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 sqlalchemy import (
    and_,
    asc,
    Boolean,
    Column,
    DateTime,
    desc,
    false,
    ForeignKey,
    func,
    Index,
    Integer,
    MetaData,
    not_,
    Numeric,
    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 ModelMapping
from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
from galaxy.model.orm.engine_factory import build_engine
from galaxy.model.orm.now import now
from galaxy.model.security import GalaxyRBACAgent

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("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("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', JSONType, 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', JSONType),
    Column('authn_id', Integer, ForeignKey("oidc_user_authnz_tokens.id"), index=True),
    Column('tokens', JSONType),
    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", JSONType()),
)


model.History.table = Table(
    "history", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, index=True, default=now, onupdate=now),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("name", TrimmedString(255)),
    Column("hid_counter", Integer, default=1),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("importing", Boolean, index=True, default=False),
    Column("genome_build", TrimmedString(40)),
    Column("importable", Boolean, default=False),
    Column("slug", TEXT),
    Column("published", Boolean, index=True, default=False),
    Index('ix_history_slug', 'slug', mysql_length=200),
)

model.HistoryUserShareAssociation.table = Table(
    "history_user_share_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True))

model.HistoryDatasetAssociation.table = Table(
    "history_dataset_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("state", TrimmedString(64), index=True, key="_state"),
    Column("copied_from_history_dataset_association_id", Integer,
           ForeignKey("history_dataset_association.id"), nullable=True),
    Column("copied_from_library_dataset_dataset_association_id", Integer,
           ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("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("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", JSONType)
)

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.ValidationError.table = Table(
    "validation_error", metadata,
    Column("id", Integer, primary_key=True),
    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("message", TrimmedString(255)),
    Column("err_type", TrimmedString(64)),
    Column("attributes", TEXT))

model.Group.table = Table(
    "galaxy_group", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("deleted", Boolean, index=True, default=False))

model.UserGroupAssociation.table = Table(
    "user_group_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

model.UserRoleAssociation.table = Table(
    "user_role_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

model.GroupRoleAssociation.table = Table(
    "group_role_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

model.Role.table = Table(
    "role", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("description", TEXT),
    Column("type", String(40), index=True),
    Column("deleted", Boolean, index=True, default=False))

model.UserQuotaAssociation.table = Table(
    "user_quota_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

model.GroupQuotaAssociation.table = Table(
    "group_quota_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("quota_id", Integer, ForeignKey("quota.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

model.Quota.table = Table(
    "quota", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("description", TEXT),
    Column("bytes", BigInteger),
    Column("operation", String(8)),
    Column("deleted", Boolean, index=True, default=False))

model.DefaultQuotaAssociation.table = Table(
    "default_quota_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("type", String(32), index=True, unique=True),
    Column("quota_id", Integer, ForeignKey("quota.id"), index=True))

model.DatasetPermissions.table = Table(
    "dataset_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.LibraryPermissions.table = Table(
    "library_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.LibraryFolderPermissions.table = Table(
    "library_folder_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.LibraryDatasetPermissions.table = Table(
    "library_dataset_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.LibraryDatasetDatasetAssociationPermissions.table = Table(
    "library_dataset_dataset_association_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_dataset_dataset_association_id", Integer,
        ForeignKey("library_dataset_dataset_association.id"),
        nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.DefaultUserPermissions.table = Table(
    "default_user_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("action", TEXT),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.DefaultHistoryPermissions.table = Table(
    "default_history_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("action", TEXT),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

model.LibraryDataset.table = Table(
    "library_dataset", metadata,
    Column("id", Integer, primary_key=True),
    # 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),
    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", JSONType))

model.ExtendedMetadataIndex.table = Table(
    "extended_metadata_index", metadata,
    Column("id", Integer, primary_key=True),
    Column("extended_metadata_id", Integer,
        ForeignKey("extended_metadata.id", onupdate="CASCADE", ondelete="CASCADE"), index=True),
    Column("path", String(255)),
    Column("value", TEXT))

model.Library.table = Table(
    "library", metadata,
    Column("id", Integer, primary_key=True),
    Column("root_folder_id", Integer, ForeignKey("library_folder.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("description", TEXT),
    Column("synopsis", TEXT))

model.LibraryFolder.table = Table(
    "library_folder", metadata,
    Column("id", Integer, primary_key=True),
    Column("parent_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", TEXT),
    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),
    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", JSONType, nullable=True),
    Column("job_messages", JSONType, 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)),
    Column("destination_id", String(255), nullable=True),
    Column("destination_params", JSONType, nullable=True),
    Column("object_store_id", TrimmedString(255), index=True),
    Column("imported", Boolean, default=False, index=True),
    Column("params", TrimmedString(255), index=True),
    Column("handler", TrimmedString(255), index=True))

model.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.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("info", JSONType, 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", JSONType, 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", JSONType, nullable=True),
    Column("info", TrimmedString(255)),
    Column("traceback", TEXT),
    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
    Column("working_directory", String(1024)),
    Column("task_runner_name", String(255)),
    Column("task_runner_external_id", String(255)),
    Column("prepare_input_files_cmd", TEXT))

model.PostJobAction.table = Table(
    "post_job_action", metadata,
    Column("id", Integer, primary_key=True),
    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True, nullable=False),
    Column("action_type", String(255), nullable=False),
    Column("output_name", String(255), nullable=True),
    Column("action_arguments", JSONType, nullable=True))

model.PostJobActionAssociation.table = Table(
    "post_job_action_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False),
    Column("post_job_action_id", Integer, ForeignKey("post_job_action.id"), index=True, nullable=False))

model.DeferredJob.table = Table(
    "deferred_job", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("state", String(64), index=True),
    Column("plugin", String(128), index=True),
    Column("params", JSONType))

model.TransferJob.table = Table(
    "transfer_job", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("state", String(64), index=True),
    Column("path", String(1024)),
    Column("info", TEXT),
    Column("pid", Integer),
    Column("socket", Integer),
    Column("params", JSONType))

model.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),
)

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),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True, nullable=False),
    Column("latest_workflow_id", Integer,
        ForeignKey("workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk'), index=True),
    Column("name", TEXT),
    Column("deleted", Boolean, default=False),
    Column("importable", Boolean, default=False),
    Column("slug", TEXT),
    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", JSONType),
    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", JSONType),
    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", JSONType),
    Column("value_from_type", TEXT),
    Column("default_value", JSONType),
    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", JSONType))

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", JSONType),
)

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),
    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", JSONType, 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")),
    Column("dataset_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("workflow_output_id", Integer, ForeignKey("workflow_output.id")),
)

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')),
    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')),
)

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')),
    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", JSONType()),
    Column("type", TrimmedString(255), index=True),
    Column("layout", JSONType()))

model.FormValues.table = Table(
    "form_values", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True),
    Column("content", JSONType()))

model.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))

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", JSONType),
    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.DatasetTagAssociation.table = Table(
    "dataset_tag_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("user_tname", TrimmedString(255), index=True),
    Column("value", TrimmedString(255), index=True),
    Column("user_value", TrimmedString(255), index=True))

model.HistoryDatasetAssociationTagAssociation.table = Table(
    "history_dataset_association_tag_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True),
    Column("tag_id", Integer, ForeignKey("tag.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("user_tname", TrimmedString(255), index=True),
    Column("value", TrimmedString(255), index=True),
    Column("user_value", TrimmedString(255), index=True))

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.
[docs]def simple_mapping(model, **kwds): mapper(model, model.table, properties=kwds)
simple_mapping(model.WorkerProcess) 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') )) mapper(model.ValidationError, model.ValidationError.table) 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, 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()))), tags=relation(model.DatasetTagAssociation, order_by=model.DatasetTagAssociation.table.c.id, backref='datasets') ) 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 ) )) # 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') 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.table.c.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.table.c.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) 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)), 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)) ), 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, primaryjoin=(model.LibraryDataset.table.c.library_dataset_dataset_association_id == model.LibraryDatasetDatasetAssociation.table.c.id)), 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, primaryjoin=(model.LibraryDatasetDatasetAssociation.table.c.library_dataset_id == model.LibraryDataset.table.c.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.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.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), output_datasets=relation(model.JobToOutputDatasetAssociation, lazy=True), any_output_dataset_deleted=column_property( 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()) ) ), any_output_dataset_collection_instances_deleted=column_property( 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()) ) ), 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) )) 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, ), 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') 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),) 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.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') 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') 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.DatasetTagAssociation, "tagged_datasets") 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 = dict((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 = dict((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) # 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) )) # 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={}) # 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 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
[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=None): """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) # 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 = ModelMapping(model_modules, engine=engine) # Create tables if needed if create_tables: metadata.create_all() # metadata.engine.commit() result.create_tables = create_tables # load local galaxy security policy result.security_agent = GalaxyRBACAgent(result) result.thread_local_log = thread_local_log return result