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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.

galaxy.model.get_uuid(uuid: Optional[Union[UUID, str]] = None) → UUID

class galaxy.model.Base(**kwargs)

Bases: object

metadata = MetaData()

registry = <sqlalchemy.orm.decl_api.registry object>

__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.

class galaxy.model.RepresentById

Bases: object

id: int

exception galaxy.model.NoConverterException(value)

Bases: Exception

__init__(value)

exception galaxy.model.ConverterDependencyException(value)

Bases: Exception

__init__(value)

galaxy.model.set_datatypes_registry(d_registry)

Set up datatypes_registry

class galaxy.model.HasTags

Bases: object

dict_collection_visible_keys = ['tags']

dict_element_visible_keys = ['tags']

tags: List[ItemTagAssociation]

to_dict(*args, **kwargs)

make_tag_string_list()

copy_tags_from(target_user, source)

property auto_propagated_tags

class galaxy.model.SerializeFilesHandler(*args, **kwds)

Bases: Protocol

serialize_files(dataset: DatasetInstance, as_dict: Dict[str, Any]) → None

__init__(*args, **kwargs)

class galaxy.model.SerializationOptions(for_edit: bool, serialize_dataset_objects: Optional[bool] = None, serialize_files_handler: Optional[SerializeFilesHandler] = None, strip_metadata_files: Optional[bool] = None)

Bases: object

__init__(for_edit: bool, serialize_dataset_objects: Optional[bool] = None, serialize_files_handler: Optional[SerializeFilesHandler] = None, strip_metadata_files: Optional[bool] = None) → None

attach_identifier(id_encoder, obj, ret_val)

get_identifier(id_encoder, obj)

get_identifier_for_id(id_encoder, obj_id)

serialize_files(dataset, as_dict)

class galaxy.model.Serializable

Bases: RepresentById

serialize(id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False) → Dict[str, Any]

Serialize model for a re-population in (potentially) another Galaxy instance.

id: int

class galaxy.model.HasName

Bases: object

get_display_name()

These objects have a name attribute can be either a string or a unicode object. If string, convert to unicode object assuming ‘utf-8’ format.

class galaxy.model.UsesCreateAndUpdateTime

Bases: object

update_time: DateTime

property seconds_since_updated

property seconds_since_created

update()

class galaxy.model.WorkerProcess(**kwargs)

Bases: Base, UsesCreateAndUpdateTime

id

server_name

hostname

pid

update_time: DateTime

__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=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

galaxy.model.cached_id(galaxy_model_object)

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

Bases: object

MAX_NUMERIC = 9999999999999999999

add_metric(plugin, metric_name, metric_value)

property metrics

set_streams(tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None)

log_str()

property stdout

property stderr

galaxy.model.calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False)

Standalone function so can be reused for postgres directly in pgcleanup.py.

class galaxy.model.UserQuotaBasicUsage(*, quota_source_label: Optional[str] = None, total_disk_usage: float)

Bases: BaseModel

quota_source_label: Optional[str]

total_disk_usage: float

class galaxy.model.UserQuotaUsage(*, quota_source_label: Optional[str] = None, total_disk_usage: float, quota_percent: Optional[float] = None, quota_bytes: Optional[int] = None, quota: Optional[str] = None)

Bases: UserQuotaBasicUsage

quota_percent: Optional[float]

quota_bytes: Optional[int]

quota: Optional[str]

class galaxy.model.User(email=None, password=None, username=None)

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

id: int

create_time

update_time

last_password_change

form_values_id

preferred_object_store_id

disk_usage

activation_token

addresses

cloudauthz

custos_auth

default_permissions

groups

histories

active_histories

galaxy_sessions

quotas

quota_source_usages

social_auth

stored_workflow_menu_entries

values

api_keys: List[APIKeys]

data_manager_histories

roles

stored_workflows

all_notifications

non_private_roles

preferences: association_proxy = 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.

email

password

external

deleted

purged

active

username

property extra_preferences

set_password_cleartext(cleartext)

Set user password to the digest of cleartext.

set_random_password(length=16)

Sets user password to a random string of the given length. :return: void

check_password(cleartext)

Check if cleartext matches user password when hashed.

system_user_pwent(real_system_username)

Gives the system user pwent entry based on e-mail or username depending on the value in real_system_username

all_roles()

Return a unique list of Roles associated with this user or any of their groups.

all_roles_exploiting_cache()

get_disk_usage(nice_size=False, quota_source_label=None)

Return byte count of disk space used by user or a human-readable string if nice_size is True.

set_disk_usage(bytes)

Manually set the disk space used by a user to bytes.

property total_disk_usage

Return byte count of disk space used by user or a human-readable string if nice_size is True.

adjust_total_disk_usage(amount, quota_source_label)

get_oidc_tokens(provider_backend)

property nice_total_disk_usage

Return byte count of disk space used in a human-readable string.

calculate_disk_usage_default_source(object_store)

Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories assigned to default quota source.

calculate_and_set_disk_usage(object_store)

Calculates and sets user disk usage.

static user_template_environment(user)

>>> 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'

static expand_user_properties(user, in_string)

is_active()

is_authenticated()

attempt_create_private_role()

dictify_usage(object_store=None) → List[UserQuotaBasicUsage]

Include object_store to include empty/unused usage info.

dictify_usage_for(quota_source_label: Optional[str]) → UserQuotaBasicUsage

quota_source_usage_for(quota_source_label: Optional[str]) → Optional[UserQuotaSourceUsage]

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault(<function datetime.utcnow>)), Column('external', Boolean(), table=<galaxy_user>, default=ColumnDefault(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=ColumnDefault(False)), Column('purged', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_user>), Column('active', Boolean(), table=<galaxy_user>, nullable=False, default=ColumnDefault(True)), Column('activation_token', TrimmedString(length=64), table=<galaxy_user>), schema=None)

class galaxy.model.PasswordResetToken(user, token=None)

Bases: Base

user_id

__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.

token

user

expiration_time

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)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

tool_id

tool_version

tool_format

tool_path

tool_directory

value

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.

active

hidden

uuid

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dynamic_tool>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault(True)), Column('active', Boolean(), table=<dynamic_tool>, default=ColumnDefault(True)), Column('value', MutableJSONType(), table=<dynamic_tool>), schema=None)

class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)

Bases: Base

__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.

class galaxy.model.JobMetricText(plugin, metric_name, metric_value)

Bases: BaseJobMetric, RepresentById

id: int

job_id

plugin

metric_name

metric_value

__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)

Bases: BaseJobMetric, RepresentById

id: int

job_id

plugin

metric_name

metric_value

__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)

Bases: BaseJobMetric, RepresentById

id: int

task_id

plugin

metric_name

metric_value

__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)

Bases: BaseJobMetric, RepresentById

id: int

task_id

plugin

metric_name

metric_value

__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)

Bases: tuple

property inp_data

Alias for field number 0

property out_data

Alias for field number 1

property out_collections

Alias for field number 2

class galaxy.model.Job

Bases: Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable

A job represents a request to run a tool given input datasets, tool parameters, and output datasets.

id: int

create_time

update_time: DateTime

history_id

library_folder_id

tool_id

tool_version

galaxy_version

dynamic_tool_id

info

copied_from_job_id

command_line

job_messages

param_filename

runner_name

job_stdout

job_stderr

tool_stdout

tool_stderr

exit_code

traceback

session_id

user_id

job_runner_name

job_runner_external_id

destination_id

destination_params

object_store_id

params

handler

preferred_object_store_id

object_store_id_overrides

user

galaxy_session

history

library_folder

parameters

input_datasets

input_dataset_collections

input_dataset_collection_elements

output_dataset_collection_instances

output_dataset_collections

post_job_actions

input_library_datasets

output_library_datasets

external_output_metadata

tasks

output_datasets

state_history

text_metrics

numeric_metrics

interactivetool_entry_points

implicit_collection_jobs_association

container

data_manager_association

history_dataset_collection_associations

workflow_invocation_step

any_output_dataset_collection_instances_deleted: column_property

any_output_dataset_deleted: column_property

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']

states

alias of JobState

terminal_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>]

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.

dependencies

state

imported

property running

property finished

io_dicts(exclude_implicit_outputs=False) → IoDicts

get_external_output_metadata()

The external_output_metadata is currently a reference from Job to JobExternalOutputMetadata. It exists for a job but not a task.

get_session_id()

get_user_id()

get_tool_id()

get_tool_version()

get_command_line()

get_dependencies()

get_param_filename()

get_parameters()

get_copied_from_job_id()

get_input_datasets()

get_output_datasets()

get_input_library_datasets()

get_output_library_datasets()

get_state()

get_info()

get_job_runner_name()

get_job_runner_external_id()

get_post_job_actions()

get_imported()

get_handler()

get_params()

get_user()

get_tasks()

get_id_tag()

Return a tag that can be useful in identifying a Job. This returns the Job’s get_id

set_session_id(session_id)

set_user_id(user_id)

set_tool_id(tool_id)

get_user_email()

set_tool_version(tool_version)

set_command_line(command_line)

set_dependencies(dependencies)

set_param_filename(param_filename)

set_parameters(parameters)

set_copied_from_job_id(job_id)

set_input_datasets(input_datasets)

set_output_datasets(output_datasets)

set_input_library_datasets(input_library_datasets)

set_output_library_datasets(output_library_datasets)

set_info(info)

set_runner_name(job_runner_name)

get_job()

set_runner_external_id(job_runner_external_id)

set_post_job_actions(post_job_actions)

set_imported(imported)

set_handler(handler)

set_params(params)

add_parameter(name, value)

add_input_dataset(name, dataset=None, dataset_id=None)

add_output_dataset(name, dataset)

add_input_dataset_collection(name, dataset_collection)

add_input_dataset_collection_element(name, dataset_collection_element)

add_output_dataset_collection(name, dataset_collection_instance)

add_implicit_output_dataset_collection(name, dataset_collection)

add_input_library_dataset(name, dataset)

add_output_library_dataset(name, dataset)

add_post_job_action(pja)

property all_entry_points_configured

set_state(state)

Save state history

get_param_values(app, ignore_errors=False)

Read encoded parameter values from the database and turn back into a dict of tool parameter values.

raw_param_dict()

check_if_output_datasets_deleted()

Return true if all of the output datasets associated with this job are in the deleted state

mark_stopped(track_jobs_in_database=False)

Mark this job as stopped

mark_deleted(track_jobs_in_database=False)

Mark this job as deleted, and mark any output datasets as discarded.

mark_failed(info='Job execution failed', blurb=None, peek=None)

Mark this job as failed, and mark any output datasets as errored.

resume(flush=True)

requires_shareable_storage(security_agent)

to_dict(view='collection', system_details=False)

Return item dictionary.

update_hdca_update_time_for_job(update_time, sa_session, supports_skip_locked)

set_final_state(final_state, supports_skip_locked)

get_destination_configuration(dest_params, config, key, default=None)

Get a destination parameter that can be defaulted back in specified config if it needs to be applied globally.

property command_version

update_output_states(supports_skip_locked)

remappable()

Check whether job is remappable when rerun

hide_outputs(flush=True)

table = Table('job', MetaData(), Column('id', Integer(), table=<job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault('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=ColumnDefault(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)

Bases: Base, JobLike, RepresentById

A task represents a single component of a job.

id: int

create_time

execution_time

update_time

command_line

param_filename

runner_name

job_stdout

job_stderr

tool_stdout

tool_stderr

exit_code

job_messages

info

traceback

job_id

task_runner_name

task_runner_external_id

text_metrics

numeric_metrics

class states(value)

Bases: str, Enum

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.

state

working_directory

job

prepare_input_files_cmd

get_param_values(app)

Read encoded parameter values from the database and turn back into a dict of tool parameter values.

get_id_tag()

Return an id tag suitable for identifying the task. This combines the task’s job id and the task’s own id.

get_command_line()

get_parameters()

get_state()

get_info()

get_working_directory()

get_task_runner_name()

get_task_runner_external_id()

get_job()

get_prepare_input_files_cmd()

get_external_output_metadata()

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()

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()

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.

get_session_id()

set_id(id)

set_command_line(command_line)

set_parameters(parameters)

set_state(state)

set_info(info)

set_working_directory(working_directory)

set_task_runner_name(task_runner_name)

set_job_runner_external_id(task_runner_external_id)

set_task_runner_external_id(task_runner_external_id)

set_job(job)

set_prepare_input_files_cmd(prepare_input_files_cmd)

table = Table('task', MetaData(), Column('id', Integer(), table=<task>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<task>, default=ColumnDefault(<function datetime.utcnow>)), Column('execution_time', DateTime(), table=<task>), Column('update_time', DateTime(), table=<task>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

job_id

__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.

name

value

copy()

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)

Bases: Base, RepresentById

id: int

job_id

dataset_id

job

__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.

name

dataset

dataset_version

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)

Bases: Base, RepresentById

id: int

job_id

dataset_id

job

__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.

name

dataset

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)

Bases: Base, RepresentById

id: int

job_id

dataset_collection_id

job

__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.

name

dataset_collection

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)

Bases: Base, RepresentById

id: int

job_id

dataset_collection_element_id

job

__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.

name

dataset_collection_element

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)

Bases: Base, RepresentById

id: int

job_id

dataset_collection_id

job

__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.

name

dataset_collection_instance

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)

Bases: Base, RepresentById

id: int

job_id

dataset_collection_id

job

__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.

name

dataset_collection

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)

Bases: Base, RepresentById

id: int

job_id

ldda_id

job

__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.

name

dataset

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)

Bases: Base, RepresentById

id: int

job_id

ldda_id

job

__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.

name

dataset

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)

Bases: Base, RepresentById

id: int

create_time

__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.

job_id

state

info

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=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

dataset_collection_id

input_dataset_collection_id

__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.

name

input_dataset_collection

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)

Bases: Base, Serializable

id: int

jobs

class populated_states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

OK = 'ok'

FAILED = 'failed'

__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.

populated_state

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=ColumnDefault('new')), schema=None)

class galaxy.model.ImplicitCollectionJobsJobAssociation(**kwargs)

Bases: Base, RepresentById

id: int

implicit_collection_jobs_id

job_id

order_index

implicit_collection_jobs

job

__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)

Bases: Base, RepresentById

id: int

workflow_step_id

__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.

action_type

output_name

action_arguments

workflow_step

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)

Bases: Base, RepresentById

id: int

post_job_action_id

__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.

job

job_id

post_job_action

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)

Bases: Base, RepresentById

id: int

job_id

history_dataset_association_id

library_dataset_dataset_association_id

is_valid

filename_in

filename_out

filename_results_code

filename_kwds

filename_override_metadata

job_runner_external_pid

__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.

job

history_dataset_association

library_dataset_dataset_association

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=ColumnDefault(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)

Bases: object

fake_dataset_association = True

__init__(dataset=None)

class galaxy.model.JobExportHistoryArchive(compressed=False, **kwd)

Bases: Base, RepresentById

id: int

job_id

history_id

dataset_id

history_attrs_filename

job

dataset

history

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.

compressed

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

static create_for_history(history, job, sa_session, object_store, compressed)

to_dict()

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=ColumnDefault(False)), Column('history_attrs_filename', TEXT(), table=<job_export_history_archive>), schema=None)

class galaxy.model.JobImportHistoryArchive(**kwargs)

Bases: Base, RepresentById

id: int

job_id

history_id

archive_dir

job

history

__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)

Bases: Base, RepresentById

id: int

task_uuid

create_time

object_type

object_id

export_metadata

__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=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

job_id

container_type

container_name

created_time

modified_time

job

__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.

container_info

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=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<job_container_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.InteractiveToolEntryPoint(requires_domain=True, configured=False, deleted=False, short_token=False, **kwd)

Bases: Base, Dictifiable, RepresentById

id: int

job_id

name

tool_port

host

port

protocol

entry_url

created_time

modified_time

job

dict_collection_visible_keys = ['id', 'job_id', 'name', 'active', 'created_time', 'modified_time', 'output_datasets_ids']

dict_element_visible_keys = ['id', 'job_id', 'name', 'active', 'created_time', 'modified_time', 'output_datasets_ids']

__init__(requires_domain=True, configured=False, deleted=False, short_token=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.

requires_domain

configured

deleted

token

info

property active

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=ColumnDefault(True)), Column('info', MutableJSONType(), table=<interactivetool_entry_point>), Column('configured', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('created_time', DateTime(), table=<interactivetool_entry_point>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<interactivetool_entry_point>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.GenomeIndexToolData(**kwargs)

Bases: Base, RepresentById

id: int

job_id

dataset_id

fasta_path

created_time

modified_time

indexer

user_id

job

dataset

user

__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=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<genome_index_tool_data>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

quotas

roles

users

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.

name

deleted

table = Table('galaxy_group', MetaData(), Column('id', Integer(), table=<galaxy_group>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_group>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<galaxy_group>), Column('deleted', Boolean(), table=<galaxy_group>, default=ColumnDefault(False)), schema=None)

class galaxy.model.UserGroupAssociation(user, group)

Bases: Base, RepresentById

id: int

user_id

group_id

create_time

update_time

__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.

user

group

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.Notification(source, category, variant, content)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

publication_time

expiration_time

user_notification_associations

__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.

source

category

variant

content

table = Table('notification', MetaData(), Column('id', Integer(), table=<notification>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<notification>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('publication_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('expiration_time', DateTime(), table=<notification>, default=ColumnDefault(datetime.datetime(2025, 3, 26, 16, 7, 9, 457437))), Column('source', String(length=32), table=<notification>), Column('category', String(length=64), table=<notification>), Column('variant', String(length=16), table=<notification>), Column('content', DoubleEncodedJsonType(), table=<notification>), schema=None)

class galaxy.model.UserNotificationAssociation(user, notification)

Bases: Base, RepresentById

id: int

user_id

notification_id

seen_time

deleted

update_time

__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.

user

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=ColumnDefault(False)), Column('update_time', DateTime(), table=<user_notification_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

galaxy.model.is_hda(d)

class galaxy.model.HistoryAudit(*args, **kwargs)

Bases: Base, RepresentById

history_id

update_time

__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.

classmethod prune(sa_session)

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=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.History(id=None, name=None, user=None)

Bases: Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable

create_time

user_id

hid_counter

genome_build

importable

slug

preferred_object_store_id

archived

archive_export_id

datasets

exports

active_datasets

dataset_collections

active_dataset_collections

visible_datasets

visible_dataset_collections

tags: List[ItemTagAssociation]

annotations

ratings

default_permissions

users_shared_with

galaxy_sessions

workflow_invocations

jobs

update_time

users_shared_with_count: column_property

average_rating: column_property

users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']

dict_element_visible_keys = ['id', 'name', 'genome_build', 'deleted', 'purged', 'archived', 'update_time', 'published', 'importable', 'slug', 'empty', 'preferred_object_store_id']

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.

id: int

name

deleted

purged

importing

published

user

init_on_load()

stage_addition(items)

property empty

property count

add_pending_items(set_output_hid=True)

add_galaxy_session(galaxy_session, association=None)

add_dataset(dataset, parent_id=None, genome_build=None, set_hid=True, quota=True)

add_datasets(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)

Optimized version of add_dataset above that minimizes database interactions when adding many datasets and collections to history at once.

add_dataset_collection(history_dataset_collection, set_hid=True)

copy(name=None, target_user=None, activatable=False, all_datasets=False)

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.

get_dataset_by_hid(hid)

property has_possible_members

property activatable_datasets

to_dict(view='collection', value_mapper=None)

Return item dictionary.

property latest_export

unhide_datasets()

resume_paused_jobs()

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_dataset_and_roles_query

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.

contents_iter(**kwds)

Fetch filtered list of contents of history.

table = Table('history', MetaData(), Column('id', Integer(), table=<history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault(1)), Column('deleted', Boolean(), table=<history>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<history>, default=ColumnDefault(False)), Column('importing', Boolean(), table=<history>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<history>), Column('importable', Boolean(), table=<history>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<history>), Column('published', Boolean(), table=<history>, default=ColumnDefault(False)), Column('preferred_object_store_id', String(length=255), table=<history>), Column('archived', Boolean(), table=<history>, default=ColumnDefault(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)

class galaxy.model.UserShareAssociation

Bases: RepresentById

user: Optional[User]

class galaxy.model.HistoryUserShareAssociation(**kwargs)

Bases: Base, UserShareAssociation

id: int

history_id

user_id

user: Optional[User]

history

__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('history_user_share_association', MetaData(), Column('id', Integer(), table=<history_user_share_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_user_share_association>), schema=None)

class galaxy.model.UserRoleAssociation(user, role)

Bases: Base, RepresentById

id: int

user_id

role_id

create_time

update_time

__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.

user

role

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.GroupRoleAssociation(group, role)

Bases: Base, RepresentById

id: int

group_id

role_id

create_time

update_time

__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.

group

role

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.Role(name=None, description=None, type=types.SYSTEM, deleted=False)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

dataset_actions

groups

users

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'description', 'type']

private_id = None

class types(value)

Bases: str, Enum

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.

name

description

type

deleted

table = Table('role', MetaData(), Column('id', Integer(), table=<role>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<role>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault(False)), schema=None)

class galaxy.model.UserQuotaSourceUsage(**kwargs)

Bases: Base, Dictifiable, RepresentById

dict_element_visible_keys = ['disk_usage', 'quota_source_label']

id: int

user_id

quota_source_label

disk_usage

user

__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=ColumnDefault(0)), schema=None)

class galaxy.model.UserQuotaAssociation(user, quota)

Bases: Base, Dictifiable, RepresentById

id: int

user_id

quota_id

create_time

update_time

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.

user

quota

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.GroupQuotaAssociation(group, quota)

Bases: Base, Dictifiable, RepresentById

id: int

group_id

quota_id

create_time

update_time

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.

group

quota

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.Quota(name=None, description=None, amount=0, operation='=', quota_source_label=None)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

deleted

default

groups

users

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.

name

description

bytes

operation

quota_source_label

get_amount()

set_amount(amount)

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<quota>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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=ColumnDefault(False)), Column('quota_source_label', String(length=32), table=<quota>), schema=None)

class galaxy.model.DefaultQuotaAssociation(type, quota)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

quota_id

dict_element_visible_keys = ['type']

class types(value)

Bases: str, Enum

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.

type

quota

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<default_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

create_time

update_time

dataset_id

__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.

action

dataset

role

role_id

table = Table('dataset_permissions', MetaData(), Column('id', Integer(), table=<dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

create_time

update_time

library_id

role_id

__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.

action

library

role

table = Table('library_permissions', MetaData(), Column('id', Integer(), table=<library_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

create_time

update_time

library_folder_id

role_id

__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.

action

folder

role

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

create_time

update_time

library_dataset_id

role_id

__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.

action

library_dataset

role

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

create_time

update_time

library_dataset_dataset_association_id

role_id

__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.

action

library_dataset_dataset_association

role

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<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)

Bases: Base, RepresentById

id: int

user_id

role_id

__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.

user

action

role

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)

Bases: Base, RepresentById

id: int

history_id

role_id

__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.

history

action

role

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.StorableObject

Bases: object

flush()

class galaxy.model.Dataset(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)

Bases: Base, StorableObject, Serializable

job_id

create_time

update_time

object_store_id

created_from_basename

total_size

actions

job

active_history_associations

purged_history_associations

active_library_associations

history_associations

library_associations

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.OK: 'ok'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.ERROR: 'error'>, <DatasetState.DEFERRED: 'deferred'>)

valid_input_states = (<DatasetState.UPLOAD: 'upload'>, <DatasetState.OK: 'ok'>, <DatasetState.NEW: 'new'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.RUNNING: 'running'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>, <DatasetState.DEFERRED: 'deferred'>)

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)

Bases: str, Enum

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: Optional[ObjectStore] = 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.

id: int

uuid

state

deleted

purged

purgable

external_filename

file_size

sources

hashes

property is_new

in_ready_state()

property shareable

Return True if placed into an objectstore not labeled as private.

ensure_shareable()

get_file_name()

property quota_source_label

property quota_source_info

set_file_name(filename)

property file_name

get_extra_files_path()

create_extra_files_path()

set_extra_files_path(extra_files_path)

property extra_files_path

extra_files_path_exists()

property store_by

extra_files_path_name_from(object_store)

property extra_files_path_name

get_size(nice_size: typing_extensions.Literal[False], calculate_size: bool = True) → int

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)

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.

get_total_size()

set_total_size()

has_data()

Detects whether there is any data

mark_deleted()

property user_can_purge

full_delete()

Remove the file and extra files, marks deleted and purged

get_access_roles(security_agent)

get_manage_permissions_roles(security_agent)

has_manage_permissions_roles(security_agent)

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=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<dataset>), Column('deleted', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purgable', Boolean(), table=<dataset>, default=ColumnDefault(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)

Bases: Base, Dictifiable, Serializable

id: int

dataset_id

source_uri

extra_files_path

transform

dataset

hashes

dict_collection_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']

dict_element_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']

copy() → DatasetSource

__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)

Bases: Base, Serializable

id: int

dataset_source_id

hash_function

hash_value

source

copy() → DatasetSourceHash

__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)

Bases: Base, Dictifiable, Serializable

id: int

dataset_id

hash_function

hash_value

extra_files_path

dataset

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

__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)

galaxy.model.datatype_for_extension(extension, datatypes_registry=None) → Data

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)

Bases: UsesCreateAndUpdateTime, object

A base class for all ‘dataset instances’, HDAs, LDAs, etc

states

alias of DatasetState

class conversion_messages(value)

Bases: str, Enum

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>

purged: bool

creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]

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, 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)

property peek

property ext

property has_deferred_data

get_dataset_state()

raw_set_dataset_state(state)

set_dataset_state(state)

property state

get_file_name() → str

set_file_name(filename: str)

property file_name: str

link_to(path)

property extra_files_path

extra_files_path_exists()

property datatype: Data

get_metadata()

property set_metadata_requires_flush

set_metadata(bunch)

property metadata

property has_metadata_files

property metadata_file_types

get_metadata_file_paths_and_extensions() → List[Tuple[str, str]]

get_dbkey()

set_dbkey(value)

property dbkey

ok_to_edit_metadata()

change_datatype(new_ext)

get_size(nice_size=False, calculate_size=True)

Returns the size of the data on disk

set_size(**kwds)

Sets and gets the size of the data on disk

get_total_size()

set_total_size()

has_data()

Detects whether there is any data

get_created_from_basename()

set_created_from_basename(created_from_basename)

property created_from_basename

property sources

property hashes

get_mime()

Returns the mime type of the data

set_peek(**kwd)

init_meta(copy_from=None)

set_meta(**kwd)

missing_meta(**kwd)

as_display_type(type, **kwd)

display_peek()

display_name()

display_info()

get_converted_files_by_type(file_type)

get_converted_dataset_deps(trans, target_ext)

Returns dict of { “dependency” => HDA }

get_converted_dataset(trans, target_ext, target_context=None, history=None)

Return converted dataset(s) if they exist, along with a dict of dependencies. If not converted yet, do so and return None (the first time). If unconvertible, raise exception.

copy_attributes(new_dataset)

Copies attributes to a new datasets, used for implicit conversions

get_metadata_dataset(dataset_ext)

Returns an HDA that points to a metadata file which contains a converted data with the requested extension.

clear_associated_files(metadata_safe=False, purge=False)

get_converter_types()

can_convert_to(format)

find_conversion_destination(accepted_formats: List[str], **kwd) → Tuple[bool, Optional[str], Optional[DatasetInstance]]

Returns ( target_ext, existing converted dataset )

add_validation_error(validation_error)

extend_validation_errors(validation_errors)

mark_deleted()

mark_undeleted()

mark_unhidden()

undeletable()

property is_ok

property is_pending

Return true if the dataset is neither ready nor in error

property source_library_dataset

property source_dataset_chain

property creating_job

get_display_applications(trans)

get_datasources(trans)

Returns datasources for dataset; if datasources are not available due to indexing, indexing is started. Return value is a dictionary with entries of type (<datasource_type> : {<datasource_name>, <indexing_message>}).

convert_dataset(trans, target_type)

Converts a dataset to the target_type and returns a message indicating status of the conversion. None is returned to indicate that dataset was converted successfully.

class galaxy.model.HistoryDatasetAssociation(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)

Bases: DatasetInstance, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable

Resource class that creates a relation between a dataset and a user history.

__init__(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)

Create a a new HDA and associate it with the given history.

hid

history

copied_from_history_dataset_association

copied_from_library_dataset_dataset_association

property user

copy_from(other_hda, new_dataset=None, include_tags=True, include_metadata=False)

copy(parent_id=None, copy_tags=None, flush=True, copy_hid=True, new_name=None)

Create a copy of this HDA.

copy_tags_to(copy_tags=None)

copy_attributes(new_dataset)

Copies attributes to a new datasets, used for implicit conversions

to_library_dataset_dataset_association(trans, target_folder, replace_dataset=None, parent_id=None, roles=None, ldda_message='', element_identifier=None)

Copy this HDA to a library optionally replacing an existing LDDA.

clear_associated_files(metadata_safe=False, purge=False)

get_access_roles(security_agent)

Return The access roles associated with this HDA’s dataset.

purge_usage_from_quota(user, quota_source_info)

Remove this HDA’s quota_amount from user’s quota.

quota_amount(user)

Return the disk space used for this HDA relevant to user quotas.

If the user has multiple instances of this dataset, it will not affect their disk usage statistic.

to_dict(view='collection', expose_dataset_path=False)

Return attributes of this HDA that are exposed using the API.

unpause_dependent_jobs(jobs=None)

property history_content_type

content_type = 'dataset'

type_id

annotations

blurb

copied_from_history_dataset_association_id

copied_from_library_dataset_dataset_association_id

copied_to_history_dataset_associations

copied_to_library_dataset_dataset_associations

create_time

creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]

dataset

dataset_id

deleted

dependent_jobs

designation

extended_metadata

extended_metadata_id

extension

hidden_beneath_collection_instance

hidden_beneath_collection_instance_id

history_id

id: int

implicitly_converted_datasets

implicitly_converted_parent_datasets

info

metadata_deferred

name

parent_id

purged: bool

ratings

table = Table('history_dataset_association', MetaData(), Column('id', Integer(), table=<history_dataset_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<history_dataset_association>), Column('create_time', DateTime(), table=<history_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<history_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<history_dataset_association>), Column('name', TrimmedString(length=255), table=<history_dataset_association>), Column('info', TrimmedString(length=255), table=<history_dataset_association>), Column('blurb', TrimmedString(length=255), table=<history_dataset_association>), Column('peek', TEXT(), table=<history_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<history_dataset_association>), Column('extension', TrimmedString(length=64), table=<history_dataset_association>), Column('metadata', MetadataType(), table=<history_dataset_association>, key='_metadata'), Column('metadata_deferred', Boolean(), table=<history_dataset_association>), Column('parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('designation', TrimmedString(length=255), table=<history_dataset_association>), Column('deleted', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('visible', Boolean(), table=<history_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association>), Column('version', Integer(), table=<history_dataset_association>, default=ColumnDefault(1)), Column('hid', Integer(), table=<history_dataset_association>), Column('purged', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<history_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<history_dataset_association>), Column('hidden_beneath_collection_instance_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_association>), schema=None)

tags: List[ItemTagAssociation]

tool_version

update_time: DateTime

validated_state

validated_state_message

version

visible

class galaxy.model.HistoryDatasetAssociationHistory(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)

Bases: Base, Serializable

id: int

__init__(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)

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_id

name

update_time

version

extension

extended_metadata_id

table = Table('history_dataset_association_history', MetaData(), Column('id', Integer(), table=<history_dataset_association_history>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_history>), Column('update_time', DateTime(), table=<history_dataset_association_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('version', Integer(), table=<history_dataset_association_history>), Column('name', TrimmedString(length=255), table=<history_dataset_association_history>), Column('extension', TrimmedString(length=64), table=<history_dataset_association_history>), Column('metadata', MetadataType(), table=<history_dataset_association_history>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association_history>), schema=None)

class galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization(hda=None, user=None, site=None)

Bases: Base, RepresentById

id: int

create_time

update_time

history_dataset_association_id

user_id

__init__(hda=None, user=None, site=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

user

site

table = Table('history_dataset_association_display_at_authorization', MetaData(), Column('id', Integer(), table=<history_dataset_association_display_at_authorization>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history_dataset_association_display_at_authorization>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association_display_at_authorization>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_display_at_authorization>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_display_at_authorization>), Column('site', TrimmedString(length=255), table=<history_dataset_association_display_at_authorization>), schema=None)

class galaxy.model.HistoryDatasetAssociationSubset(hda, subset, location)

Bases: Base, RepresentById

id: int

history_dataset_association_id

history_dataset_association_subset_id

__init__(hda, subset, location)

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.

hda

subset

location

table = Table('history_dataset_association_subset', MetaData(), Column('id', Integer(), table=<history_dataset_association_subset>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('history_dataset_association_subset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('location', Unicode(length=255), table=<history_dataset_association_subset>), schema=None)

class galaxy.model.Library(name=None, description=None, synopsis=None, root_folder=None)

Bases: Base, Dictifiable, HasName, Serializable

id: int

root_folder_id

create_time

update_time

deleted

purged

actions

permitted_actions = <galaxy.util.bunch.Bunch object>

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time']

__init__(name=None, description=None, synopsis=None, root_folder=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.

name

description

synopsis

root_folder

to_dict(view='collection', value_mapper=None)

We prepend an F to folders.

get_active_folders(folder, folders=None)

get_access_roles(security_agent)

table = Table('library', MetaData(), Column('id', Integer(), table=<library>, primary_key=True, nullable=False), Column('root_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library>), Column('create_time', DateTime(), table=<library>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<library>), Column('deleted', Boolean(), table=<library>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library>, default=ColumnDefault(False)), Column('description', TEXT(), table=<library>), Column('synopsis', TEXT(), table=<library>), schema=None)

class galaxy.model.LibraryFolder(name=None, description=None, item_count=0, order_id=None, genome_build=None)

Bases: Base, Dictifiable, HasName, Serializable

id: int

parent_id

create_time

update_time

deleted

purged

folders

parent

active_folders

datasets

active_datasets

library_root

actions

dict_element_visible_keys = ['id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted']

__init__(name=None, description=None, item_count=0, order_id=None, genome_build=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.

name

description

item_count

order_id

genome_build

add_library_dataset(library_dataset, genome_build=None)

add_folder(folder)

property activatable_library_datasets

to_dict(view='collection', value_mapper=None)

Return item dictionary.

property library_path

property parent_library

table = Table('library_folder', MetaData(), Column('id', Integer(), table=<library_folder>, primary_key=True, nullable=False), Column('parent_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder>), Column('create_time', DateTime(), table=<library_folder>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TEXT(), table=<library_folder>), Column('description', TEXT(), table=<library_folder>), Column('order_id', Integer(), table=<library_folder>), Column('item_count', Integer(), table=<library_folder>), Column('deleted', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<library_folder>), schema=None)

class galaxy.model.LibraryDataset(**kwargs)

Bases: Base, Serializable

id: int

library_dataset_dataset_association_id

folder_id

order_id

create_time

update_time

deleted

purged

folder

library_dataset_dataset_association

expired_datasets

actions

upload_options = [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]

get_info()

set_info(info)

property info

get_name()

set_name(name)

property name

display_name()

to_dict(view='collection')

__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('library_dataset', MetaData(), Column('id', Integer(), table=<library_dataset>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset>), Column('order_id', Integer(), table=<library_dataset>), Column('create_time', DateTime(), table=<library_dataset>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TrimmedString(length=255), table=<library_dataset>), Column('info', TrimmedString(length=255), table=<library_dataset>), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)

class galaxy.model.LibraryDatasetDatasetAssociation(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)

Bases: DatasetInstance, HasName, Serializable

__init__(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)

copied_from_history_dataset_association_id

copied_from_library_dataset_dataset_association_id

library_dataset

user

to_history_dataset_association(target_history, parent_id=None, add_to_history=False, visible=None)

copy(parent_id=None, target_folder=None, flush=True)

clear_associated_files(metadata_safe=False, purge=False)

get_access_roles(security_agent)

get_manage_permissions_roles(security_agent)

has_manage_permissions_roles(security_agent)

to_dict(view='collection')

update_parent_folder_update_times()

actions

blurb

copied_from_history_dataset_association

copied_from_library_dataset_dataset_association

copied_to_history_dataset_associations

copied_to_library_dataset_dataset_associations

create_time

creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]]

dataset

dataset_id

deleted

dependent_jobs

designation

extended_metadata

extended_metadata_id

extension

id: int

implicitly_converted_datasets

implicitly_converted_parent_datasets

info

library_dataset_id

message

metadata_deferred

name

parent_id

table = Table('library_dataset_dataset_association', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_association>, primary_key=True, nullable=False), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<library_dataset_dataset_association>), Column('create_time', DateTime(), table=<library_dataset_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<library_dataset_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<library_dataset_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('name', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('info', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('blurb', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('peek', TEXT(), table=<library_dataset_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<library_dataset_dataset_association>), Column('extension', TrimmedString(length=64), table=<library_dataset_dataset_association>), Column('metadata', MetadataType(), table=<library_dataset_dataset_association>, key='_metadata'), Column('metadata_deferred', Boolean(), table=<library_dataset_dataset_association>), Column('parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('designation', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<library_dataset_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<library_dataset_dataset_association>), Column('visible', Boolean(), table=<library_dataset_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<library_dataset_dataset_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association>), Column('message', TrimmedString(length=255), table=<library_dataset_dataset_association>), schema=None)

tags

tool_version

update_time: DateTime

user_id

validated_state

validated_state_message

visible

purged: bool

class galaxy.model.ExtendedMetadata(data)

Bases: Base, RepresentById

id: int

children

__init__(data)

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.

data

table = Table('extended_metadata', MetaData(), Column('id', Integer(), table=<extended_metadata>, primary_key=True, nullable=False), Column('data', MutableJSONType(), table=<extended_metadata>), schema=None)

class galaxy.model.ExtendedMetadataIndex(extended_metadata, path, value)

Bases: Base, RepresentById

id: int

extended_metadata_id

__init__(extended_metadata, path, 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.

extended_metadata

path

value

table = Table('extended_metadata_index', MetaData(), Column('id', Integer(), table=<extended_metadata_index>, primary_key=True, nullable=False), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<extended_metadata_index>), Column('path', String(length=255), table=<extended_metadata_index>), Column('value', TEXT(), table=<extended_metadata_index>), schema=None)

class galaxy.model.LibraryInfoAssociation(library, form_definition, info, inheritable=False)

Bases: Base, RepresentById

id: int

library_id

form_definition_id

form_values_id

deleted

__init__(library, form_definition, info, inheritable=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.

library

template

info

inheritable

table = Table('library_info_association', MetaData(), Column('id', Integer(), table=<library_info_association>, primary_key=True, nullable=False), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_info_association>), Column('inheritable', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), schema=None)

class galaxy.model.LibraryFolderInfoAssociation(folder, form_definition, info, inheritable=False)

Bases: Base, RepresentById

id: int

library_folder_id

form_definition_id

form_values_id

deleted

__init__(folder, form_definition, info, inheritable=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.

folder

template

info

inheritable

table = Table('library_folder_info_association', MetaData(), Column('id', Integer(), table=<library_folder_info_association>, primary_key=True, nullable=False), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_folder_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_folder_info_association>), Column('inheritable', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), schema=None)

class galaxy.model.LibraryDatasetDatasetInfoAssociation(library_dataset_dataset_association, form_definition, info)

Bases: Base, RepresentById

id: int

library_dataset_dataset_association_id

form_definition_id

form_values_id

deleted

__init__(library_dataset_dataset_association, form_definition, info)

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

template

info

property inheritable

table = Table('library_dataset_dataset_info_association', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_info_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_dataset_dataset_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_dataset_dataset_info_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_info_association>, default=ColumnDefault(False)), schema=None)

class galaxy.model.ImplicitlyConvertedDatasetAssociation(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)

Bases: Base, RepresentById

create_time

update_time

hda_id

ldda_id

hda_parent_id

ldda_parent_id

__init__(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True)

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.

id: int

dataset

dataset_ldda

parent_hda

parent_ldda

type

deleted

metadata_safe

clear(purge=False, delete_dataset=True)

table = Table('implicitly_converted_dataset_association', MetaData(), Column('id', Integer(), table=<implicitly_converted_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<implicitly_converted_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('hda_parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('deleted', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(False)), Column('metadata_safe', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(True)), Column('type', TrimmedString(length=255), table=<implicitly_converted_dataset_association>), schema=None)

class galaxy.model.InnerCollectionFilter(column, operator_function, expected_value)

Bases: tuple

property column

Alias for field number 0

property operator_function

Alias for field number 1

property expected_value

Alias for field number 2

produce_filter(table)

class galaxy.model.DatasetCollection(id=None, collection_type=None, populated=True, element_count=None)

Bases: Base, Dictifiable, UsesAnnotations, Serializable

populated_state_message

create_time

update_time

elements

dict_collection_visible_keys = ['id', 'collection_type']

dict_element_visible_keys = ['id', 'collection_type']

populated_states

alias of DatasetCollectionPopulatedState

__init__(id=None, collection_type=None, populated=True, element_count=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.

id: int

collection_type

populated_state

element_count

property dataset_states_and_extensions_summary

property has_deferred_data

property populated_optimized

property populated

property dataset_action_tuples

property element_identifiers_extensions_and_paths

property element_identifiers_extensions_paths_and_metadata_files: List[List[Any]]

property waiting_for_elements

mark_as_populated()

handle_population_failed(message)

finalize(collection_type_description)

property dataset_instances

property dataset_elements

dataset_elements_and_identifiers(identifiers=None)

property first_dataset_element

property state

validate()

copy(destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)

replace_failed_elements(replacements)

set_from_dict(new_data)

property has_subcollections

table = Table('dataset_collection', MetaData(), Column('id', Integer(), table=<dataset_collection>, primary_key=True, nullable=False), Column('collection_type', Unicode(length=255), table=<dataset_collection>, nullable=False), Column('populated_state', TrimmedString(length=64), table=<dataset_collection>, nullable=False, default=ColumnDefault('ok')), Column('populated_state_message', TEXT(), table=<dataset_collection>), Column('element_count', Integer(), table=<dataset_collection>), Column('create_time', DateTime(), table=<dataset_collection>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_collection>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.DatasetCollectionInstance

Bases: HasName, UsesCreateAndUpdateTime

property state

property populated

property dataset_instances

display_name()

set_from_dict(new_data)

Set object attributes to the values in dictionary new_data limiting to only those keys in dict_element_visible_keys.

Returns a dictionary of the keys, values that have been changed.

property has_deferred_data

update_time: DateTime

class galaxy.model.HistoryDatasetCollectionAssociation(deleted=False, visible=True, **kwd)

Bases: Base, DatasetCollectionInstance, HasTags, Dictifiable, UsesAnnotations, Serializable

Associates a DatasetCollection with a History.

id: int

collection_id

history_id

name

hid

copied_from_history_dataset_collection_association_id

implicit_output_name

job_id

implicit_collection_jobs_id

create_time

update_time: DateTime

collection

history

copied_from_history_dataset_collection_association

copied_to_history_dataset_collection_association

implicit_collection_jobs

job

tags: List[ItemTagAssociation]

annotations

ratings

creating_job_associations

dict_dbkeysandextensions_visible_keys = ['dbkeys', 'extensions']

editable_keys = ('name', 'deleted', 'visible')

__init__(deleted=False, visible=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.

deleted

visible

implicit_input_collections

property history_content_type

content_type = 'dataset_collection'

type_id

property job_source_type

property job_state_summary

Aggregate counts of jobs by state, stored in a JobStateSummary object.

property job_state_summary_dict

property dataset_dbkeys_and_extensions_summary

property job_source_id

touch()

to_hda_representative(multiple=False)

to_dict(view='collection')

Return item dictionary.

add_implicit_input_collection(name, history_dataset_collection)

find_implicit_input_collection(name)

copy(element_destination=None, dataset_instance_attributes=None, flush=True, set_hid=True, minimize_copies=False)

Create a copy of this history dataset collection association. Copy underlying collection.

property waiting_for_elements

contains_collection(collection_id)

Checks to see that the indicated collection is a member of the hdca by using a recursive CTE sql query to find the collection’s parents and checking to see if any of the parents are associated with this hdca

table = Table('history_dataset_collection_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<history_dataset_collection_association>), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<history_dataset_collection_association>), Column('hid', Integer(), table=<history_dataset_collection_association>), Column('visible', Boolean(), table=<history_dataset_collection_association>), Column('deleted', Boolean(), table=<history_dataset_collection_association>, default=ColumnDefault(False)), Column('copied_from_history_dataset_collection_association_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_association>), Column('implicit_output_name', Unicode(length=255), table=<history_dataset_collection_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<history_dataset_collection_association>), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<history_dataset_collection_association>), Column('create_time', DateTime(), table=<history_dataset_collection_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_collection_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.LibraryDatasetCollectionAssociation(deleted=False, **kwd)

Bases: Base, DatasetCollectionInstance, RepresentById

Associates a DatasetCollection with a library folder.

id: int

collection_id

folder_id

name

collection

folder

tags

annotations

ratings

editable_keys = ('name', 'deleted')

__init__(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.

deleted

to_dict(view='collection')

table = Table('library_dataset_collection_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<library_dataset_collection_association>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<library_dataset_collection_association>), Column('deleted', Boolean(), table=<library_dataset_collection_association>, default=ColumnDefault(False)), schema=None)

class galaxy.model.DatasetCollectionElement(id=None, collection=None, element=None, element_index=None, element_identifier=None)

Bases: Base, Dictifiable, Serializable

Associates a DatasetInstance (hda or ldda) with a DatasetCollection.

dataset_collection_id

hda_id

ldda_id

child_collection_id

dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']

dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']

UNINITIALIZED_ELEMENT = <object object>

__init__(id=None, collection=None, element=None, element_index=None, element_identifier=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.

hda

ldda

child_collection

id: int

collection

element_index

element_identifier

property element_type

property is_collection

property element_object

property dataset_instance

property dataset

first_dataset_instance()

property dataset_instances

property has_deferred_data

copy_to_collection(collection, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)

table = Table('dataset_collection_element', MetaData(), Column('id', Integer(), table=<dataset_collection_element>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>, nullable=False), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<dataset_collection_element>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<dataset_collection_element>), Column('child_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>), Column('element_index', Integer(), table=<dataset_collection_element>), Column('element_identifier', Unicode(length=255), table=<dataset_collection_element>), schema=None)

class galaxy.model.Event(**kwargs)

Bases: