns it.
It also saves the future next_id into the DB.
:rtype: int
:returns: the next history id
"""
session = object_session(self)
table = self.table
trans = session.begin()
try:
if "postgres" not in session.bind.dialect.name:
next_hid = select([table.c.hid_counter], table.c.id == model.cached_id(self)).with_for_update().scalar()
table.update(table.c.id == self.id).execute(hid_counter=(next_hid + n))
else:
stmt = table.update().where(table.c.id == model.cached_id(self)).values(hid_counter=(table.c.hid_counter + n)).returning(table.c.hid_counter)
next_hid = session.execute(stmt).scalar() - n
trans.commit()
return next_hid
except Exception:
trans.rollback()
raise
model.History._next_hid = db_next_hid # type: ignore
def _workflow_invocation_update(self):
session = object_session(self)
table = self.table
now_val = now()
stmt = table.update().values(update_time=now_val).where(and_(table.c.id == self.id, table.c.update_time < now_val))
session.execute(stmt)
model.WorkflowInvocation.update = _workflow_invocation_update # type: ignore
[docs]class GalaxyModelMapping(SharedModelMapping):
security_agent: GalaxyRBACAgent
thread_local_log: Optional[local]
create_tables: bool
User: Type
GalaxySession: Type
[docs]def init(file_path, url, engine_options=None, create_tables=False, map_install_models=False,
database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True,
slow_query_log_threshold=0, thread_local_log: Optional[local] = None, log_query_counts=False) -> GalaxyModelMapping:
"""Connect mappings to the database"""
if engine_options is None:
engine_options = {}
# Connect dataset to the file path
model.Dataset.file_path = file_path
# Connect dataset to object store
model.Dataset.object_store = object_store
# Use PBKDF2 password hashing?
model.User.use_pbkdf2 = use_pbkdf2
# Load the appropriate db module
engine = build_engine(url, engine_options, database_query_profiling_proxy, trace_logger, slow_query_log_threshold, thread_local_log=thread_local_log, log_query_counts=log_query_counts)
# Connect the metadata to the database.
metadata.bind = engine
model_modules = [model]
if map_install_models:
import galaxy.model.tool_shed_install.mapping # noqa: F401
from galaxy.model import tool_shed_install
galaxy.model.tool_shed_install.mapping.init(url=url, engine_options=engine_options, create_tables=create_tables)
model_modules.append(tool_shed_install)
result = GalaxyModelMapping(model_modules, engine=engine)
# Create tables if needed
if create_tables:
metadata.create_all()
install_timestamp_triggers(engine)
install_views(engine)
result.create_tables = create_tables
# load local galaxy security policy
result.security_agent = GalaxyRBACAgent(result)
result.thread_local_log = thread_local_log
return result