galaxy.model package
Galaxy data model classes
Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
- galaxy.model.now()
Return a new datetime representing UTC day and time.
- class galaxy.model.ConfigurationTemplateEnvironmentSecret[source]
Bases:
TypedDict
- type: typing_extensions.Literal[secret]
- class galaxy.model.ConfigurationTemplateEnvironmentVariable[source]
Bases:
TypedDict
- type: typing_extensions.Literal[variable]
- class galaxy.model.Base(**kwargs: Any)[source]
Bases:
DeclarativeBase
,object
- metadata: ClassVar[MetaData] = MetaData()
Refers to the
_schema.MetaData
collection that will be used for new_schema.Table
objects.See also
orm_declarative_metadata
- registry: ClassVar[_RegistryType] = <sqlalchemy.orm.decl_api.registry object>
Refers to the
_orm.registry
in use where new_orm.Mapper
objects will be associated.
- __init__(**kwargs: Any) None
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.HasTags[source]
Bases:
object
- dict_collection_visible_keys = ['tags']
- dict_element_visible_keys = ['tags']
- property auto_propagated_tags
- class galaxy.model.SerializeFilesHandler(*args, **kwargs)[source]
Bases:
Protocol
- __init__(*args, **kwargs)
- class galaxy.model.SerializationOptions(for_edit: bool, serialize_dataset_objects: bool | None = None, serialize_files_handler: SerializeFilesHandler | None = None, strip_metadata_files: bool | None = None)[source]
Bases:
object
- class galaxy.model.Serializable[source]
Bases:
RepresentById
- serialize(id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False) Dict[str, Any] [source]
Serialize model for a re-population in (potentially) another Galaxy instance.
- class galaxy.model.UsesCreateAndUpdateTime[source]
Bases:
object
- property seconds_since_updated
- property seconds_since_created
- class galaxy.model.WorkerProcess(**kwargs)[source]
Bases:
Base
,UsesCreateAndUpdateTime
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('worker_process', MetaData(), Column('id', Integer(), table=<worker_process>, primary_key=True, nullable=False), Column('server_name', String(length=255), table=<worker_process>), Column('hostname', String(length=255), table=<worker_process>), Column('pid', Integer(), table=<worker_process>), Column('update_time', DateTime(), table=<worker_process>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- galaxy.model.cached_id(galaxy_model_object)[source]
Get model object id attribute without a firing a database query.
Useful to fetching the id of a typical Galaxy model object after a flush, where SA is going to mark the id attribute as unloaded but we know the id is immutable and so we can use the database identity to fetch.
With Galaxy’s default SA initialization - any flush marks all attributes as unloaded - even objects completely unrelated to the flushed changes and even attributes we know to be immutable like id. See test_galaxy_mapping.py for verification of this behavior. This method is a workaround that uses the fact that we know all Galaxy objects use the id attribute as identity and SA internals (_sa_instance_state) to infer the previously loaded ID value. I tried digging into the SA internals extensively and couldn’t find a way to get the previously loaded values after a flush to allow a generalization of this for other attributes.
- class galaxy.model.JobLike[source]
Bases:
object
- MAX_NUMERIC = 9999999999999999999
- property metrics
- property stdout
- property stderr
- galaxy.model.calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False)[source]
Standalone function so can be reused for postgres directly in pgcleanup.py.
- class galaxy.model.UserQuotaBasicUsage(*, quota_source_label: str | None = None, total_disk_usage: float)[source]
Bases:
BaseModel
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {'quota_source_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'total_disk_usage': FieldInfo(annotation=float, required=True)}
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- class galaxy.model.UserQuotaUsage(*, quota_source_label: str | None = None, total_disk_usage: float, quota_percent: float | None = None, quota_bytes: int | None = None, quota: str | None = None)[source]
Bases:
UserQuotaBasicUsage
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {'quota': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'quota_bytes': FieldInfo(annotation=Union[int, NoneType], required=False, default=None), 'quota_percent': FieldInfo(annotation=Union[float, NoneType], required=False, default=None), 'quota_source_label': FieldInfo(annotation=Union[str, NoneType], required=False, default=None), 'total_disk_usage': FieldInfo(annotation=float, required=True)}
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- class galaxy.model.UserObjectstoreUsage(*, object_store_id: str, total_disk_usage: float)[source]
Bases:
BaseModel
- model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}
A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
- model_config: ClassVar[ConfigDict] = {}
Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
- model_fields: ClassVar[dict[str, FieldInfo]] = {'object_store_id': FieldInfo(annotation=str, required=True), 'total_disk_usage': FieldInfo(annotation=float, required=True)}
Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
This replaces Model.__fields__ from Pydantic V1.
- class galaxy.model.User(email=None, password=None, username=None)[source]
Bases:
Base
,Dictifiable
,RepresentById
Data for a Galaxy user or admin and relations to their histories, credentials, and roles.
- use_pbkdf2 = True
- bootstrap_admin_user = False
- addresses: Mapped[List[UserAddress]]
- cloudauthz: Mapped[List[CloudAuthz]]
- custos_auth: Mapped[List[CustosAuthnzToken]]
- default_permissions: Mapped[List[DefaultUserPermissions]]
- groups: Mapped[List[UserGroupAssociation]]
- galaxy_sessions: Mapped[List[GalaxySession]]
- object_stores: Mapped[List[UserObjectStore]]
- file_sources: Mapped[List[UserFileSource]]
- quotas: Mapped[List[UserQuotaAssociation]]
- quota_source_usages: Mapped[List[UserQuotaSourceUsage]]
- social_auth: Mapped[List[UserAuthnzToken]]
- values: Mapped[List[FormValues]]
- data_manager_histories: Mapped[List[DataManagerHistoryAssociation]]
- roles: Mapped[List[UserRoleAssociation]]
- stored_workflows: Mapped[List[StoredWorkflow]]
- all_notifications: Mapped[List[UserNotificationAssociation]]
- non_private_roles: Mapped[List[UserRoleAssociation]]
- preferences: AssociationProxy[Any] = ColumnAssociationProxyInstance(AssociationProxy('_preferences', 'value'))
- dict_collection_visible_keys = ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']
- dict_element_visible_keys = ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change', 'preferred_object_store_id']
- __init__(email=None, password=None, username=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property extra_preferences
- set_random_password(length=16)[source]
Sets user password to a random string of the given length. :return: void
- system_user_pwent(real_system_username)[source]
Gives the system user pwent entry based on e-mail or username depending on the value in real_system_username
- all_roles()[source]
Return a unique list of Roles associated with this user or any of their groups.
- get_disk_usage(nice_size=False, quota_source_label=None)[source]
Return byte count of disk space used by user or a human-readable string if nice_size is True.
- property total_disk_usage
Return byte count of disk space used by user or a human-readable string if nice_size is True.
- property nice_total_disk_usage
Return byte count of disk space used in a human-readable string.
- calculate_disk_usage_default_source(object_store)[source]
Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories assigned to default quota source.
- static user_template_environment(user)[source]
>>> env = User.user_template_environment(None) >>> env['__user_email__'] 'Anonymous' >>> env['__user_id__'] 'Anonymous' >>> user = User('foo@example.com') >>> user.id = 6 >>> user.username = 'foo2' >>> env = User.user_template_environment(user) >>> env['__user_id__'] '6' >>> env['__user_name__'] 'foo2'
- dictify_objectstore_usage() List[UserObjectstoreUsage] [source]
- dictify_usage(object_store=None) List[UserQuotaBasicUsage] [source]
Include object_store to include empty/unused usage info.
- dictify_usage_for(quota_source_label: str | None) UserQuotaBasicUsage [source]
- current_galaxy_session
- table = Table('galaxy_user', MetaData(), Column('id', Integer(), table=<galaxy_user>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_user>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('email', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('username', TrimmedString(length=255), table=<galaxy_user>), Column('password', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('last_password_change', DateTime(), table=<galaxy_user>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('external', Boolean(), table=<galaxy_user>, default=ScalarElementColumnDefault(False)), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<galaxy_user>), Column('preferred_object_store_id', String(length=255), table=<galaxy_user>), Column('deleted', Boolean(), table=<galaxy_user>, default=ScalarElementColumnDefault(False)), Column('purged', Boolean(), table=<galaxy_user>, default=ScalarElementColumnDefault(False)), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_user>), Column('active', Boolean(), table=<galaxy_user>, nullable=False, default=ScalarElementColumnDefault(True)), Column('activation_token', TrimmedString(length=64), table=<galaxy_user>), schema=None)
- class galaxy.model.PasswordResetToken(user, token=None)[source]
Bases:
Base
- __init__(user, token=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('password_reset_token', MetaData(), Column('token', String(length=32), table=<password_reset_token>, primary_key=True, nullable=False), Column('expiration_time', DateTime(), table=<password_reset_token>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<password_reset_token>), schema=None)
- class galaxy.model.DynamicTool(active=True, hidden=True, **kwd)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_collection_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
- dict_element_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
- __init__(active=True, hidden=True, **kwd)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dynamic_tool', MetaData(), Column('id', Integer(), table=<dynamic_tool>, primary_key=True, nullable=False), Column('uuid', UUIDType(), table=<dynamic_tool>), Column('create_time', DateTime(), table=<dynamic_tool>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dynamic_tool>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('tool_id', Unicode(length=255), table=<dynamic_tool>), Column('tool_version', Unicode(length=255), table=<dynamic_tool>), Column('tool_format', Unicode(length=255), table=<dynamic_tool>), Column('tool_path', Unicode(length=255), table=<dynamic_tool>), Column('tool_directory', Unicode(length=255), table=<dynamic_tool>), Column('hidden', Boolean(), table=<dynamic_tool>, default=ScalarElementColumnDefault(True)), Column('active', Boolean(), table=<dynamic_tool>, default=ScalarElementColumnDefault(True)), Column('value', MutableJSONType(), table=<dynamic_tool>), schema=None)
- class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)[source]
Bases:
Base
- __init__(plugin, metric_name, metric_value)[source]
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.JobMetricText(plugin, metric_name, metric_value)[source]
Bases:
BaseJobMetric
,RepresentById
- __init__(plugin, metric_name, metric_value)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_metric_text', MetaData(), Column('id', Integer(), table=<job_metric_text>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_text>), Column('plugin', Unicode(length=255), table=<job_metric_text>), Column('metric_name', Unicode(length=255), table=<job_metric_text>), Column('metric_value', Unicode(length=1023), table=<job_metric_text>), schema=None)
- class galaxy.model.JobMetricNumeric(plugin, metric_name, metric_value)[source]
Bases:
BaseJobMetric
,RepresentById
- __init__(plugin, metric_name, metric_value)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_metric_numeric', MetaData(), Column('id', Integer(), table=<job_metric_numeric>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_numeric>), Column('plugin', Unicode(length=255), table=<job_metric_numeric>), Column('metric_name', Unicode(length=255), table=<job_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<job_metric_numeric>), schema=None)
- class galaxy.model.TaskMetricText(plugin, metric_name, metric_value)[source]
Bases:
BaseJobMetric
,RepresentById
- __init__(plugin, metric_name, metric_value)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('task_metric_text', MetaData(), Column('id', Integer(), table=<task_metric_text>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_text>), Column('plugin', Unicode(length=255), table=<task_metric_text>), Column('metric_name', Unicode(length=255), table=<task_metric_text>), Column('metric_value', Unicode(length=1023), table=<task_metric_text>), schema=None)
- class galaxy.model.TaskMetricNumeric(plugin, metric_name, metric_value)[source]
Bases:
BaseJobMetric
,RepresentById
- __init__(plugin, metric_name, metric_value)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('task_metric_numeric', MetaData(), Column('id', Integer(), table=<task_metric_numeric>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_numeric>), Column('plugin', Unicode(length=255), table=<task_metric_numeric>), Column('metric_name', Unicode(length=255), table=<task_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<task_metric_numeric>), schema=None)
- class galaxy.model.IoDicts(inp_data, out_data, out_collections)[source]
Bases:
tuple
- inp_data: Dict[str, DatasetInstance | None]
Alias for field number 0
- out_data: Dict[str, DatasetInstance]
Alias for field number 1
- out_collections: Dict[str, DatasetCollectionInstance | DatasetCollection]
Alias for field number 2
- class galaxy.model.Job[source]
Bases:
Base
,JobLike
,UsesCreateAndUpdateTime
,Dictifiable
,Serializable
A job represents a request to run a tool given input datasets, tool parameters, and output datasets.
- galaxy_session: Mapped[GalaxySession | None]
- library_folder: Mapped[LibraryFolder | None]
- parameters
- input_datasets: Mapped[List[JobToInputDatasetAssociation]]
- input_dataset_collections: Mapped[List[JobToInputDatasetCollectionAssociation]]
- input_dataset_collection_elements: Mapped[List[JobToInputDatasetCollectionElementAssociation]]
- output_dataset_collection_instances: Mapped[List[JobToOutputDatasetCollectionAssociation]]
- output_dataset_collections: Mapped[List[JobToImplicitOutputDatasetCollectionAssociation]]
- post_job_actions: Mapped[List[PostJobActionAssociation]]
- input_library_datasets: Mapped[List[JobToInputLibraryDatasetAssociation]]
- output_library_datasets: Mapped[List[JobToOutputLibraryDatasetAssociation]]
- external_output_metadata: Mapped[List[JobExternalOutputMetadata]]
- output_datasets: Mapped[List[JobToOutputDatasetAssociation]]
- state_history: Mapped[List[JobStateHistory]]
- text_metrics: Mapped[List[JobMetricText]]
- numeric_metrics: Mapped[List[JobMetricNumeric]]
- interactivetool_entry_points: Mapped[List[InteractiveToolEntryPoint]]
- implicit_collection_jobs_association: Mapped[List[ImplicitCollectionJobsJobAssociation]]
- container: Mapped[JobContainerAssociation | None]
- data_manager_association: Mapped[DataManagerJobAssociation | None]
- history_dataset_collection_associations: Mapped[List[HistoryDatasetCollectionAssociation]]
- workflow_invocation_step: Mapped[WorkflowInvocationStep | None]
- any_output_dataset_collection_instances_deleted
- any_output_dataset_deleted
- dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']
- dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version', 'command_version', 'copied_from_job_id']
- terminal_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>]
- finished_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>, <JobState.DELETING: 'deleting'>]
- non_ready_states = [<JobState.NEW: 'new'>, <JobState.RESUBMITTED: 'resubmitted'>, <JobState.UPLOAD: 'upload'>, <JobState.WAITING: 'waiting'>, <JobState.QUEUED: 'queued'>, <JobState.RUNNING: 'running'>]
job states where the job hasn’t finished and the model may still change
- __init__()
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property running
- property finished
- get_external_output_metadata()[source]
The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task.
- get_id_tag()[source]
Return a tag that can be useful in identifying a Job. This returns the Job’s get_id
- property all_entry_points_configured
- set_state(state: JobState) bool [source]
Save state history. Returns True if state has changed, else False.
- get_param_values(app, ignore_errors=False)[source]
Read encoded parameter values from the database and turn back into a dict of tool parameter values.
- check_if_output_datasets_deleted()[source]
Return true if all of the output datasets associated with this job are in the deleted state
- mark_deleted(track_jobs_in_database=False)[source]
Mark this job as deleted, and mark any output datasets as discarded.
- mark_failed(info='Job execution failed', blurb=None, peek=None)[source]
Mark this job as failed, and mark any output datasets as errored.
- get_destination_configuration(dest_params, config, key, default=None)[source]
Get a destination parameter that can be defaulted back in specified config if it needs to be applied globally.
- property command_version
- table = Table('job', MetaData(), Column('id', Integer(), table=<job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<job>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<job>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<job>), Column('tool_id', String(length=255), table=<job>), Column('tool_version', TEXT(), table=<job>, default=ScalarElementColumnDefault('1.0.0')), Column('galaxy_version', String(length=64), table=<job>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<job>), Column('state', String(length=64), table=<job>), Column('info', TrimmedString(length=255), table=<job>), Column('copied_from_job_id', Integer(), table=<job>), Column('command_line', TEXT(), table=<job>), Column('dependencies', MutableJSONType(), table=<job>), Column('job_messages', MutableJSONType(), table=<job>), Column('param_filename', String(length=1024), table=<job>), Column('runner_name', String(length=255), table=<job>), Column('job_stdout', TEXT(), table=<job>), Column('job_stderr', TEXT(), table=<job>), Column('tool_stdout', TEXT(), table=<job>), Column('tool_stderr', TEXT(), table=<job>), Column('exit_code', Integer(), table=<job>), Column('traceback', TEXT(), table=<job>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<job>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<job>), Column('job_runner_name', String(length=255), table=<job>), Column('job_runner_external_id', String(length=255), table=<job>), Column('destination_id', String(length=255), table=<job>), Column('destination_params', MutableJSONType(), table=<job>), Column('object_store_id', TrimmedString(length=255), table=<job>), Column('imported', Boolean(), table=<job>, default=ScalarElementColumnDefault(False)), Column('params', TrimmedString(length=255), table=<job>), Column('handler', TrimmedString(length=255), table=<job>), Column('preferred_object_store_id', String(length=255), table=<job>), Column('object_store_id_overrides', JSONType(), table=<job>), schema=None)
- class galaxy.model.Task(job, working_directory, prepare_files_cmd)[source]
Bases:
Base
,JobLike
,RepresentById
A task represents a single component of a job.
- text_metrics: Mapped[List[TaskMetricText]]
- numeric_metrics: Mapped[List[TaskMetricNumeric]]
- class states(value)[source]
-
An enumeration.
- NEW = 'new'
- WAITING = 'waiting'
- QUEUED = 'queued'
- RUNNING = 'running'
- OK = 'ok'
- ERROR = 'error'
- DELETED = 'deleted'
- __init__(job, working_directory, prepare_files_cmd)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- get_param_values(app)[source]
Read encoded parameter values from the database and turn back into a dict of tool parameter values.
- get_id_tag()[source]
Return an id tag suitable for identifying the task. This combines the task’s job id and the task’s own id.
- get_external_output_metadata()[source]
The external_output_metadata is currently a backref to JobExternalOutputMetadata. It exists for a job but not a task, and when a task is cancelled its corresponding parent Job will be cancelled. So None is returned now, but that could be changed to self.get_job().get_external_output_metadata().
- get_job_runner_name()[source]
Since runners currently access Tasks the same way they access Jobs, this method just refers to this instance’s runner.
- get_job_runner_external_id()[source]
Runners will use the same methods to get information about the Task class as they will about the Job class, so this method just returns the task’s external id.
- table = Table('task', MetaData(), Column('id', Integer(), table=<task>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<task>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('execution_time', DateTime(), table=<task>), Column('update_time', DateTime(), table=<task>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<task>), Column('command_line', TEXT(), table=<task>), Column('param_filename', String(length=1024), table=<task>), Column('runner_name', String(length=255), table=<task>), Column('job_stdout', TEXT(), table=<task>), Column('job_stderr', TEXT(), table=<task>), Column('tool_stdout', TEXT(), table=<task>), Column('tool_stderr', TEXT(), table=<task>), Column('exit_code', Integer(), table=<task>), Column('job_messages', MutableJSONType(), table=<task>), Column('info', TrimmedString(length=255), table=<task>), Column('traceback', TEXT(), table=<task>), Column('job_id', Integer(), ForeignKey('job.id'), table=<task>, nullable=False), Column('working_directory', String(length=1024), table=<task>), Column('task_runner_name', String(length=255), table=<task>), Column('task_runner_external_id', String(length=255), table=<task>), Column('prepare_input_files_cmd', TEXT(), table=<task>), schema=None)
- class galaxy.model.JobParameter(name, value)[source]
Bases:
Base
,RepresentById
- __init__(name, value)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_parameter', MetaData(), Column('id', Integer(), table=<job_parameter>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_parameter>), Column('name', String(length=255), table=<job_parameter>), Column('value', TEXT(), table=<job_parameter>), schema=None)
- class galaxy.model.JobToInputDatasetAssociation(name, dataset)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset: Mapped[HistoryDatasetAssociation]
- table = Table('job_to_input_dataset', MetaData(), Column('id', Integer(), table=<job_to_input_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_input_dataset>), Column('dataset_version', Integer(), table=<job_to_input_dataset>), Column('name', String(length=255), table=<job_to_input_dataset>), schema=None)
- class galaxy.model.JobToOutputDatasetAssociation(name, dataset)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset: Mapped[HistoryDatasetAssociation]
- property item
- table = Table('job_to_output_dataset', MetaData(), Column('id', Integer(), table=<job_to_output_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_output_dataset>), Column('name', String(length=255), table=<job_to_output_dataset>), schema=None)
- class galaxy.model.JobToInputDatasetCollectionAssociation(name, dataset_collection)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset_collection)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset_collection: Mapped[HistoryDatasetCollectionAssociation]
- table = Table('job_to_input_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_input_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_input_dataset_collection>), Column('name', String(length=255), table=<job_to_input_dataset_collection>), schema=None)
- class galaxy.model.JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset_collection_element)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset_collection_element: Mapped[DatasetCollectionElement]
- table = Table('job_to_input_dataset_collection_element', MetaData(), Column('id', Integer(), table=<job_to_input_dataset_collection_element>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection_element>), Column('dataset_collection_element_id', Integer(), ForeignKey('dataset_collection_element.id'), table=<job_to_input_dataset_collection_element>), Column('name', Unicode(length=255), table=<job_to_input_dataset_collection_element>), schema=None)
- class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset_collection_instance)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset_collection_instance: Mapped[HistoryDatasetCollectionAssociation]
- property item
- table = Table('job_to_output_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_output_dataset_collection>), schema=None)
- class galaxy.model.JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset_collection)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset_collection: Mapped[DatasetCollection]
- table = Table('job_to_implicit_output_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_implicit_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_implicit_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<job_to_implicit_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_implicit_output_dataset_collection>), schema=None)
- class galaxy.model.JobToInputLibraryDatasetAssociation(name, dataset)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset: Mapped[LibraryDatasetDatasetAssociation]
- table = Table('job_to_input_library_dataset', MetaData(), Column('id', Integer(), table=<job_to_input_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_input_library_dataset>), Column('name', Unicode(length=255), table=<job_to_input_library_dataset>), schema=None)
- class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)[source]
Bases:
Base
,RepresentById
- __init__(name, dataset)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- dataset: Mapped[LibraryDatasetDatasetAssociation]
- table = Table('job_to_output_library_dataset', MetaData(), Column('id', Integer(), table=<job_to_output_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_output_library_dataset>), Column('name', Unicode(length=255), table=<job_to_output_library_dataset>), schema=None)
- class galaxy.model.JobStateHistory(job)[source]
Bases:
Base
,RepresentById
- __init__(job)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_state_history', MetaData(), Column('id', Integer(), table=<job_state_history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job_state_history>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_state_history>), Column('state', String(length=64), table=<job_state_history>), Column('info', TrimmedString(length=255), table=<job_state_history>), schema=None)
- class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)[source]
Bases:
Base
,RepresentById
- __init__(name, input_dataset_collection)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- input_dataset_collection: Mapped[HistoryDatasetCollectionAssociation | None]
- table = Table('implicitly_created_dataset_collection_inputs', MetaData(), Column('id', Integer(), table=<implicitly_created_dataset_collection_inputs>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('input_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('name', Unicode(length=255), table=<implicitly_created_dataset_collection_inputs>), schema=None)
- class galaxy.model.ImplicitCollectionJobs(populated_state=None)[source]
Bases:
Base
,Serializable
- jobs: Mapped[List[ImplicitCollectionJobsJobAssociation]]
- __init__(populated_state=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property job_list
- table = Table('implicit_collection_jobs', MetaData(), Column('id', Integer(), table=<implicit_collection_jobs>, primary_key=True, nullable=False), Column('populated_state', TrimmedString(length=64), table=<implicit_collection_jobs>, nullable=False, default=ScalarElementColumnDefault('new')), schema=None)
- class galaxy.model.ImplicitCollectionJobsJobAssociation(**kwargs)[source]
Bases:
Base
,RepresentById
- implicit_collection_jobs
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('implicit_collection_jobs_job_association', MetaData(), Column('id', Integer(), table=<implicit_collection_jobs_job_association>, primary_key=True, nullable=False), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<implicit_collection_jobs_job_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<implicit_collection_jobs_job_association>), Column('order_index', Integer(), table=<implicit_collection_jobs_job_association>, nullable=False), schema=None)
- class galaxy.model.PostJobAction(action_type, workflow_step=None, output_name=None, action_arguments=None)[source]
Bases:
Base
,RepresentById
- __init__(action_type, workflow_step=None, output_name=None, action_arguments=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- workflow_step: Mapped[WorkflowStep | None]
- table = Table('post_job_action', MetaData(), Column('id', Integer(), table=<post_job_action>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<post_job_action>), Column('action_type', String(length=255), table=<post_job_action>, nullable=False), Column('output_name', String(length=255), table=<post_job_action>), Column('action_arguments', MutableJSONType(), table=<post_job_action>), schema=None)
- class galaxy.model.PostJobActionAssociation(pja, job=None, job_id=None)[source]
Bases:
Base
,RepresentById
- __init__(pja, job=None, job_id=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- post_job_action: Mapped[PostJobAction]
- table = Table('post_job_action_association', MetaData(), Column('id', Integer(), table=<post_job_action_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<post_job_action_association>, nullable=False), Column('post_job_action_id', Integer(), ForeignKey('post_job_action.id'), table=<post_job_action_association>, nullable=False), schema=None)
- class galaxy.model.JobExternalOutputMetadata(job=None, dataset=None)[source]
Bases:
Base
,RepresentById
- __init__(job=None, dataset=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- history_dataset_association: Mapped[HistoryDatasetAssociation | None]
- library_dataset_dataset_association: Mapped[LibraryDatasetDatasetAssociation | None]
- property dataset
- table = Table('job_external_output_metadata', MetaData(), Column('id', Integer(), table=<job_external_output_metadata>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_external_output_metadata>), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_external_output_metadata>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_external_output_metadata>), Column('is_valid', Boolean(), table=<job_external_output_metadata>, default=ScalarElementColumnDefault(True)), Column('filename_in', String(length=255), table=<job_external_output_metadata>), Column('filename_out', String(length=255), table=<job_external_output_metadata>), Column('filename_results_code', String(length=255), table=<job_external_output_metadata>), Column('filename_kwds', String(length=255), table=<job_external_output_metadata>), Column('filename_override_metadata', String(length=255), table=<job_external_output_metadata>), Column('job_runner_external_pid', String(length=255), table=<job_external_output_metadata>), schema=None)
- class galaxy.model.FakeDatasetAssociation(dataset=None)[source]
Bases:
object
- fake_dataset_association = True
- class galaxy.model.JobExportHistoryArchive(compressed=False, **kwd)[source]
Bases:
Base
,RepresentById
- ATTRS_FILENAME_HISTORY = 'history_attrs.txt'
- __init__(compressed=False, **kwd)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property fda
- property temp_directory
- property up_to_date
Return False, if a new export should be generated for corresponding history.
- property ready
- property preparing
- property export_name
- table = Table('job_export_history_archive', MetaData(), Column('id', Integer(), table=<job_export_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_export_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_export_history_archive>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<job_export_history_archive>), Column('compressed', Boolean(), table=<job_export_history_archive>, default=ScalarElementColumnDefault(False)), Column('history_attrs_filename', TEXT(), table=<job_export_history_archive>), schema=None)
- class galaxy.model.JobImportHistoryArchive(**kwargs)[source]
Bases:
Base
,RepresentById
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_import_history_archive', MetaData(), Column('id', Integer(), table=<job_import_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_import_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_import_history_archive>), Column('archive_dir', TEXT(), table=<job_import_history_archive>), schema=None)
- class galaxy.model.StoreExportAssociation(**kwargs)[source]
Bases:
Base
,RepresentById
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('store_export_association', MetaData(), Column('id', Integer(), table=<store_export_association>, primary_key=True, nullable=False), Column('task_uuid', UUIDType(), table=<store_export_association>), Column('create_time', DateTime(), table=<store_export_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('object_type', TrimmedString(length=32), table=<store_export_association>), Column('object_id', Integer(), table=<store_export_association>), Column('export_metadata', JSONType(), table=<store_export_association>), schema=None)
- class galaxy.model.JobContainerAssociation(**kwd)[source]
Bases:
Base
,RepresentById
- __init__(**kwd)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('job_container_association', MetaData(), Column('id', Integer(), table=<job_container_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_container_association>), Column('container_type', TEXT(), table=<job_container_association>), Column('container_name', TEXT(), table=<job_container_association>), Column('container_info', MutableJSONType(), table=<job_container_association>), Column('created_time', DateTime(), table=<job_container_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<job_container_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.InteractiveToolEntryPoint(requires_domain=True, requires_path_in_url=False, configured=False, deleted=False, **kwd)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_collection_visible_keys = ['id', 'job_id', 'name', 'label', 'active', 'created_time', 'modified_time', 'output_datasets_ids']
- dict_element_visible_keys = ['id', 'job_id', 'name', 'label', 'active', 'created_time', 'modified_time', 'output_datasets_ids']
- __init__(requires_domain=True, requires_path_in_url=False, configured=False, deleted=False, **kwd)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property active
- property class_id
- property output_datasets_ids
- table = Table('interactivetool_entry_point', MetaData(), Column('id', Integer(), table=<interactivetool_entry_point>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<interactivetool_entry_point>), Column('name', TEXT(), table=<interactivetool_entry_point>), Column('token', TEXT(), table=<interactivetool_entry_point>), Column('tool_port', Integer(), table=<interactivetool_entry_point>), Column('host', TEXT(), table=<interactivetool_entry_point>), Column('port', Integer(), table=<interactivetool_entry_point>), Column('protocol', TEXT(), table=<interactivetool_entry_point>), Column('entry_url', TEXT(), table=<interactivetool_entry_point>), Column('requires_domain', Boolean(), table=<interactivetool_entry_point>, default=ScalarElementColumnDefault(True)), Column('requires_path_in_url', Boolean(), table=<interactivetool_entry_point>, default=ScalarElementColumnDefault(False)), Column('requires_path_in_header_named', TEXT(), table=<interactivetool_entry_point>), Column('info', MutableJSONType(), table=<interactivetool_entry_point>), Column('configured', Boolean(), table=<interactivetool_entry_point>, default=ScalarElementColumnDefault(False)), Column('deleted', Boolean(), table=<interactivetool_entry_point>, default=ScalarElementColumnDefault(False)), Column('created_time', DateTime(), table=<interactivetool_entry_point>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<interactivetool_entry_point>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('label', TEXT(), table=<interactivetool_entry_point>), schema=None)
- class galaxy.model.GenomeIndexToolData(**kwargs)[source]
Bases:
Base
,RepresentById
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('genome_index_tool_data', MetaData(), Column('id', Integer(), table=<genome_index_tool_data>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<genome_index_tool_data>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<genome_index_tool_data>), Column('fasta_path', String(length=255), table=<genome_index_tool_data>), Column('created_time', DateTime(), table=<genome_index_tool_data>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<genome_index_tool_data>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('indexer', String(length=64), table=<genome_index_tool_data>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<genome_index_tool_data>), schema=None)
- class galaxy.model.Group(name=None)[source]
Bases:
Base
,Dictifiable
,RepresentById
- quotas: Mapped[List[GroupQuotaAssociation]]
- roles: Mapped[List[GroupRoleAssociation]]
- users: Mapped[List[UserGroupAssociation]]
- dict_collection_visible_keys = ['id', 'name']
- dict_element_visible_keys = ['id', 'name']
- __init__(name=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('galaxy_group', MetaData(), Column('id', Integer(), table=<galaxy_group>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_group>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<galaxy_group>), Column('deleted', Boolean(), table=<galaxy_group>, default=ScalarElementColumnDefault(False)), schema=None)
- class galaxy.model.UserGroupAssociation(user, group)[source]
Bases:
Base
,RepresentById
- __init__(user, group)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('user_group_association', MetaData(), Column('id', Integer(), table=<user_group_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_group_association>), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<user_group_association>), Column('create_time', DateTime(), table=<user_group_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.Notification(source, category, variant, content)[source]
Bases:
Base
,Dictifiable
,RepresentById
- user_notification_associations: Mapped[List[UserNotificationAssociation]]
- __init__(source, category, variant, content)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('notification', MetaData(), Column('id', Integer(), table=<notification>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<notification>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<notification>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('publication_time', DateTime(), table=<notification>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('expiration_time', DateTime(), table=<notification>, default=ScalarElementColumnDefault(datetime.datetime(2025, 5, 21, 9, 42, 1, 471350))), Column('source', String(length=32), table=<notification>), Column('category', String(length=64), table=<notification>), Column('variant', String(length=16), table=<notification>), Column('dispatched', Boolean(), table=<notification>, nullable=False, default=ScalarElementColumnDefault(False)), Column('galaxy_url', String(length=255), table=<notification>), Column('content', DoubleEncodedJsonType(), table=<notification>), schema=None)
- class galaxy.model.UserNotificationAssociation(user, notification)[source]
Bases:
Base
,RepresentById
- __init__(user, notification)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- notification: Mapped[Notification]
- table = Table('user_notification_association', MetaData(), Column('id', Integer(), table=<user_notification_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_notification_association>), Column('notification_id', Integer(), ForeignKey('notification.id'), table=<user_notification_association>), Column('seen_time', DateTime(), table=<user_notification_association>), Column('deleted', Boolean(), table=<user_notification_association>, default=ScalarElementColumnDefault(False)), Column('update_time', DateTime(), table=<user_notification_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.HistoryAudit(*args, **kwargs)[source]
Bases:
Base
- __init__(*args, **kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('history_audit', MetaData(), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_audit>, primary_key=True, nullable=False), Column('update_time', DateTime(), table=<history_audit>, primary_key=True, nullable=False, default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.History(id=None, name=None, user=None)[source]
Bases:
Base
,HasTags
,Dictifiable
,UsesAnnotations
,HasName
,Serializable
,UsesCreateAndUpdateTime
- datasets: Mapped[List[HistoryDatasetAssociation]]
- exports: Mapped[List[JobExportHistoryArchive]]
- active_datasets: Mapped[List[HistoryDatasetAssociation]]
- dataset_collections: Mapped[List[HistoryDatasetCollectionAssociation]]
- active_dataset_collections: Mapped[List[HistoryDatasetCollectionAssociation]]
- visible_datasets: Mapped[List[HistoryDatasetAssociation]]
- visible_dataset_collections: Mapped[List[HistoryDatasetCollectionAssociation]]
- tags: Mapped[List[HistoryTagAssociation]]
- annotations: Mapped[List[HistoryAnnotationAssociation]]
- ratings: Mapped[List[HistoryRatingAssociation]]
- default_permissions: Mapped[List[DefaultHistoryPermissions]]
- galaxy_sessions
- workflow_invocations: Mapped[List[WorkflowInvocation]]
- average_rating
- dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
- dict_element_visible_keys = ['id', 'name', 'archived', 'create_time', 'deleted', 'empty', 'genome_build', 'hid_counter', 'importable', 'preferred_object_store_id', 'purged', 'published', 'slug', 'tags', 'update_time', 'username']
- default_name = 'Unnamed history'
- __init__(id=None, name=None, user=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property empty
- property username
- property count
- add_datasets(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)[source]
Optimized version of add_dataset above that minimizes database interactions when adding many datasets and collections to history at once.
- copy(name=None, target_user=None, activatable=False, all_datasets=False)[source]
Return a copy of this history using the given name and target_user. If activatable, copy only non-deleted datasets. If all_datasets, copy non-deleted, deleted, and purged datasets.
- property has_possible_members
- property activatable_datasets
- property latest_export
- property paused_jobs
- disk_size
Return a query scalar that will get any history’s size in bytes by summing the ‘total_size’s of all non-purged, unique datasets within it.
- property disk_nice_size
Returns human readable size of history on disk.
- property active_datasets_and_roles
- property active_visible_datasets_and_roles
- property active_visible_dataset_collections
- property active_contents
Return all active contents ordered by hid.
- table = Table('history', MetaData(), Column('id', Integer(), table=<history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history>), Column('name', TrimmedString(length=255), table=<history>), Column('hid_counter', Integer(), table=<history>, default=ScalarElementColumnDefault(1)), Column('deleted', Boolean(), table=<history>, default=ScalarElementColumnDefault(False)), Column('purged', Boolean(), table=<history>, default=ScalarElementColumnDefault(False)), Column('importing', Boolean(), table=<history>, default=ScalarElementColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<history>), Column('importable', Boolean(), table=<history>, default=ScalarElementColumnDefault(False)), Column('slug', TEXT(), table=<history>), Column('published', Boolean(), table=<history>, default=ScalarElementColumnDefault(False)), Column('preferred_object_store_id', String(length=255), table=<history>), Column('archived', Boolean(), table=<history>, default=ScalarElementColumnDefault(False), server_default=DefaultClause(<sqlalchemy.sql.elements.False_ object>, for_update=False)), Column('archive_export_id', Integer(), ForeignKey('store_export_association.id'), table=<history>), schema=None)
Bases:
RepresentById
Bases:
Base
,UserShareAssociation
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- class galaxy.model.UserRoleAssociation(user, role)[source]
Bases:
Base
,RepresentById
- __init__(user, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('user_role_association', MetaData(), Column('id', Integer(), table=<user_role_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<user_role_association>), Column('create_time', DateTime(), table=<user_role_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.GroupRoleAssociation(group, role)[source]
Bases:
Base
,RepresentById
- __init__(group, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('group_role_association', MetaData(), Column('id', Integer(), table=<group_role_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<group_role_association>), Column('create_time', DateTime(), table=<group_role_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.Role(name=None, description=None, type=types.SYSTEM, deleted=False)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dataset_actions: Mapped[List[DatasetPermissions]]
- groups: Mapped[List[GroupRoleAssociation]]
- users: Mapped[List[UserRoleAssociation]]
- dict_collection_visible_keys = ['id', 'name']
- dict_element_visible_keys = ['id', 'name', 'description', 'type']
- private_id = None
- class types(value)[source]
-
An enumeration.
- PRIVATE = 'private'
- SYSTEM = 'system'
- USER = 'user'
- ADMIN = 'admin'
- SHARING = 'sharing'
- __init__(name=None, description=None, type=types.SYSTEM, deleted=False)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('role', MetaData(), Column('id', Integer(), table=<role>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<role>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<role>), Column('description', TEXT(), table=<role>), Column('type', String(length=40), table=<role>), Column('deleted', Boolean(), table=<role>, default=ScalarElementColumnDefault(False)), schema=None)
- class galaxy.model.UserQuotaSourceUsage(**kwargs)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_element_visible_keys = ['disk_usage', 'quota_source_label']
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('user_quota_source_usage', MetaData(), Column('id', Integer(), table=<user_quota_source_usage>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_source_usage>), Column('quota_source_label', String(length=32), table=<user_quota_source_usage>), Column('disk_usage', Numeric(precision=15, scale=0), table=<user_quota_source_usage>, nullable=False, default=ScalarElementColumnDefault(0)), schema=None)
- class galaxy.model.UserQuotaAssociation(user, quota)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_element_visible_keys = ['user']
- __init__(user, quota)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('user_quota_association', MetaData(), Column('id', Integer(), table=<user_quota_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<user_quota_association>), Column('create_time', DateTime(), table=<user_quota_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_quota_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.GroupQuotaAssociation(group, quota)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_element_visible_keys = ['group']
- __init__(group, quota)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('group_quota_association', MetaData(), Column('id', Integer(), table=<group_quota_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<group_quota_association>), Column('create_time', DateTime(), table=<group_quota_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_quota_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), schema=None)
- class galaxy.model.Quota(name=None, description=None, amount=0, operation='=', quota_source_label=None)[source]
Bases:
Base
,Dictifiable
,RepresentById
- default: Mapped[List[DefaultQuotaAssociation]]
- groups: Mapped[List[GroupQuotaAssociation]]
- users: Mapped[List[UserQuotaAssociation]]
- dict_collection_visible_keys = ['id', 'name', 'quota_source_label']
- dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups', 'quota_source_label']
- valid_operations = ('+', '-', '=')
- __init__(name=None, description=None, amount=0, operation='=', quota_source_label=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- property amount
- property display_amount
- table = Table('quota', MetaData(), Column('id', Integer(), table=<quota>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<quota>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<quota>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<quota>), Column('description', TEXT(), table=<quota>), Column('bytes', BigInteger(), table=<quota>), Column('operation', String(length=8), table=<quota>), Column('deleted', Boolean(), table=<quota>, default=ScalarElementColumnDefault(False)), Column('quota_source_label', String(length=32), table=<quota>), schema=None)
- class galaxy.model.DefaultQuotaAssociation(type, quota)[source]
Bases:
Base
,Dictifiable
,RepresentById
- dict_element_visible_keys = ['type']
- class types(value)[source]
-
An enumeration.
- UNREGISTERED = 'unregistered'
- REGISTERED = 'registered'
- __init__(type, quota)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('default_quota_association', MetaData(), Column('id', Integer(), table=<default_quota_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<default_quota_association>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<default_quota_association>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('type', String(length=32), table=<default_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<default_quota_association>), schema=None)
- class galaxy.model.DatasetPermissions(action, dataset, role=None, role_id=None)[source]
Bases:
Base
,RepresentById
- __init__(action, dataset, role=None, role_id=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_permissions', MetaData(), Column('id', Integer(), table=<dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset_permissions>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_permissions>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<dataset_permissions>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<dataset_permissions>), schema=None)
- class galaxy.model.LibraryPermissions(action, library_item, role)[source]
Bases:
Base
,RepresentById
- __init__(action, library_item, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('library_permissions', MetaData(), Column('id', Integer(), table=<library_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_permissions>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_permissions>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_permissions>), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_permissions>), schema=None)
- class galaxy.model.LibraryFolderPermissions(action, library_item, role)[source]
Bases:
Base
,RepresentById
- __init__(action, library_item, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- folder: Mapped[LibraryFolder | None]
- table = Table('library_folder_permissions', MetaData(), Column('id', Integer(), table=<library_folder_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_folder_permissions>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder_permissions>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_folder_permissions>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_folder_permissions>), schema=None)
- class galaxy.model.LibraryDatasetPermissions(action, library_item, role)[source]
Bases:
Base
,RepresentById
- __init__(action, library_item, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- library_dataset: Mapped[LibraryDataset | None]
- table = Table('library_dataset_permissions', MetaData(), Column('id', Integer(), table=<library_dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_permissions>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_permissions>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_permissions>), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_permissions>), schema=None)
- class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)[source]
Bases:
Base
,RepresentById
- __init__(action, library_item, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- library_dataset_dataset_association: Mapped[LibraryDatasetDatasetAssociation]
- table = Table('library_dataset_dataset_association_permissions', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_association_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_dataset_association_permissions>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association_permissions>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_dataset_association_permissions>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_dataset_association_permissions>), schema=None)
- class galaxy.model.DefaultUserPermissions(user, action, role)[source]
Bases:
Base
,RepresentById
- __init__(user, action, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('default_user_permissions', MetaData(), Column('id', Integer(), table=<default_user_permissions>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<default_user_permissions>), Column('action', TEXT(), table=<default_user_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_user_permissions>), schema=None)
- class galaxy.model.DefaultHistoryPermissions(history, action, role)[source]
Bases:
Base
,RepresentById
- __init__(history, action, role)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('default_history_permissions', MetaData(), Column('id', Integer(), table=<default_history_permissions>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<default_history_permissions>), Column('action', TEXT(), table=<default_history_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_history_permissions>), schema=None)
- class galaxy.model.Dataset(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)[source]
Bases:
Base
,StorableObject
,Serializable
- actions: Mapped[List[DatasetPermissions]]
- active_history_associations: Mapped[List[HistoryDatasetAssociation]]
- purged_history_associations: Mapped[List[HistoryDatasetAssociation]]
- active_library_associations: Mapped[List[LibraryDatasetDatasetAssociation]]
- history_associations: Mapped[List[HistoryDatasetAssociation]]
- library_associations: Mapped[List[LibraryDatasetDatasetAssociation]]
- states
alias of
DatasetState
- non_ready_states = (<DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)
- ready_states = (<DatasetState.ERROR: 'error'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>, <DatasetState.OK: 'ok'>, <DatasetState.DISCARDED: 'discarded'>)
- valid_input_states = (<DatasetState.SETTING_METADATA: 'setting_metadata'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.RUNNING: 'running'>, <DatasetState.NEW: 'new'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.OK: 'ok'>, <DatasetState.QUEUED: 'queued'>)
- no_data_states = (<DatasetState.PAUSED: 'paused'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)
- terminal_states = (<DatasetState.OK: 'ok'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.ERROR: 'error'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>)
- class conversion_messages(value)[source]
-
An enumeration.
- PENDING = 'pending'
- NO_DATA = 'no data'
- NO_CHROMOSOME = 'no chromosome'
- NO_CONVERTER = 'no converter'
- NO_TOOL = 'no tool'
- DATA = 'data'
- ERROR = 'error'
- OK = 'ok'
- permitted_actions = <galaxy.util.bunch.Bunch object>
- file_path = '/tmp/'
- object_store = None
- engine = None
- __init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- sources: Mapped[List[DatasetSource]]
- hashes: Mapped[List[DatasetHash]]
- property is_new
Return True if placed into an objectstore not labeled as
private
.
- property quota_source_label
- property quota_source_info
- property device_source_label
- property device_source_info
- property extra_files_path
- property store_by
- property extra_files_path_name
- get_size(nice_size: typing_extensions.Literal[False], calculate_size: bool = True) int [source]
- get_size(nice_size: typing_extensions.Literal[True], calculate_size: bool = True) str
Returns the size of the data on disk
- set_size(no_extra_files=False)[source]
Sets the size of the data on disk.
If the caller is sure there are no extra files, pass no_extra_files as True to optimize subsequent calls to get_total_size or set_total_size - potentially avoiding both a database flush and check against the file system.
- property user_can_purge
- table = Table('dataset', MetaData(), Column('id', Integer(), table=<dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<dataset>), Column('create_time', DateTime(), table=<dataset>, default=CallableColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=CallableColumnDefault(<function datetime.utcnow>), default=CallableColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<dataset>), Column('deleted', Boolean(), table=<dataset>, default=ScalarElementColumnDefault(False)), Column('purged', Boolean(), table=<dataset>, default=ScalarElementColumnDefault(False)), Column('purgable', Boolean(), table=<dataset>, default=ScalarElementColumnDefault(True)), Column('object_store_id', TrimmedString(length=255), table=<dataset>), Column('external_filename', TEXT(), table=<dataset>), Column('_extra_files_path', TEXT(), table=<dataset>), Column('created_from_basename', TEXT(), table=<dataset>), Column('file_size', Numeric(precision=15, scale=0), table=<dataset>), Column('total_size', Numeric(precision=15, scale=0), table=<dataset>), Column('uuid', UUIDType(), table=<dataset>), schema=None)
- class galaxy.model.DatasetSource(**kwargs)[source]
Bases:
Base
,Dictifiable
,Serializable
- transform: Mapped[List[TransformAction] | None]
- hashes: Mapped[List[DatasetSourceHash]]
- dict_collection_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']
- dict_element_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']
- copy() DatasetSource [source]
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_source', MetaData(), Column('id', Integer(), table=<dataset_source>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_source>), Column('source_uri', TEXT(), table=<dataset_source>), Column('extra_files_path', TEXT(), table=<dataset_source>), Column('transform', MutableJSONType(), table=<dataset_source>), schema=None)
- class galaxy.model.DatasetSourceHash(**kwargs)[source]
Bases:
Base
,Serializable
- source: Mapped[DatasetSource | None]
- copy() DatasetSourceHash [source]
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_source_hash', MetaData(), Column('id', Integer(), table=<dataset_source_hash>, primary_key=True, nullable=False), Column('dataset_source_id', Integer(), ForeignKey('dataset_source.id'), table=<dataset_source_hash>), Column('hash_function', TEXT(), table=<dataset_source_hash>), Column('hash_value', TEXT(), table=<dataset_source_hash>), schema=None)
- class galaxy.model.DatasetHash(**kwargs)[source]
Bases:
Base
,Dictifiable
,Serializable
- dict_collection_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
- dict_element_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
- copy() DatasetHash [source]
- __init__(**kwargs)
A simple constructor that allows initialization from kwargs.
Sets attributes on the constructed instance using the names and values in
kwargs
.Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.
- table = Table('dataset_hash', MetaData(), Column('id', Integer(), table=<dataset_hash>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_hash>), Column('hash_function', TEXT(), table=<dataset_hash>), Column('hash_value', TEXT(), table=<dataset_hash>), Column('extra_files_path', TEXT(), table=<dataset_hash>), schema=None)
- class galaxy.model.DatasetInstance(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validated_state=DatasetValidatedState.UNKNOWN, validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True, metadata_deferred=False, creating_job_id=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None)[source]
Bases:
RepresentById
,UsesCreateAndUpdateTime
,object
A base class for all ‘dataset instances’, HDAs, LDAs, etc
- states
alias of
DatasetState
- class conversion_messages(value)
-
An enumeration.
- PENDING = 'pending'
- NO_DATA = 'no data'
- NO_CHROMOSOME = 'no chromosome'
- NO_CONVERTER = 'no converter'
- NO_TOOL = 'no tool'
- DATA = 'data'
- ERROR = 'error'
- OK = 'ok'
- permitted_actions = <galaxy.util.bunch.Bunch object>
- creating_job_associations: List[JobToOutputDatasetCollectionAssociation | JobToOutputDatasetAssociation]
- copied_from_history_dataset_association: HistoryDatasetAssociation | None
- copied_from_library_dataset_dataset_association: LibraryDatasetDatasetAssociation | None
- dependent_jobs: List[JobToInputLibraryDatasetAssociation]
- implicitly_converted_datasets: List[ImplicitlyConvertedDatasetAssociation]
- implicitly_converted_parent_datasets: List[ImplicitlyConvertedDatasetAssociation]
- validated_states
alias of
DatasetValidatedState
- __init__(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, <