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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

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

metadata = 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.

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.

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

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

disk_usage

activation_token

addresses

cloudauthz

custos_auth

default_permissions

groups

histories

active_histories

galaxy_sessions

quotas

social_auth

stored_workflow_menu_entries

values

api_keys: List[APIKeys]

data_manager_histories

roles

stored_workflows

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']

__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)

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)

property nice_total_disk_usage

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

calculate_disk_usage()

Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories.

calculate_and_set_disk_usage()

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()

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

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']

class states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

RESUBMITTED = 'resubmitted'

UPLOAD = 'upload'

WAITING = 'waiting'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

ERROR = 'error'

FAILED = 'failed'

PAUSED = 'paused'

DELETING = 'deleting'

DELETED = 'deleted'

DELETED_NEW = 'deleted_new'

STOPPING = 'stop'

STOPPED = 'stopped'

SKIPPED = 'skipped'

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

non_ready_states = [<states.NEW: 'new'>, <states.RESUBMITTED: 'resubmitted'>, <states.UPLOAD: 'upload'>, <states.WAITING: 'waiting'>, <states.QUEUED: 'queued'>, <states.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)

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>), 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)

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

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', 'update_time', 'published', 'importable', 'slug', 'empty']

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)), 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.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='=')

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

deleted

default

groups

users

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups']

valid_operations = ('+', '-', '=')

__init__(name=None, description=None, amount=0, operation='=')

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

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)), 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

class states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

UPLOAD = 'upload'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

EMPTY = 'empty'

ERROR = 'error'

PAUSED = 'paused'

SETTING_METADATA = 'setting_metadata'

FAILED_METADATA = 'failed_metadata'

DEFERRED = 'deferred'

DISCARDED = 'discarded'

classmethod values()

non_ready_states = (<states.NEW: 'new'>, <states.UPLOAD: 'upload'>, <states.QUEUED: 'queued'>, <states.RUNNING: 'running'>, <states.SETTING_METADATA: 'setting_metadata'>)

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

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

terminal_states = (<states.OK: 'ok'>, <states.EMPTY: 'empty'>, <states.ERROR: 'error'>, <states.DEFERRED: 'deferred'>, <states.DISCARDED: 'discarded'>, <states.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()

get_file_name()

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=False, calculate_size=True)

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='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

class states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

UPLOAD = 'upload'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

EMPTY = 'empty'

ERROR = 'error'

PAUSED = 'paused'

SETTING_METADATA = 'setting_metadata'

FAILED_METADATA = 'failed_metadata'

DEFERRED = 'deferred'

DISCARDED = 'discarded'

classmethod values()

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]]

class validated_states(value)

Bases: str, Enum

An enumeration.

UNKNOWN = 'unknown'

INVALID = 'invalid'

OK = 'ok'

__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='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)

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)

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']

class populated_states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

OK = 'ok'

FAILED = 'failed'

__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

job_state_summary

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_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: Base, RepresentById

id: int

create_time

update_time

history_id

user_id

message

session_id

tool_id

history

user

galaxy_session

__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('event', MetaData(), Column('id', Integer(), table=<event>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<event>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<event>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<event>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<event>), Column('message', TrimmedString(length=1024), table=<event>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<event>), Column('tool_id', String(length=255), table=<event>), schema=None)

class galaxy.model.GalaxySession(is_valid=False, **kwd)

Bases: Base, RepresentById

id: int

create_time

update_time

user_id

remote_host

remote_addr

referer

current_history_id

session_key

prev_session_id

disk_usage

current_history

histories

user

__init__(is_valid=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.

is_valid

last_action

add_history(history, association=None)

get_disk_usage()

set_disk_usage(bytes)

property total_disk_usage

table = Table('galaxy_session', MetaData(), Column('id', Integer(), table=<galaxy_session>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_session>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<galaxy_session>), Column('remote_host', String(length=255), table=<galaxy_session>), Column('remote_addr', String(length=255), table=<galaxy_session>), Column('referer', TEXT(), table=<galaxy_session>), Column('current_history_id', Integer(), ForeignKey('history.id'), table=<galaxy_session>), Column('session_key', TrimmedString(length=255), table=<galaxy_session>), Column('is_valid', Boolean(), table=<galaxy_session>, default=ColumnDefault(False)), Column('prev_session_id', Integer(), table=<galaxy_session>), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_session>), Column('last_action', DateTime(), table=<galaxy_session>), schema=None)

class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)

Bases: Base, RepresentById

id: int

create_time

session_id

history_id

__init__(galaxy_session, history)

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.

galaxy_session

history

table = Table('galaxy_session_to_history', MetaData(), Column('id', Integer(), table=<galaxy_session_to_history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_session_to_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<galaxy_session_to_history>), Column('history_id', Integer(), ForeignKey('history.id'), table=<galaxy_session_to_history>), schema=None)

class galaxy.model.UCI

Bases: object

__init__()

class galaxy.model.StoredWorkflow(user=None, name=None, slug=None, create_time=None, update_time=None, published=False, latest_workflow_id=None, workflow=None, hidden=False)

Bases: Base, HasTags, Dictifiable, RepresentById

StoredWorkflow represents the root node of a tree of objects that compose a workflow, including workflow revisions, steps, and subworkflows. It is responsible for the metadata associated with a workflow including owner, name, published, and create/update time.

Each time a workflow is modified a revision is created, represented by a new galaxy.model.Workflow instance. See galaxy.model.Workflow for more information

id: int

user_id

latest_workflow_id

deleted

importable

from_path

tags: List[ItemTagAssociation]

owner_tags

annotations

ratings

users_shared_with

average_rating: column_property

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

dict_collection_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'importable', 'deleted', 'hidden']

dict_element_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'importable', 'deleted', 'hidden']

__init__(user=None, name=None, slug=None, create_time=None, update_time=None, published=False, latest_workflow_id=None, workflow=None, hidden=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.

user

name

slug

create_time

update_time

published

latest_workflow

workflows

hidden

get_internal_version(version)

show_in_tool_panel(user_id)

copy_tags_from(target_user, source_workflow)

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

Return item dictionary.

table = Table('stored_workflow', MetaData(), Column('id', Integer(), table=<stored_workflow>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<stored_workflow>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<stored_workflow>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow>, nullable=False), Column('latest_workflow_id', Integer(), ForeignKey('workflow.id'), table=<stored_workflow>), Column('name', TEXT(), table=<stored_workflow>), Column('deleted', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), Column('hidden', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<stored_workflow>), Column('from_path', TEXT(), table=<stored_workflow>), Column('published', Boolean(), table=<stored_workflow>, default=ColumnDefault(False)), schema=None)

class galaxy.model.Workflow(uuid=None)

Bases: Base, Dictifiable, RepresentById

Workflow represents a revision of a galaxy.model.StoredWorkflow. A new instance is created for each workflow revision and provides a common parent for the workflow steps.

See galaxy.model.WorkflowStep for more information

id: int

create_time

update_time

stored_workflow_id

parent_workflow_id

name

has_cycles

has_errors

reports_config

creator_metadata

license

source_metadata

steps: List[WorkflowStep]

parent_workflow_steps

stored_workflow

step_count: column_property

dict_collection_visible_keys = ['name', 'has_cycles', 'has_errors']

dict_element_visible_keys = ['name', 'has_cycles', 'has_errors']

input_step_types = ['data_input', 'data_collection_input', 'parameter_input']

__init__(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.

uuid

has_outputs_defined()

Returns true or false indicating whether or not a workflow has outputs defined.

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

Return item dictionary.

property steps_by_id

step_by_index(order_index: int)

step_by_label(label)

property input_steps

property workflow_outputs

workflow_output_for(output_label)

property workflow_output_labels

property top_level_workflow

If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it.

property top_level_stored_workflow

If this workflow is not attached to stored workflow directly, recursively grab its parents until it is the top level workflow which must have a stored workflow associated with it and then grab that stored workflow.

copy(user=None)

Copy a workflow for a new StoredWorkflow object.

Pass user if user-specific information needed.

log_str()

table = Table('workflow', MetaData(), Column('id', Integer(), table=<workflow>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<workflow>), Column('parent_workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow>), Column('name', TEXT(), table=<workflow>), Column('has_cycles', Boolean(), table=<workflow>), Column('has_errors', Boolean(), table=<workflow>), Column('reports_config', JSONType(), table=<workflow>), Column('creator_metadata', JSONType(), table=<workflow>), Column('license', TEXT(), table=<workflow>), Column('source_metadata', JSONType(), table=<workflow>), Column('uuid', UUIDType(), table=<workflow>), schema=None)

class galaxy.model.WorkflowStep

Bases: Base, RepresentById

WorkflowStep represents a tool or subworkflow, its inputs, annotations, and any outputs that are flagged as workflow outputs.

See galaxy.model.WorkflowStepInput and galaxy.model.WorkflowStepConnection for more information.

id: int

create_time

update_time

workflow_id

subworkflow_id

dynamic_tool_id

type: str

tool_id

tool_version

tool_inputs

tool_errors

position

config

order_index: int

when_expression

label

temp_input_connections: Optional[Dict[str, Union[Dict[str, Any], List[Dict[str, Any]]]]]

subworkflow: Optional[Workflow]

dynamic_tool

tags

annotations

post_job_actions

inputs

workflow_outputs

output_connections

workflow

module: Optional[WorkflowModule]

state: Optional[DefaultToolState]

upgrade_messages: Optional[Dict]

STEP_TYPE_TO_INPUT_TYPE = {'data_collection_input': 'dataset_collection', 'data_input': 'dataset', 'parameter_input': 'parameter'}

DEFAULT_POSITION = {'left': 0, 'top': 0}

__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.

uuid

init_on_load()

property tool_uuid

property input_type

property input_default_value

property input_optional

setup_inputs_by_name()

property inputs_by_name

get_input(input_name)

get_or_add_input(input_name)

add_connection(input_name, output_name, output_step, input_subworkflow_step_index=None)

property input_connections

property unique_workflow_outputs

property content_id

property input_connections_by_name

setup_input_connections_by_name()

create_or_update_workflow_output(output_name, label, uuid)

workflow_output_for(output_name)

copy_to(copied_step, step_mapping, user=None)

log_str()

clear_module_extras()

table = Table('workflow_step', MetaData(), Column('id', Integer(), table=<workflow_step>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_step>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_step>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>, nullable=False), Column('subworkflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<workflow_step>), Column('type', String(length=64), table=<workflow_step>), Column('tool_id', TEXT(), table=<workflow_step>), Column('tool_version', TEXT(), table=<workflow_step>), Column('tool_inputs', JSONType(), table=<workflow_step>), Column('tool_errors', JSONType(), table=<workflow_step>), Column('position', MutableJSONType(), table=<workflow_step>), Column('config', JSONType(), table=<workflow_step>), Column('order_index', Integer(), table=<workflow_step>), Column('when_expression', JSONType(), table=<workflow_step>), Column('uuid', UUIDType(), table=<workflow_step>), Column('label', Unicode(length=255), table=<workflow_step>), schema=None)

class galaxy.model.WorkflowStepInput(workflow_step)

Bases: Base, RepresentById

id: int

workflow_step_id

name

merge_type

scatter_type

value_from

value_from_type

default_value

runtime_value

connections

__init__(workflow_step)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

workflow_step

default_value_set

copy(copied_step)

table = Table('workflow_step_input', MetaData(), Column('id', Integer(), table=<workflow_step_input>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_input>), Column('name', TEXT(), table=<workflow_step_input>), Column('merge_type', TEXT(), table=<workflow_step_input>), Column('scatter_type', TEXT(), table=<workflow_step_input>), Column('value_from', MutableJSONType(), table=<workflow_step_input>), Column('value_from_type', TEXT(), table=<workflow_step_input>), Column('default_value', MutableJSONType(), table=<workflow_step_input>), Column('default_value_set', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), Column('runtime_value', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), schema=None)

class galaxy.model.WorkflowStepConnection(**kwargs)

Bases: Base, RepresentById

id: int

output_step_id

input_step_input_id

output_name

input_subworkflow_step_id

input_step_input

input_subworkflow_step

output_step

NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'

property non_data_connection

property input_name

property input_step: Optional[WorkflowStep]

property input_step_id

copy()

__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('workflow_step_connection', MetaData(), Column('id', Integer(), table=<workflow_step_connection>, primary_key=True, nullable=False), Column('output_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), Column('input_step_input_id', Integer(), ForeignKey('workflow_step_input.id'), table=<workflow_step_connection>), Column('output_name', TEXT(), table=<workflow_step_connection>), Column('input_subworkflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), schema=None)

class galaxy.model.WorkflowOutput(workflow_step, output_name=None, label=None, uuid=None)

Bases: Base, Serializable

id: int

workflow_step_id

__init__(workflow_step, output_name=None, label=None, 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.

workflow_step

output_name

label

uuid

copy(copied_step)

table = Table('workflow_output', MetaData(), Column('id', Integer(), table=<workflow_output>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_output>, nullable=False), Column('output_name', String(length=255), table=<workflow_output>), Column('label', Unicode(length=255), table=<workflow_output>), Column('uuid', UUIDType(), table=<workflow_output>), schema=None)

class galaxy.model.StoredWorkflowUserShareAssociation(**kwargs)

Bases: Base, UserShareAssociation

id: int

stored_workflow_id

user_id

user: Optional[User]

stored_workflow

__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('stored_workflow_user_share_connection', MetaData(), Column('id', Integer(), table=<stored_workflow_user_share_connection>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_user_share_connection>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_user_share_connection>), schema=None)

class galaxy.model.StoredWorkflowMenuEntry(**kwargs)

Bases: Base, RepresentById

id: int

stored_workflow_id

user_id

order_index

stored_workflow

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('stored_workflow_menu_entry', MetaData(), Column('id', Integer(), table=<stored_workflow_menu_entry>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_menu_entry>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_menu_entry>), Column('order_index', Integer(), table=<stored_workflow_menu_entry>), schema=None)

class galaxy.model.WorkflowInvocation(**kwargs)

Bases: Base, UsesCreateAndUpdateTime, Dictifiable, Serializable

id: int

create_time

update_time: DateTime

workflow_id

state

scheduler

handler

uuid

history_id

history

input_parameters

step_states

input_step_parameters

input_datasets

input_dataset_collections

subworkflow_invocations

steps

workflow: Workflow

output_dataset_collections

output_datasets

output_values

messages

dict_collection_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']

dict_element_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']

class states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

READY = 'ready'

SCHEDULED = 'scheduled'

CANCELLED = 'cancelled'

FAILED = 'failed'

non_terminal_states = [<states.NEW: 'new'>, <states.READY: 'ready'>]

create_subworkflow_invocation_for_step(step)

attach_subworkflow_invocation_for_step(step, subworkflow_invocation)

get_subworkflow_invocation_for_step(step)

get_subworkflow_invocation_association_for_step(step)

property active

Indicates the workflow invocation is somehow active - and in particular valid actions may be performed on its WorkflowInvocationSteps.

cancel()

fail()

step_states_by_step_id()

step_invocations_by_step_id()

step_invocation_for_step_id(step_id: int) → Optional[WorkflowInvocationStep]

step_invocation_for_label(label)

static poll_unhandled_workflow_ids(sa_session)

static poll_active_workflow_ids(sa_session, scheduler=None, handler=None)

add_output(workflow_output, step, output_object)

get_output_object(label)

get_input_object(label)

property output_associations

property input_associations

to_dict(view='collection', value_mapper=None, step_details=False, legacy_job_state=False)

Return item dictionary.

add_input(content, step_id=None, step=None)

add_message(message: InvocationMessageUnion)

property resource_parameters

has_input_for_step(step_id)

set_handler(handler)

log_str()

__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('workflow_invocation', MetaData(), Column('id', Integer(), table=<workflow_invocation>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_invocation>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_invocation>, nullable=False), Column('state', TrimmedString(length=64), table=<workflow_invocation>), Column('scheduler', TrimmedString(length=255), table=<workflow_invocation>), Column('handler', TrimmedString(length=255), table=<workflow_invocation>), Column('uuid', UUIDType(), table=<workflow_invocation>), Column('history_id', Integer(), ForeignKey('history.id'), table=<workflow_invocation>), schema=None)

class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation(**kwargs)

Bases: Base, Dictifiable, RepresentById

id: int

workflow_invocation_id

subworkflow_invocation_id

workflow_step_id

subworkflow_invocation

workflow_step

parent_workflow_invocation

dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']

dict_element_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']

__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('workflow_invocation_to_subworkflow_invocation_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_to_subworkflow_invocation_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('subworkflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), schema=None)

class galaxy.model.WorkflowInvocationMessage(**kwargs)

Bases: Base, Dictifiable, Serializable

id: int

workflow_invocation_id

reason

details

output_name

workflow_step_id

dependent_workflow_step_id

job_id

hda_id

hdca_id

workflow_invocation

workflow_step

dependent_workflow_step

property workflow_step_index

property dependent_workflow_step_index

property history_id

__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('workflow_invocation_message', MetaData(), Column('id', Integer(), table=<workflow_invocation_message>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_message>, nullable=False), Column('reason', String(length=32), table=<workflow_invocation_message>), Column('details', TrimmedString(length=255), table=<workflow_invocation_message>), Column('output_name', String(length=255), table=<workflow_invocation_message>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_message>), Column('dependent_workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_message>), Column('job_id', Integer(), ForeignKey('job.id'), table=<workflow_invocation_message>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_message>), Column('hdca_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_message>), schema=None)

class galaxy.model.WorkflowInvocationStep(**kwargs)

Bases: Base, Dictifiable, Serializable

id: int

create_time

update_time

workflow_invocation_id

workflow_step_id

state

job_id

implicit_collection_jobs_id

action

workflow_step

job

implicit_collection_jobs

output_dataset_collections

output_datasets

workflow_invocation

output_value

order_index

subworkflow_invocation_id: column_property

dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']

dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']

class states(value)

Bases: str, Enum

An enumeration.

NEW = 'new'

READY = 'ready'

SCHEDULED = 'scheduled'

property is_new

add_output(output_name, output_object)

property jobs

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

Return item dictionary.

__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('workflow_invocation_step', MetaData(), Column('id', Integer(), table=<workflow_invocation_step>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_invocation_step>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation_step>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_step>, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_step>, nullable=False), Column('state', TrimmedString(length=64), table=<workflow_invocation_step>), Column('job_id', Integer(), ForeignKey('job.id'), table=<workflow_invocation_step>), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<workflow_invocation_step>), Column('action', MutableJSONType(), table=<workflow_invocation_step>), schema=None)

class galaxy.model.WorkflowRequestInputParameter(**kwargs)

Bases: Base, Dictifiable, Serializable

Workflow-related parameters not tied to steps or inputs.

id: int

workflow_invocation_id

name

value

type

workflow_invocation

dict_collection_visible_keys = ['id', 'name', 'value', 'type']

class types(value)

Bases: str, Enum

An enumeration.

REPLACEMENT_PARAMETERS = 'replacements'

STEP_PARAMETERS = 'step'

META_PARAMETERS = 'meta'

RESOURCE_PARAMETERS = 'resource'

__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('workflow_request_input_parameters', MetaData(), Column('id', Integer(), table=<workflow_request_input_parameters>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_parameters>), Column('name', Unicode(length=255), table=<workflow_request_input_parameters>), Column('value', TEXT(), table=<workflow_request_input_parameters>), Column('type', Unicode(length=255), table=<workflow_request_input_parameters>), schema=None)

class galaxy.model.WorkflowRequestStepState(**kwargs)

Bases: Base, Dictifiable, Serializable

Workflow step value parameters.

id: int

workflow_invocation_id

workflow_step_id

value

workflow_step

workflow_invocation

dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']

__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('workflow_request_step_states', MetaData(), Column('id', Integer(), table=<workflow_request_step_states>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_step_states>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_step_states>), Column('value', MutableJSONType(), table=<workflow_request_step_states>), schema=None)

class galaxy.model.WorkflowRequestToInputDatasetAssociation(**kwargs)

Bases: Base, Dictifiable, Serializable

Workflow step input dataset parameters.

id: int

name

workflow_invocation_id

workflow_step_id

dataset_id

workflow_step

dataset

workflow_invocation

history_content_type = 'dataset'

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']

__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('workflow_request_to_input_dataset', MetaData(), Column('id', Integer(), table=<workflow_request_to_input_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_request_to_input_dataset>), schema=None)

class galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation(**kwargs)

Bases: Base, Dictifiable, Serializable

Workflow step input dataset collection parameters.

id: int

name

workflow_invocation_id

workflow_step_id

dataset_collection_id

workflow_step

dataset_collection

workflow_invocation

history_content_type = 'dataset_collection'

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']

__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('workflow_request_to_input_collection_dataset', MetaData(), Column('id', Integer(), table=<workflow_request_to_input_collection_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_collection_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_collection_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_collection_dataset>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_request_to_input_collection_dataset>), schema=None)

class galaxy.model.WorkflowRequestInputStepParameter(**kwargs)

Bases: Base, Dictifiable, Serializable

Workflow step parameter inputs.

id: int

workflow_invocation_id

workflow_step_id

parameter_value

workflow_step

workflow_invocation

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']

__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('workflow_request_input_step_parameter', MetaData(), Column('id', Integer(), table=<workflow_request_input_step_parameter>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_step_parameter>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_input_step_parameter>), Column('parameter_value', MutableJSONType(), table=<workflow_request_input_step_parameter>), schema=None)

class galaxy.model.WorkflowInvocationOutputDatasetAssociation(**kwargs)

Bases: Base, Dictifiable, Serializable

Represents links to output datasets for the workflow.

id: int

workflow_invocation_id

workflow_step_id

dataset_id

workflow_output_id

workflow_invocation

workflow_step

dataset

workflow_output

history_content_type = 'dataset'

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']

__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('workflow_invocation_output_dataset_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_association>), schema=None)

class galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation(**kwargs)

Bases: Base, Dictifiable, Serializable

Represents links to output dataset collections for the workflow.

id: int

workflow_invocation_id

workflow_step_id

dataset_collection_id

workflow_output_id

workflow_invocation

workflow_step

dataset_collection

workflow_output

history_content_type = 'dataset_collection'

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']

__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('workflow_invocation_output_dataset_collection_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_collection_association>), schema=None)

class galaxy.model.WorkflowInvocationOutputValue(**kwargs)

Bases: Base, Dictifiable, Serializable

Represents a link to a specified or computed workflow parameter.

id: int

workflow_invocation_id

workflow_step_id

workflow_output_id

value

workflow_invocation

workflow_invocation_step

workflow_step

workflow_output

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'value']

__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('workflow_invocation_output_value', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_value>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_value>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_value>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_value>), Column('value', MutableJSONType(), table=<workflow_invocation_output_value>), schema=None)

class galaxy.model.WorkflowInvocationStepOutputDatasetAssociation(**kwargs)

Bases: Base, Dictifiable, RepresentById

Represents links to output datasets for the workflow.

id: int

workflow_invocation_step_id

dataset_id

output_name

workflow_invocation_step

dataset

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']

__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('workflow_invocation_step_output_dataset_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_step_output_dataset_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_association>), schema=None)

class galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation(**kwargs)

Bases: Base, Dictifiable, RepresentById

Represents links to output dataset collections for the workflow.

id: int

workflow_invocation_step_id

workflow_step_id

dataset_collection_id

output_name

workflow_invocation_step

dataset_collection

dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']

__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('workflow_invocation_step_output_dataset_collection_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_collection_association>), schema=None)

class galaxy.model.MetadataFile(dataset=None, name=None, uuid=None)

Bases: Base, StorableObject, Serializable

id: int

hda_id

lda_id

create_time

update_time

object_store_id

deleted

purged

__init__(dataset=None, name=None, 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.

uuid

history_dataset

library_dataset

name

property dataset: Optional[Dataset]

update_from_file(file_name)

property file_name

table = Table('metadata_file', MetaData(), Column('id', Integer(), table=<metadata_file>, primary_key=True, nullable=False), Column('name', TEXT(), table=<metadata_file>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<metadata_file>), Column('lda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<metadata_file>), Column('create_time', DateTime(), table=<metadata_file>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<metadata_file>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('object_store_id', TrimmedString(length=255), table=<metadata_file>), Column('uuid', UUIDType(), table=<metadata_file>), Column('deleted', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), schema=None)

class galaxy.model.FormDefinition(**kwargs)

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

name

desc

form_definition_current_id

fields

type

layout

form_definition_current

supported_field_types = [<class 'galaxy.util.form_builder.AddressField'>, <class 'galaxy.util.form_builder.CheckboxField'>, <class 'galaxy.util.form_builder.PasswordField'>, <class 'galaxy.util.form_builder.SelectField'>, <class 'galaxy.util.form_builder.TextArea'>, <class 'galaxy.util.form_builder.TextField'>, <class 'galaxy.util.form_builder.WorkflowField'>, <class 'galaxy.util.form_builder.WorkflowMappingField'>, <class 'galaxy.util.form_builder.HistoryField'>]

class types(value)

Bases: str, Enum

An enumeration.

USER_INFO = 'User Information'

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']

to_dict(user=None, values=None, security=None)

Return item dictionary.

grid_fields(grid_index)

__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('form_definition', MetaData(), Column('id', Integer(), table=<form_definition>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_definition>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_definition>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TrimmedString(length=255), table=<form_definition>, nullable=False), Column('desc', TEXT(), table=<form_definition>), Column('form_definition_current_id', Integer(), ForeignKey('form_definition_current.id'), table=<form_definition>, nullable=False), Column('fields', MutableJSONType(), table=<form_definition>), Column('type', TrimmedString(length=255), table=<form_definition>), Column('layout', MutableJSONType(), table=<form_definition>), schema=None)

class galaxy.model.FormDefinitionCurrent(form_definition=None)

Bases: Base, RepresentById

id: int

create_time

update_time

latest_form_id

deleted

forms

__init__(form_definition=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.

latest_form

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

class galaxy.model.FormValues(form_def=None, content=None)

Bases: Base, RepresentById

id: int

create_time

update_time

form_definition_id

__init__(form_def=None, content=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.

form_definition

content

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

class galaxy.model.UserAddress(**kwargs)

Bases: Base, RepresentById

id: int

create_time

update_time

user_id

desc

name

institution

address

city

state

postal_code

country

phone

deleted

purged

user

to_dict(trans)

__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_address', MetaData(), Column('id', Integer(), table=<user_address>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_address>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_address>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_address>), Column('desc', TrimmedString(length=255), table=<user_address>), Column('name', TrimmedString(length=255), table=<user_address>, nullable=False), Column('institution', TrimmedString(length=255), table=<user_address>), Column('address', TrimmedString(length=255), table=<user_address>, nullable=False), Column('city', TrimmedString(length=255), table=<user_address>, nullable=False), Column('state', TrimmedString(length=255), table=<user_address>, nullable=False), Column('postal_code', TrimmedString(length=255), table=<user_address>, nullable=False), Column('country', TrimmedString(length=255), table=<user_address>, nullable=False), Column('phone', TrimmedString(length=255), table=<user_address>), Column('deleted', Boolean(), table=<user_address>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<user_address>, default=ColumnDefault(False)), schema=None)

class galaxy.model.PSAAssociation(**kwargs)

Bases: Base, AssociationMixin, RepresentById

id: int

server_url

handle

secret

issued

lifetime

assoc_type

sa_session = None

save()

classmethod store(server_url, association)

Create an Association instance

classmethod get(*args, **kwargs)

Get an Association instance

classmethod remove(ids_to_delete)

Remove an Association instance

__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('psa_association', MetaData(), Column('id', Integer(), table=<psa_association>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_association>), Column('handle', VARCHAR(length=255), table=<psa_association>), Column('secret', VARCHAR(length=255), table=<psa_association>), Column('issued', Integer(), table=<psa_association>), Column('lifetime', Integer(), table=<psa_association>), Column('assoc_type', VARCHAR(length=64), table=<psa_association>), schema=None)

class galaxy.model.PSACode(email, code)

Bases: Base, CodeMixin, RepresentById

id: int

sa_session = None

__init__(email, code)

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

code

save()

classmethod get_code(code)

table = Table('psa_code', MetaData(), Column('id', Integer(), table=<psa_code>, primary_key=True, nullable=False), Column('email', VARCHAR(length=200), table=<psa_code>), Column('code', VARCHAR(length=32), table=<psa_code>), schema=None)

class galaxy.model.PSANonce(server_url, timestamp, salt)

Bases: Base, NonceMixin, RepresentById

id: int

sa_session = None

__init__(server_url, timestamp, salt)

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.

server_url

timestamp

salt

save()

classmethod use(server_url, timestamp, salt)

Create a Nonce instance

table = Table('psa_nonce', MetaData(), Column('id', Integer(), table=<psa_nonce>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_nonce>), Column('timestamp', Integer(), table=<psa_nonce>), Column('salt', VARCHAR(length=40), table=<psa_nonce>), schema=None)

class galaxy.model.PSAPartial(token, data, next_step, backend)

Bases: Base, PartialMixin, RepresentById

id: int

sa_session = None

__init__(token, data, next_step, backend)

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

data

next_step

backend

save()

classmethod load(token)

classmethod destroy(token)

table = Table('psa_partial', MetaData(), Column('id', Integer(), table=<psa_partial>, primary_key=True, nullable=False), Column('token', VARCHAR(length=32), table=<psa_partial>), Column('data', TEXT(), table=<psa_partial>), Column('next_step', Integer(), table=<psa_partial>), Column('backend', VARCHAR(length=32), table=<psa_partial>), schema=None)

class galaxy.model.UserAuthnzToken(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)

Bases: Base, UserMixin, RepresentById

id: int

user

sa_session = None

__init__(provider, uid, extra_data=None, lifetime=None, assoc_type=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.

provider

uid

user_id

extra_data

lifetime

assoc_type

get_id_token(strategy)

set_extra_data(extra_data=None)

save()

classmethod username_max_length()

Return the max length for username

classmethod user_model()

Return the user model

classmethod changed(user)

The given user instance is ready to be saved

classmethod user_query()

classmethod user_exists(*args, **kwargs)

Return True/False if a User instance exists with the given arguments. Arguments are directly passed to filter() manager method.

classmethod get_username(user)

Return the username for given user

classmethod create_user(*args, **kwargs)

This is used by PSA authnz, do not use directly. Prefer using the user manager.

classmethod get_user(pk)

Return user instance for given id

classmethod get_users_by_email(email)

Return users instances for given email address

classmethod get_social_auth(provider, uid)

Return UserSocialAuth for given provider and uid

classmethod get_social_auth_for_user(user, provider=None, id=None)

Return all the UserSocialAuth instances for given user

classmethod create_social_auth(user, uid, provider)

Create a UserSocialAuth instance for given user

table = Table('oidc_user_authnz_tokens', MetaData(), Column('id', Integer(), table=<oidc_user_authnz_tokens>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<oidc_user_authnz_tokens>), Column('uid', VARCHAR(length=255), table=<oidc_user_authnz_tokens>), Column('provider', VARCHAR(length=32), table=<oidc_user_authnz_tokens>), Column('extra_data', MutableJSONType(), table=<oidc_user_authnz_tokens>), Column('lifetime', Integer(), table=<oidc_user_authnz_tokens>), Column('assoc_type', VARCHAR(length=64), table=<oidc_user_authnz_tokens>), schema=None)

class galaxy.model.CustosAuthnzToken(**kwargs)

Bases: Base, RepresentById

id: int

user_id

external_user_id

provider

access_token

id_token

refresh_token

expiration_time

refresh_expiration_time

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('custos_authnz_token', MetaData(), Column('id', Integer(), table=<custos_authnz_token>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<custos_authnz_token>), Column('external_user_id', String(length=64), table=<custos_authnz_token>), Column('provider', String(length=255), table=<custos_authnz_token>), Column('access_token', Text(), table=<custos_authnz_token>), Column('id_token', Text(), table=<custos_authnz_token>), Column('refresh_token', Text(), table=<custos_authnz_token>), Column('expiration_time', DateTime(), table=<custos_authnz_token>), Column('refresh_expiration_time', DateTime(), table=<custos_authnz_token>), schema=None)

class galaxy.model.CloudAuthz(user_id, provider, config, authn_id, description=None)

Bases: Base

id

tokens

create_time

user

authn

__init__(user_id, provider, config, authn_id, description=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.

user_id

provider

config

authn_id

last_update

last_activity

description

equals(user_id, provider, authn_id, config)

table = Table('cloudauthz', MetaData(), Column('id', Integer(), table=<cloudauthz>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<cloudauthz>), Column('provider', String(length=255), table=<cloudauthz>), Column('config', MutableJSONType(), table=<cloudauthz>), Column('authn_id', Integer(), ForeignKey('oidc_user_authnz_tokens.id'), table=<cloudauthz>), Column('tokens', MutableJSONType(), table=<cloudauthz>), Column('last_update', DateTime(), table=<cloudauthz>), Column('last_activity', DateTime(), table=<cloudauthz>), Column('description', TEXT(), table=<cloudauthz>), Column('create_time', DateTime(), table=<cloudauthz>, default=ColumnDefault(<function datetime.utcnow>)), schema=None)

class galaxy.model.Page(**kwargs)

Bases: Base, HasTags, Dictifiable, RepresentById

id: int

create_time

update_time

user_id

latest_revision_id

title

deleted

importable

slug

published

user

revisions

latest_revision

tags: List[ItemTagAssociation]

annotations

ratings

users_shared_with

average_rating: column_property

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

dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted', 'username', 'email_hash']

to_dict(view='element')

Return item dictionary.

property username

property email_hash

__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('page', MetaData(), Column('id', Integer(), table=<page>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<page>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<page>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page>, nullable=False), Column('latest_revision_id', Integer(), ForeignKey('page_revision.id'), table=<page>), Column('title', TEXT(), table=<page>), Column('deleted', Boolean(), table=<page>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<page>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<page>), Column('published', Boolean(), table=<page>, default=ColumnDefault(False)), schema=None)

class galaxy.model.PageRevision

Bases: Base, Dictifiable, RepresentById

id: int

create_time

update_time

page_id

title

content

page

DEFAULT_CONTENT_FORMAT = 'html'

dict_element_visible_keys = ['id', 'page_id', 'title', 'content', 'content_format']

__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.

content_format

to_dict(view='element')

Return item dictionary.

table = Table('page_revision', MetaData(), Column('id', Integer(), table=<page_revision>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<page_revision>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<page_revision>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_revision>, nullable=False), Column('title', TEXT(), table=<page_revision>), Column('content', TEXT(), table=<page_revision>), Column('content_format', TrimmedString(length=32), table=<page_revision>), schema=None)

class galaxy.model.PageUserShareAssociation(**kwargs)

Bases: Base, UserShareAssociation

id: int

page_id

user_id

user: Optional[User]

page

__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('page_user_share_association', MetaData(), Column('id', Integer(), table=<page_user_share_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_user_share_association>), schema=None)

class galaxy.model.Visualization(**kwd)

Bases: Base, HasTags, RepresentById

id: int

create_time

update_time

user_id

latest_revision_id

title

type

dbkey

deleted

importable

slug

published

user

revisions

latest_revision

tags: List[ItemTagAssociation]

annotations

ratings

users_shared_with

average_rating: column_property

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

__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.

copy(user=None, title=None)

Provide copy of visualization with only its latest revision.

table = Table('visualization', MetaData(), Column('id', Integer(), table=<visualization>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<visualization>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<visualization>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization>, nullable=False), Column('latest_revision_id', Integer(), ForeignKey('visualization_revision.id'), table=<visualization>), Column('title', TEXT(), table=<visualization>), Column('type', TEXT(), table=<visualization>), Column('dbkey', TEXT(), table=<visualization>), Column('deleted', Boolean(), table=<visualization>, default=ColumnDefault(False)), Column('importable', Boolean(), table=<visualization>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<visualization>), Column('published', Boolean(), table=<visualization>, default=ColumnDefault(False)), schema=None)

class galaxy.model.VisualizationRevision(**kwargs)

Bases: Base, RepresentById

id: int

create_time

update_time

visualization_id

title

dbkey

config

visualization

copy(visualization=None)

Returns a copy of this 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.

table = Table('visualization_revision', MetaData(), Column('id', Integer(), table=<visualization_revision>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<visualization_revision>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<visualization_revision>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_revision>, nullable=False), Column('title', TEXT(), table=<visualization_revision>), Column('dbkey', TEXT(), table=<visualization_revision>), Column('config', MutableJSONType(), table=<visualization_revision>), schema=None)

class galaxy.model.VisualizationUserShareAssociation(**kwargs)

Bases: Base, UserShareAssociation

id: int

visualization_id

user_id

user: Optional[User]

visualization

__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('visualization_user_share_association', MetaData(), Column('id', Integer(), table=<visualization_user_share_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_user_share_association>), schema=None)

class galaxy.model.Tag(**kwargs)

Bases: Base, RepresentById

id: int

type

parent_id

name

children

parent

__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('tag', MetaData(), Column('id', Integer(), table=<tag>, primary_key=True, nullable=False), Column('type', Integer(), table=<tag>), Column('parent_id', Integer(), ForeignKey('tag.id'), table=<tag>), Column('name', TrimmedString(length=255), table=<tag>), schema=None)

class galaxy.model.ItemTagAssociation

Bases: Dictifiable

dict_collection_visible_keys = ['id', 'user_tname', 'user_value']

dict_element_visible_keys = ['id', 'user_tname', 'user_value']

associated_item_names: List[str] = ['History', 'HistoryDatasetAssociation', 'LibraryDatasetDatasetAssociation', 'Page', 'WorkflowStep', 'StoredWorkflow', 'Visualization', 'HistoryDatasetCollection', 'LibraryDatasetCollection', 'Tool']

user_tname: Column

user_value = Column(None, TrimmedString(length=255), table=None)

copy(cls=None)

class galaxy.model.HistoryTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

history_id

tag_id

user_id

user_tname: Column

value

history

tag

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('history_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_tag_association>), Column('id', Integer(), table=<history_tag_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_tag_association>), Column('value', TrimmedString(length=255), table=<history_tag_association>), schema=None)

user_value

class galaxy.model.HistoryDatasetAssociationTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

history_dataset_association_id

tag_id

user_id

user_tname: Column

value

history_dataset_association

tag

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('history_dataset_association_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('id', Integer(), table=<history_dataset_association_tag_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), schema=None)

user_value

class galaxy.model.LibraryDatasetDatasetAssociationTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

library_dataset_dataset_association_id

tag_id

user_id

user_tname: Column

value

library_dataset_dataset_association

tag

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('library_dataset_dataset_association_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('id', Integer(), table=<library_dataset_dataset_association_tag_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), schema=None)

user_value

class galaxy.model.PageTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

page_id

tag_id

user_id

user_tname: Column

value

page

tag

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('page_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<page_tag_association>), Column('id', Integer(), table=<page_tag_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<page_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_tag_association>), Column('user_tname', TrimmedString(length=255), table=<page_tag_association>), Column('value', TrimmedString(length=255), table=<page_tag_association>), schema=None)

user_value

class galaxy.model.WorkflowStepTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

workflow_step_id

tag_id

user_id

user_tname: Column

value

workflow_step

tag

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('workflow_step_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<workflow_step_tag_association>), Column('id', Integer(), table=<workflow_step_tag_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<workflow_step_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_tag_association>), Column('user_tname', TrimmedString(length=255), table=<workflow_step_tag_association>), Column('value', TrimmedString(length=255), table=<workflow_step_tag_association>), schema=None)

user_value

class galaxy.model.StoredWorkflowTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

stored_workflow_id

tag_id

user_id

user_tname: Column

value

stored_workflow

tag

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('stored_workflow_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<stored_workflow_tag_association>), Column('id', Integer(), table=<stored_workflow_tag_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<stored_workflow_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_tag_association>), Column('user_tname', TrimmedString(length=255), table=<stored_workflow_tag_association>), Column('value', TrimmedString(length=255), table=<stored_workflow_tag_association>), schema=None)

user_value

class galaxy.model.VisualizationTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

visualization_id

tag_id

user_id

user_tname: Column

value

visualization

tag

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('visualization_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<visualization_tag_association>), Column('id', Integer(), table=<visualization_tag_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<visualization_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_tag_association>), Column('user_tname', TrimmedString(length=255), table=<visualization_tag_association>), Column('value', TrimmedString(length=255), table=<visualization_tag_association>), schema=None)

user_value

class galaxy.model.HistoryDatasetCollectionTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

history_dataset_collection_id

tag_id

user_id

user_tname: Column

value

dataset_collection

tag

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('history_dataset_collection_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('id', Integer(), table=<history_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), schema=None)

user_value

class galaxy.model.LibraryDatasetCollectionTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

library_dataset_collection_id

tag_id

user_id

user_tname: Column

value

dataset_collection

tag

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('library_dataset_collection_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('id', Integer(), table=<library_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), schema=None)

user_value

class galaxy.model.ToolTagAssociation(**kwargs)

Bases: Base, ItemTagAssociation, RepresentById

id: int

tool_id

tag_id

user_id

user_tname: Column

value

tag

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('tool_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<tool_tag_association>), Column('id', Integer(), table=<tool_tag_association>, primary_key=True, nullable=False), Column('tool_id', TrimmedString(length=255), table=<tool_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<tool_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<tool_tag_association>), Column('user_tname', TrimmedString(length=255), table=<tool_tag_association>), Column('value', TrimmedString(length=255), table=<tool_tag_association>), schema=None)

user_value

class galaxy.model.HistoryAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

id: int

history_id

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

user_id

annotation

history

user

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('history_dataset_association_annotation_association', MetaData(), Column('id', Integer(), table=<history_dataset_association_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_association_annotation_association>), schema=None)

id: int

history_dataset_association_id

user_id

annotation

hda

user

class galaxy.model.StoredWorkflowAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('stored_workflow_annotation_association', MetaData(), Column('id', Integer(), table=<stored_workflow_annotation_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_annotation_association>), Column('annotation', TEXT(), table=<stored_workflow_annotation_association>), schema=None)

id: int

stored_workflow_id

user_id

annotation

stored_workflow

user

class galaxy.model.WorkflowStepAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('workflow_step_annotation_association', MetaData(), Column('id', Integer(), table=<workflow_step_annotation_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_annotation_association>), Column('annotation', TEXT(), table=<workflow_step_annotation_association>), schema=None)

id: int

workflow_step_id

user_id

annotation

workflow_step

user

class galaxy.model.PageAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('page_annotation_association', MetaData(), Column('id', Integer(), table=<page_annotation_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_annotation_association>), Column('annotation', TEXT(), table=<page_annotation_association>), schema=None)

id: int

page_id

user_id

annotation

page

user

class galaxy.model.VisualizationAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('visualization_annotation_association', MetaData(), Column('id', Integer(), table=<visualization_annotation_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_annotation_association>), Column('annotation', TEXT(), table=<visualization_annotation_association>), schema=None)

id: int

visualization_id

user_id

annotation

visualization

user

class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('history_dataset_collection_annotation_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_collection_annotation_association>), schema=None)

id: int

history_dataset_collection_id

user_id

annotation

history_dataset_collection

user

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('library_dataset_collection_annotation_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<library_dataset_collection_annotation_association>), schema=None)

id: int

library_dataset_collection_id

user_id

annotation

dataset_collection

user

class galaxy.model.Vault(**kwargs)

Bases: Base

__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('vault', MetaData(), Column('key', Text(), table=<vault>, primary_key=True, nullable=False), Column('parent_key', Text(), ForeignKey('vault.key'), table=<vault>), Column('value', Text(), table=<vault>), Column('create_time', DateTime(), table=<vault>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<vault>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

key

parent_key

children

parent

value

create_time

update_time

class galaxy.model.ItemRatingAssociation(user, item, rating=0)

Bases: Base

__init__(user, item, rating=0)

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.HistoryRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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

id: int

history_id

user_id

rating

history

user

class galaxy.model.HistoryDatasetAssociationRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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_dataset_association_rating_association', MetaData(), Column('id', Integer(), table=<history_dataset_association_rating_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_rating_association>), Column('rating', Integer(), table=<history_dataset_association_rating_association>), schema=None)

id: int

history_dataset_association_id

user_id

rating

history_dataset_association

user

class galaxy.model.StoredWorkflowRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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('stored_workflow_rating_association', MetaData(), Column('id', Integer(), table=<stored_workflow_rating_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_rating_association>), Column('rating', Integer(), table=<stored_workflow_rating_association>), schema=None)

id: int

stored_workflow_id

user_id

rating

stored_workflow

user

class galaxy.model.PageRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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('page_rating_association', MetaData(), Column('id', Integer(), table=<page_rating_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_rating_association>), Column('rating', Integer(), table=<page_rating_association>), schema=None)

id: int

page_id

user_id

rating

page

user

class galaxy.model.VisualizationRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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('visualization_rating_association', MetaData(), Column('id', Integer(), table=<visualization_rating_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_rating_association>), Column('rating', Integer(), table=<visualization_rating_association>), schema=None)

id: int

visualization_id

user_id

rating

visualization

user

class galaxy.model.HistoryDatasetCollectionRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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_dataset_collection_rating_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_rating_association>), Column('rating', Integer(), table=<history_dataset_collection_rating_association>), schema=None)

id: int

history_dataset_collection_id

user_id

rating

dataset_collection

user

class galaxy.model.LibraryDatasetCollectionRatingAssociation(user, item, rating=0)

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

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_collection_rating_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_rating_association>), Column('rating', Integer(), table=<library_dataset_collection_rating_association>), schema=None)

id: int

library_dataset_collection_id

user_id

rating

dataset_collection

user

class galaxy.model.DataManagerHistoryAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

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

id: int

create_time

update_time

history_id

user_id

history

user

class galaxy.model.DataManagerJobAssociation(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

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

id: int

create_time

update_time

job_id

data_manager_id

job

class galaxy.model.UserPreference(name=None, value=None)

Bases: Base, RepresentById

table = Table('user_preference', MetaData(), Column('id', Integer(), table=<user_preference>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_preference>), Column('name', Unicode(length=255), table=<user_preference>), Column('value', Text(), table=<user_preference>), schema=None)

id: int

user_id

__init__(name=None, value=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

value

class galaxy.model.UserAction(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('user_action', MetaData(), Column('id', Integer(), table=<user_action>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_action>, default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_action>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<user_action>), Column('action', Unicode(length=255), table=<user_action>), Column('context', Unicode(length=512), table=<user_action>), Column('params', Unicode(length=1024), table=<user_action>), schema=None)

id: int

create_time

user_id

session_id

action

context

params

user

class galaxy.model.APIKeys(**kwargs)

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

Sets attributes on the constructed instance using the names and values in kwargs.

Only keys that are present as attributes of the instance’s class are allowed. These could be, for example, any mapped columns or relationships.

table = Table('api_keys', MetaData(), Column('id', Integer(), table=<api_keys>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<api_keys>, default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<api_keys>), Column('key', TrimmedString(length=32), table=<api_keys>), Column('deleted', Boolean(), table=<api_keys>, default=ColumnDefault(False)), schema=None)

id: int

create_time

user_id

key

user

deleted

galaxy.model.copy_list(lst, *args, **kwds)

class galaxy.model.CleanupEvent(**kwargs)

Bases: Base

__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('cleanup_event', MetaData(), Column('id', Integer(), table=<cleanup_event>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event>, default=ColumnDefault(<function datetime.utcnow>)), Column('message', TrimmedString(length=1024), table=<cleanup_event>), schema=None)

id

create_time

message

class galaxy.model.CleanupEventDatasetAssociation(**kwargs)

Bases: Base

__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('cleanup_event_dataset_association', MetaData(), Column('id', Integer(), table=<cleanup_event_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<cleanup_event_dataset_association>), schema=None)

id

create_time

cleanup_event_id

dataset_id

class galaxy.model.CleanupEventMetadataFileAssociation(**kwargs)

Bases: Base

__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('cleanup_event_metadata_file_association', MetaData(), Column('id', Integer(), table=<cleanup_event_metadata_file_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_metadata_file_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_metadata_file_association>), Column('metadata_file_id', Integer(), ForeignKey('metadata_file.id'), table=<cleanup_event_metadata_file_association>), schema=None)

id

create_time

cleanup_event_id

metadata_file_id

class galaxy.model.CleanupEventHistoryAssociation(**kwargs)

Bases: Base

__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('cleanup_event_history_association', MetaData(), Column('id', Integer(), table=<cleanup_event_history_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_history_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_history_association>), Column('history_id', Integer(), ForeignKey('history.id'), table=<cleanup_event_history_association>), schema=None)

id

create_time

cleanup_event_id

history_id

class galaxy.model.CleanupEventHistoryDatasetAssociationAssociation(**kwargs)

Bases: Base

__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('cleanup_event_hda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_hda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_hda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_hda_association>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<cleanup_event_hda_association>), schema=None)

id

create_time

cleanup_event_id

hda_id

class galaxy.model.CleanupEventLibraryAssociation(**kwargs)

Bases: Base

__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('cleanup_event_library_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_association>), Column('library_id', Integer(), ForeignKey('library.id'), table=<cleanup_event_library_association>), schema=None)

id

create_time

cleanup_event_id

library_id

class galaxy.model.CleanupEventLibraryFolderAssociation(**kwargs)

Bases: Base

__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('cleanup_event_library_folder_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_folder_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_folder_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_folder_association>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<cleanup_event_library_folder_association>), schema=None)

id

create_time

cleanup_event_id

library_folder_id

class galaxy.model.CleanupEventLibraryDatasetAssociation(**kwargs)

Bases: Base

__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('cleanup_event_library_dataset_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_dataset_association>), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<cleanup_event_library_dataset_association>), schema=None)

id

create_time

cleanup_event_id

library_dataset_id

class galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation(**kwargs)

Bases: Base

__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('cleanup_event_ldda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_ldda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_ldda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_ldda_association>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<cleanup_event_ldda_association>), schema=None)

id

create_time

cleanup_event_id

ldda_id

class galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation(**kwargs)

Bases: Base

__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('cleanup_event_icda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_icda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_icda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_icda_association>), Column('icda_id', Integer(), ForeignKey('implicitly_converted_dataset_association.id'), table=<cleanup_event_icda_association>), schema=None)

id

create_time

cleanup_event_id

icda_id

galaxy.model.receive_init(target, args, kwargs)

Listens for the ‘init’ event. This is not called when ‘target’ is loaded from the database. https://docs.sqlalchemy.org/en/14/orm/events.html#sqlalchemy.orm.InstanceEvents.init

Addresses SQLAlchemy 2.0 compatibility issue: see inline documentation for add_object_to_object_session in galaxy.model.orm.util.

Subpackages

• galaxy.model.dataset_collections package
  • Subpackages
    • galaxy.model.dataset_collections.types package
      • DatasetCollectionType
      • BaseDatasetCollectionType
      • Submodules
      • galaxy.model.dataset_collections.types.list module
      • galaxy.model.dataset_collections.types.paired module
  • Submodules
  • galaxy.model.dataset_collections.builder module
    • build_collection()
    • set_collection_elements()
    • CollectionBuilder
      • CollectionBuilder.__init__()
      • CollectionBuilder.replace_elements_in_collection()
      • CollectionBuilder.get_level()
      • CollectionBuilder.add_dataset()
      • CollectionBuilder.build_elements()
      • CollectionBuilder.build()
    • BoundCollectionBuilder
      • BoundCollectionBuilder.__init__()
      • BoundCollectionBuilder.populate_partial()
      • BoundCollectionBuilder.populate()
  • galaxy.model.dataset_collections.matching module
    • CollectionsToMatch
      • CollectionsToMatch.__init__()
      • CollectionsToMatch.add()
      • CollectionsToMatch.has_collections()
      • CollectionsToMatch.items()
    • MatchingCollections
      • MatchingCollections.__init__()
      • MatchingCollections.slice_collections()
      • MatchingCollections.subcollection_mapping_type()
      • MatchingCollections.structure
      • MatchingCollections.map_over_action_tuples()
      • MatchingCollections.is_mapped_over()
      • MatchingCollections.for_collections()
  • galaxy.model.dataset_collections.registry module
    • DatasetCollectionTypesRegistry
      • DatasetCollectionTypesRegistry.__init__()
      • DatasetCollectionTypesRegistry.get()
      • DatasetCollectionTypesRegistry.prototype()
  • galaxy.model.dataset_collections.structure module
    • Leaf
      • Leaf.children_known
      • Leaf.is_leaf
      • Leaf.clone()
      • Leaf.multiply()
      • Leaf.sliced_collection_type()
    • BaseTree
      • BaseTree.__init__()
    • UninitializedTree
      • UninitializedTree.children_known
      • UninitializedTree.clone()
      • UninitializedTree.is_leaf
      • UninitializedTree.multiply()
    • Tree
      • Tree.children_known
      • Tree.__init__()
      • Tree.for_dataset_collection()
      • Tree.walk_collections()
      • Tree.is_leaf
      • Tree.can_match()
      • Tree.multiply()
      • Tree.clone()
    • tool_output_to_structure()
    • dict_map()
    • get_structure()
  • galaxy.model.dataset_collections.subcollections module
    • split_dataset_collection_instance()
  • galaxy.model.dataset_collections.type_description module
    • CollectionTypeDescriptionFactory
      • CollectionTypeDescriptionFactory.__init__()
      • CollectionTypeDescriptionFactory.for_collection_type()
    • CollectionTypeDescription
      • CollectionTypeDescription.__init__()
      • CollectionTypeDescription.collection_type
      • CollectionTypeDescription.child_collection_type()
      • CollectionTypeDescription.child_collection_type_description()
      • CollectionTypeDescription.effective_collection_type_description()
      • CollectionTypeDescription.effective_collection_type()
      • CollectionTypeDescription.has_subcollections_of_type()
      • CollectionTypeDescription.is_subcollection_of_type()
      • CollectionTypeDescription.can_match_type()
      • CollectionTypeDescription.subcollection_type_description()
      • CollectionTypeDescription.has_subcollections()
      • CollectionTypeDescription.rank_collection_type()
      • CollectionTypeDescription.rank_type_plugin()
      • CollectionTypeDescription.dimension
      • CollectionTypeDescription.multiply()
    • map_over_collection_type()
• galaxy.model.migrations package
  • DatabaseConfig
    • DatabaseConfig.url
    • DatabaseConfig.template
    • DatabaseConfig.encoding
  • NoVersionTableError
    • NoVersionTableError.__init__()
  • IncorrectVersionError
    • IncorrectVersionError.__init__()
  • OutdatedDatabaseError
    • OutdatedDatabaseError.__init__()
  • InvalidModelIdError
    • InvalidModelIdError.__init__()
  • RevisionNotFoundError
    • RevisionNotFoundError.__init__()
  • AlembicManager
    • AlembicManager.is_at_revision()
    • AlembicManager.__init__()
    • AlembicManager.stamp_model_head()
    • AlembicManager.stamp_revision()
    • AlembicManager.upgrade()
    • AlembicManager.is_under_version_control()
    • AlembicManager.is_up_to_date()
    • AlembicManager.get_model_db_head()
    • AlembicManager.get_model_script_head()
    • AlembicManager.db_heads
  • DatabaseStateCache
    • DatabaseStateCache.__init__()
    • DatabaseStateCache.tables
    • DatabaseStateCache.is_database_empty()
    • DatabaseStateCache.contains_only_kombu_tables()
    • DatabaseStateCache.has_alembic_version_table()
    • DatabaseStateCache.has_sqlalchemymigrate_version_table()
    • DatabaseStateCache.is_last_sqlalchemymigrate_version()
  • metadata_contains_only_kombu_tables()
  • verify_databases_via_script()
  • verify_databases()
  • DatabaseStateVerifier
    • DatabaseStateVerifier.__init__()
    • DatabaseStateVerifier.is_auto_migrate
    • DatabaseStateVerifier.db_state
    • DatabaseStateVerifier.alembic_manager
    • DatabaseStateVerifier.run()
  • get_last_sqlalchemymigrate_version()
  • get_url_string()
  • get_alembic_manager()
  • get_metadata()
  • load_metadata()
  • listify()
  • get_gxy_metadata()
  • get_tsi_metadata()
  • Submodules
  • galaxy.model.migrations.scripts module
    • DatabaseDoesNotExistError
      • DatabaseDoesNotExistError.__init__()
    • DatabaseNotInitializedError
      • DatabaseNotInitializedError.__init__()
    • verify_database_is_initialized()
    • get_configuration()
    • get_configuration_from_file()
    • add_db_urls_to_command_arguments()
    • invoke_alembic()
    • LegacyScriptsException
      • LegacyScriptsException.__init__()
    • LegacyManageDb
      • LegacyManageDb.LEGACY_CONFIG_FILE_ARG_NAMES
      • LegacyManageDb.__init__()
      • LegacyManageDb.get_gxy_version()
      • LegacyManageDb.get_gxy_db_version()
      • LegacyManageDb.run_upgrade()
      • LegacyManageDb.rename_config_argument()
    • get_alembic_cfg()
    • get_alembic_manager()
  • galaxy.model.migrations.util module
    • drop_column()
    • create_index()
    • drop_index()
    • column_exists()
    • index_exists()
• galaxy.model.orm package
  • Submodules
  • galaxy.model.orm.engine_factory module
    • reset_request_query_counts()
    • log_request_query_counts()
    • stripwd()
    • pretty_stack()
    • build_engine()
    • set_sqlite_connect_args()
  • galaxy.model.orm.now module
    • now()
  • galaxy.model.orm.scripts module
    • get_config()
    • manage_db()
  • galaxy.model.orm.util module
    • add_object_to_object_session()
    • add_object_to_session()
    • get_object_session()
• galaxy.model.store package
  • StoreAppProtocol
    • StoreAppProtocol.datatypes_registry
    • StoreAppProtocol.object_store
    • StoreAppProtocol.security
    • StoreAppProtocol.tag_handler
    • StoreAppProtocol.model
    • StoreAppProtocol.file_sources
    • StoreAppProtocol.workflow_contents_manager
    • StoreAppProtocol.__init__()
  • ImportDiscardedDataType
    • ImportDiscardedDataType.FORBID
    • ImportDiscardedDataType.ALLOW
    • ImportDiscardedDataType.FORCE
  • ImportOptions
    • ImportOptions.__init__()
    • ImportOptions.allow_edit
    • ImportOptions.allow_library_creation
    • ImportOptions.allow_dataset_object_edit
    • ImportOptions.discarded_data
  • SessionlessContext
    • SessionlessContext.__init__()
    • SessionlessContext.flush()
    • SessionlessContext.add()
    • SessionlessContext.query()
  • replace_metadata_file()
  • ModelImportStore
    • ModelImportStore.archive_dir
    • ModelImportStore.__init__()
    • ModelImportStore.app
    • ModelImportStore.workflow_paths()
    • ModelImportStore.defines_new_history()
    • ModelImportStore.new_history_properties()
    • ModelImportStore.datasets_properties()
    • ModelImportStore.library_properties()
    • ModelImportStore.invocations_properties()
    • ModelImportStore.collections_properties()
    • ModelImportStore.jobs_properties()
    • ModelImportStore.implicit_collection_jobs_properties()
    • ModelImportStore.object_key
    • ModelImportStore.file_source_root
    • ModelImportStore.trust_hid()
    • ModelImportStore.target_history()
    • ModelImportStore.perform_import()
  • ObjectImportTracker
    • ObjectImportTracker.__init__()
    • ObjectImportTracker.libraries_by_key
    • ObjectImportTracker.hdas_by_key
    • ObjectImportTracker.hdas_by_id
    • ObjectImportTracker.hdcas_by_key
    • ObjectImportTracker.hdcas_by_id
    • ObjectImportTracker.dces_by_key
    • ObjectImportTracker.dces_by_id
    • ObjectImportTracker.lddas_by_key
    • ObjectImportTracker.hda_copied_from_sinks
    • ObjectImportTracker.hdca_copied_from_sinks
    • ObjectImportTracker.jobs_by_key
    • ObjectImportTracker.requires_hid
    • ObjectImportTracker.find_hda()
    • ObjectImportTracker.find_hdca()
    • ObjectImportTracker.find_dce()
  • FileTracebackException
    • FileTracebackException.__init__()
  • get_import_model_store_for_directory()
  • DictImportModelStore
    • DictImportModelStore.object_key
    • DictImportModelStore.__init__()
    • DictImportModelStore.archive_dir
    • DictImportModelStore.defines_new_history()
    • DictImportModelStore.new_history_properties()
    • DictImportModelStore.datasets_properties()
    • DictImportModelStore.collections_properties()
    • DictImportModelStore.library_properties()
    • DictImportModelStore.jobs_properties()
    • DictImportModelStore.implicit_collection_jobs_properties()
    • DictImportModelStore.invocations_properties()
    • DictImportModelStore.workflow_paths()
    • DictImportModelStore.app
  • get_import_model_store_for_dict()
  • BaseDirectoryImportModelStore
    • BaseDirectoryImportModelStore.file_source_root
    • BaseDirectoryImportModelStore.defines_new_history()
    • BaseDirectoryImportModelStore.new_history_properties()
    • BaseDirectoryImportModelStore.datasets_properties()
    • BaseDirectoryImportModelStore.collections_properties()
    • BaseDirectoryImportModelStore.library_properties()
    • BaseDirectoryImportModelStore.jobs_properties()
    • BaseDirectoryImportModelStore.implicit_collection_jobs_properties()
    • BaseDirectoryImportModelStore.invocations_properties()
    • BaseDirectoryImportModelStore.workflow_paths()
    • BaseDirectoryImportModelStore.app
    • BaseDirectoryImportModelStore.archive_dir
  • restore_times()
  • DirectoryImportModelStore1901
    • DirectoryImportModelStore1901.object_key
    • DirectoryImportModelStore1901.__init__()
    • DirectoryImportModelStore1901.archive_dir
    • DirectoryImportModelStore1901.trust_hid()
    • DirectoryImportModelStore1901.app
  • DirectoryImportModelStoreLatest
    • DirectoryImportModelStoreLatest.object_key
    • DirectoryImportModelStoreLatest.__init__()
    • DirectoryImportModelStoreLatest.archive_dir
    • DirectoryImportModelStoreLatest.app
  • BagArchiveImportModelStore
    • BagArchiveImportModelStore.__init__()
    • BagArchiveImportModelStore.app
    • BagArchiveImportModelStore.archive_dir
  • ModelExportStore
    • ModelExportStore.export_history()
    • ModelExportStore.export_library()
    • ModelExportStore.export_library_folder()
    • ModelExportStore.export_workflow_invocation()
    • ModelExportStore.add_dataset_collection()
    • ModelExportStore.add_dataset()
  • DirectoryModelExportStore
    • DirectoryModelExportStore.__init__()
    • DirectoryModelExportStore.app
    • DirectoryModelExportStore.file_sources
    • DirectoryModelExportStore.workflows_directory
    • DirectoryModelExportStore.serialize_files()
    • DirectoryModelExportStore.exported_key()
    • DirectoryModelExportStore.push_metadata_files()
    • DirectoryModelExportStore.export_job()
    • DirectoryModelExportStore.export_jobs()
    • DirectoryModelExportStore.export_history()
    • DirectoryModelExportStore.export_library()
    • DirectoryModelExportStore.export_library_folder()
    • DirectoryModelExportStore.export_library_folder_contents()
    • DirectoryModelExportStore.export_workflow_invocation()
    • DirectoryModelExportStore.add_job_output_dataset_associations()
    • DirectoryModelExportStore.export_collection()
    • DirectoryModelExportStore.add_dataset_collection()
    • DirectoryModelExportStore.add_dataset()
  • WriteCrates
    • WriteCrates.included_invocations
    • WriteCrates.export_directory
    • WriteCrates.included_datasets
    • WriteCrates.dataset_id_to_path
    • WriteCrates.workflows_directory
  • WorkflowInvocationOnlyExportStore
    • WorkflowInvocationOnlyExportStore.export_history()
    • WorkflowInvocationOnlyExportStore.export_library()
    • WorkflowInvocationOnlyExportStore.only_invocation
    • WorkflowInvocationOnlyExportStore.app
    • WorkflowInvocationOnlyExportStore.file_sources
    • WorkflowInvocationOnlyExportStore.included_datasets
    • WorkflowInvocationOnlyExportStore.included_collections
    • WorkflowInvocationOnlyExportStore.included_libraries
    • WorkflowInvocationOnlyExportStore.included_library_folders
    • WorkflowInvocationOnlyExportStore.included_invocations
    • WorkflowInvocationOnlyExportStore.collection_datasets
    • WorkflowInvocationOnlyExportStore.collections_attrs
    • WorkflowInvocationOnlyExportStore.dataset_id_to_path
    • WorkflowInvocationOnlyExportStore.job_output_dataset_associations
  • BcoExportOptions
    • BcoExportOptions.galaxy_url
    • BcoExportOptions.galaxy_version
    • BcoExportOptions.merge_history_metadata
    • BcoExportOptions.override_environment_variables
    • BcoExportOptions.override_empirical_error
    • BcoExportOptions.override_algorithmic_error
    • BcoExportOptions.override_xref
    • BcoExportOptions.__init__()
  • BcoModelExportStore
    • BcoModelExportStore.__init__()
    • BcoModelExportStore.app
    • BcoModelExportStore.file_sources
    • BcoModelExportStore.included_datasets
    • BcoModelExportStore.included_collections
    • BcoModelExportStore.included_libraries
    • BcoModelExportStore.included_library_folders
    • BcoModelExportStore.included_invocations
    • BcoModelExportStore.collection_datasets
    • BcoModelExportStore.collections_attrs
    • BcoModelExportStore.dataset_id_to_path
    • BcoModelExportStore.job_output_dataset_associations
  • ROCrateModelExportStore
    • ROCrateModelExportStore.__init__()
    • ROCrateModelExportStore.app
    • ROCrateModelExportStore.file_sources
    • ROCrateModelExportStore.included_datasets
    • ROCrateModelExportStore.included_collections
    • ROCrateModelExportStore.included_libraries
    • ROCrateModelExportStore.included_library_folders
    • ROCrateModelExportStore.included_invocations
    • ROCrateModelExportStore.collection_datasets
    • ROCrateModelExportStore.collections_attrs
    • ROCrateModelExportStore.dataset_id_to_path
    • ROCrateModelExportStore.job_output_dataset_associations
  • ROCrateArchiveModelExportStore
    • ROCrateArchiveModelExportStore.__init__()
    • ROCrateArchiveModelExportStore.out_file
    • ROCrateArchiveModelExportStore.file_source_uri
  • TarModelExportStore
    • TarModelExportStore.__init__()
    • TarModelExportStore.out_file
    • TarModelExportStore.file_source_uri
  • BagDirectoryModelExportStore
    • BagDirectoryModelExportStore.app
    • BagDirectoryModelExportStore.file_sources
    • BagDirectoryModelExportStore.included_datasets
    • BagDirectoryModelExportStore.included_collections
    • BagDirectoryModelExportStore.included_libraries
    • BagDirectoryModelExportStore.included_library_folders
    • BagDirectoryModelExportStore.included_invocations
    • BagDirectoryModelExportStore.collection_datasets
    • BagDirectoryModelExportStore.collections_attrs
    • BagDirectoryModelExportStore.dataset_id_to_path
    • BagDirectoryModelExportStore.job_output_dataset_associations
    • BagDirectoryModelExportStore.__init__()
  • BagArchiveModelExportStore
    • BagArchiveModelExportStore.__init__()
    • BagArchiveModelExportStore.file_source_uri
  • get_export_store_factory()
  • tar_export_directory()
  • get_export_dataset_filename()
  • imported_store_for_metadata()
  • source_to_import_store()
  • payload_to_source_uri()
  • Submodules
  • galaxy.model.store.build_objects module
    • main()
  • galaxy.model.store.discover module
    • MaxDiscoveredFilesExceededError
    • ModelPersistenceContext
      • ModelPersistenceContext.job_working_directory
      • ModelPersistenceContext.max_discovered_files
      • ModelPersistenceContext.discovered_file_count
      • ModelPersistenceContext.create_dataset()
      • ModelPersistenceContext.finalize_storage()
      • ModelPersistenceContext.set_datasets_metadata()
      • ModelPersistenceContext.populate_collection_elements()
      • ModelPersistenceContext.add_tags_to_datasets()
      • ModelPersistenceContext.update_object_store_with_datasets()
      • ModelPersistenceContext.tag_handler
      • ModelPersistenceContext.user
      • ModelPersistenceContext.sa_session
      • ModelPersistenceContext.permission_provider
      • ModelPersistenceContext.get_implicit_collection_jobs_association_id()
      • ModelPersistenceContext.job
      • ModelPersistenceContext.metadata_source_provider
      • ModelPersistenceContext.object_store
      • ModelPersistenceContext.flush_per_n_datasets
      • ModelPersistenceContext.input_dbkey
      • ModelPersistenceContext.add_library_dataset_to_folder()
      • ModelPersistenceContext.create_library_folder()
      • ModelPersistenceContext.add_output_dataset_association()
      • ModelPersistenceContext.add_datasets_to_history()
      • ModelPersistenceContext.job_id()
      • ModelPersistenceContext.persist_object()
      • ModelPersistenceContext.persist_library_folder()
      • ModelPersistenceContext.flush()
      • ModelPersistenceContext.increment_discovered_file_count()
    • PermissionProvider
      • PermissionProvider.permissions
      • PermissionProvider.set_default_hda_permissions()
      • PermissionProvider.copy_dataset_permissions()
    • UnusedPermissionProvider
      • UnusedPermissionProvider.copy_dataset_permissions()
    • MetadataSourceProvider
      • MetadataSourceProvider.get_metadata_source()
    • UnusedMetadataSourceProvider
      • UnusedMetadataSourceProvider.get_metadata_source()
    • SessionlessModelPersistenceContext
      • SessionlessModelPersistenceContext.__init__()
      • SessionlessModelPersistenceContext.discovered_file_count
      • SessionlessModelPersistenceContext.job_working_directory
      • SessionlessModelPersistenceContext.tag_handler
      • SessionlessModelPersistenceContext.sa_session
      • SessionlessModelPersistenceContext.user
      • SessionlessModelPersistenceContext.job
      • SessionlessModelPersistenceContext.permission_provider
      • SessionlessModelPersistenceContext.metadata_source_provider
      • SessionlessModelPersistenceContext.object_store
      • SessionlessModelPersistenceContext.flush_per_n_datasets
      • SessionlessModelPersistenceContext.add_tags_to_datasets()
      • SessionlessModelPersistenceContext.add_library_dataset_to_folder()
      • SessionlessModelPersistenceContext.get_library_folder()
      • SessionlessModelPersistenceContext.get_hdca()
      • SessionlessModelPersistenceContext.create_hdca()
      • SessionlessModelPersistenceContext.create_library_folder()
      • SessionlessModelPersistenceContext.persist_library_folder()
      • SessionlessModelPersistenceContext.add_datasets_to_history()
      • SessionlessModelPersistenceContext.persist_object()
      • SessionlessModelPersistenceContext.flush()
      • SessionlessModelPersistenceContext.add_output_dataset_association()
      • SessionlessModelPersistenceContext.get_implicit_collection_jobs_association_id()
    • persist_extra_files()
    • persist_target_to_export_store()
    • persist_elements_to_hdca()
    • persist_elements_to_folder()
    • persist_hdas()
    • get_required_item()
    • validate_and_normalize_target()
    • replace_request_syntax_sugar()
    • DiscoveredFile
      • DiscoveredFile.path
      • DiscoveredFile.collector
      • DiscoveredFile.match
      • DiscoveredFile.discovered_state()
    • DiscoveredResultState
      • DiscoveredResultState.info
      • DiscoveredResultState.state
    • DiscoveredDeferredFile
      • DiscoveredDeferredFile.collector
      • DiscoveredDeferredFile.match
      • DiscoveredDeferredFile.discovered_state()
      • DiscoveredDeferredFile.path
    • discovered_file_for_element()
    • discover_target_directory()
    • JsonCollectedDatasetMatch
      • JsonCollectedDatasetMatch.__init__()
      • JsonCollectedDatasetMatch.designation
      • JsonCollectedDatasetMatch.element_identifiers
      • JsonCollectedDatasetMatch.raw_element_identifiers
      • JsonCollectedDatasetMatch.name
      • JsonCollectedDatasetMatch.dbkey
      • JsonCollectedDatasetMatch.ext
      • JsonCollectedDatasetMatch.visible
      • JsonCollectedDatasetMatch.link_data
      • JsonCollectedDatasetMatch.tag_list
      • JsonCollectedDatasetMatch.object_id
      • JsonCollectedDatasetMatch.sources
      • JsonCollectedDatasetMatch.hashes
      • JsonCollectedDatasetMatch.created_from_basename
      • JsonCollectedDatasetMatch.extra_files
      • JsonCollectedDatasetMatch.effective_state
    • RegexCollectedDatasetMatch
      • RegexCollectedDatasetMatch.__init__()
    • DiscoveredFileError
      • DiscoveredFileError.error_message
      • DiscoveredFileError.collector
      • DiscoveredFileError.match
      • DiscoveredFileError.path
      • DiscoveredFileError.discovered_state()
  • galaxy.model.store.load_objects module
    • main()
• galaxy.model.tool_shed_install package
  • now()
  • Base
    • Base.registry
    • Base.metadata
    • Base.__init__()
  • ToolShedRepository
    • ToolShedRepository.update_time
    • ToolShedRepository.includes_datatypes
    • ToolShedRepository.tool_versions
    • ToolShedRepository.tool_dependencies
    • ToolShedRepository.required_repositories
    • ToolShedRepository.dict_collection_visible_keys
    • ToolShedRepository.dict_element_visible_keys
    • ToolShedRepository.installation_status
      • ToolShedRepository.installation_status.NEW
      • ToolShedRepository.installation_status.CLONING
      • ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS
      • ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES
      • ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES
      • ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES
      • ToolShedRepository.installation_status.INSTALLED
      • ToolShedRepository.installation_status.DEACTIVATED
      • ToolShedRepository.installation_status.ERROR
      • ToolShedRepository.installation_status.UNINSTALLED
    • ToolShedRepository.states
      • ToolShedRepository.states.INSTALLING
      • ToolShedRepository.states.OK
      • ToolShedRepository.states.WARNING
      • ToolShedRepository.states.ERROR
      • ToolShedRepository.states.UNINSTALLED
    • ToolShedRepository.__init__()
    • ToolShedRepository.id
    • ToolShedRepository.create_time
    • ToolShedRepository.tool_shed
    • ToolShedRepository.name
    • ToolShedRepository.description
    • ToolShedRepository.owner
    • ToolShedRepository.installed_changeset_revision
    • ToolShedRepository.changeset_revision
    • ToolShedRepository.ctx_rev
    • ToolShedRepository.metadata_
    • ToolShedRepository.tool_shed_status
    • ToolShedRepository.deleted
    • ToolShedRepository.uninstalled
    • ToolShedRepository.dist_to_shed
    • ToolShedRepository.status
    • ToolShedRepository.error_message
    • ToolShedRepository.as_dict()
    • ToolShedRepository.can_install
    • ToolShedRepository.can_reset_metadata
    • ToolShedRepository.can_uninstall
    • ToolShedRepository.can_deactivate
    • ToolShedRepository.can_reinstall_or_activate
    • ToolShedRepository.get_sharable_url()
    • ToolShedRepository.shed_config_filename
    • ToolShedRepository.get_shed_config_dict()
    • ToolShedRepository.get_tool_relative_path()
    • ToolShedRepository.guess_shed_config()
    • ToolShedRepository.has_readme_files
    • ToolShedRepository.has_repository_dependencies
    • ToolShedRepository.has_repository_dependencies_only_if_compiling_contained_td
    • ToolShedRepository.in_error_state
    • ToolShedRepository.includes_data_managers
    • ToolShedRepository.includes_tools
    • ToolShedRepository.includes_tools_for_display_in_tool_panel
    • ToolShedRepository.includes_tool_dependencies
    • ToolShedRepository.installed_repository_dependencies
    • ToolShedRepository.installed_tool_dependencies
    • ToolShedRepository.is_deprecated_in_tool_shed
    • ToolShedRepository.is_deactivated_or_installed
    • ToolShedRepository.is_installed
    • ToolShedRepository.is_latest_installable_revision
    • ToolShedRepository.is_new
    • ToolShedRepository.missing_repository_dependencies
    • ToolShedRepository.missing_tool_dependencies
    • ToolShedRepository.repo_files_directory()
    • ToolShedRepository.repo_path()
    • ToolShedRepository.repository_dependencies
    • ToolShedRepository.repository_dependencies_being_installed
    • ToolShedRepository.repository_dependencies_missing_or_being_installed
    • ToolShedRepository.repository_dependencies_with_installation_errors
    • ToolShedRepository.requires_prior_installation_of
    • ToolShedRepository.revision_update_available
    • ToolShedRepository.to_dict()
    • ToolShedRepository.tool_dependencies_being_installed
    • ToolShedRepository.tool_dependencies_installed_or_in_error
    • ToolShedRepository.tool_dependencies_missing_or_being_installed
    • ToolShedRepository.tool_dependencies_with_installation_errors
    • ToolShedRepository.tool_shed_path_name
    • ToolShedRepository.tuples_of_repository_dependencies_needed_for_compiling_td
    • ToolShedRepository.uninstalled_repository_dependencies
    • ToolShedRepository.uninstalled_tool_dependencies
    • ToolShedRepository.upgrade_available
    • ToolShedRepository.table
  • RepositoryRepositoryDependencyAssociation
    • RepositoryRepositoryDependencyAssociation.id
    • RepositoryRepositoryDependencyAssociation.create_time
    • RepositoryRepositoryDependencyAssociation.update_time
    • RepositoryRepositoryDependencyAssociation.repository
    • RepositoryRepositoryDependencyAssociation.repository_dependency
    • RepositoryRepositoryDependencyAssociation.__init__()
    • RepositoryRepositoryDependencyAssociation.tool_shed_repository_id
    • RepositoryRepositoryDependencyAssociation.repository_dependency_id
    • RepositoryRepositoryDependencyAssociation.table
  • RepositoryDependency
    • RepositoryDependency.id
    • RepositoryDependency.create_time
    • RepositoryDependency.update_time
    • RepositoryDependency.repository
    • RepositoryDependency.__init__()
    • RepositoryDependency.tool_shed_repository_id
    • RepositoryDependency.table
  • ToolDependency
    • ToolDependency.id
    • ToolDependency.create_time
    • ToolDependency.update_time
    • ToolDependency.tool_shed_repository
    • ToolDependency.installation_status
    • ToolDependency.states
      • ToolDependency.states.INSTALLING
      • ToolDependency.states.OK
      • ToolDependency.states.WARNING
      • ToolDependency.states.ERROR
      • ToolDependency.states.UNINSTALLED
    • ToolDependency.__init__()
    • ToolDependency.tool_shed_repository_id
    • ToolDependency.name
    • ToolDependency.table
    • ToolDependency.version
    • ToolDependency.type
    • ToolDependency.status
    • ToolDependency.error_message
    • ToolDependency.can_install
    • ToolDependency.can_uninstall
    • ToolDependency.can_update
    • ToolDependency.in_error_state
    • ToolDependency.installation_directory()
    • ToolDependency.is_installed
  • ToolVersion
    • ToolVersion.__init__()
    • ToolVersion.table
    • ToolVersion.id
    • ToolVersion.create_time
    • ToolVersion.update_time
    • ToolVersion.tool_id
    • ToolVersion.tool_shed_repository_id
    • ToolVersion.parent_tool_association
    • ToolVersion.child_tool_association
    • ToolVersion.tool_shed_repository
    • ToolVersion.dict_element_visible_keys
    • ToolVersion.to_dict()
  • ToolVersionAssociation
    • ToolVersionAssociation.__init__()
    • ToolVersionAssociation.table
    • ToolVersionAssociation.id
    • ToolVersionAssociation.tool_id
    • ToolVersionAssociation.parent_id
  • Submodules
  • galaxy.model.tool_shed_install.mapping module
    • init()
    • create_database_objects()
    • configure_model_mapping()
• galaxy.model.triggers package
  • Submodules
  • galaxy.model.triggers.history_update_time_field module
    • install_timestamp_triggers()
    • drop_timestamp_triggers()
    • get_timestamp_install_sql()
    • get_timestamp_drop_sql()
    • build_pg_timestamp_fn()
    • build_pg_trigger()
    • build_timestamp_trigger()
    • build_drop_trigger()
    • get_trigger_name()
  • galaxy.model.triggers.update_audit_table module
    • install()
    • remove()
    • get_trigger_name()
  • galaxy.model.triggers.utils module
    • execute_statements()
• galaxy.model.unittest_utils package
  • GalaxyDataTestApp
    • GalaxyDataTestApp.file_sources
    • GalaxyDataTestApp.__init__()
    • GalaxyDataTestApp.security
    • GalaxyDataTestApp.model
    • GalaxyDataTestApp.security_agent
    • GalaxyDataTestApp.init_datatypes()
  • GalaxyDataTestConfig
    • GalaxyDataTestConfig.__init__()
    • GalaxyDataTestConfig.root
    • GalaxyDataTestConfig.data_dir
    • GalaxyDataTestConfig.security
    • GalaxyDataTestConfig.database_connection
  • Submodules
  • galaxy.model.unittest_utils.data_app module
    • GalaxyDataTestConfig
      • GalaxyDataTestConfig.__init__()
      • GalaxyDataTestConfig.root
      • GalaxyDataTestConfig.data_dir
      • GalaxyDataTestConfig.security
      • GalaxyDataTestConfig.database_connection
    • GalaxyDataTestApp
      • GalaxyDataTestApp.file_sources
      • GalaxyDataTestApp.__init__()
      • GalaxyDataTestApp.security
      • GalaxyDataTestApp.model
      • GalaxyDataTestApp.security_agent
      • GalaxyDataTestApp.init_datatypes()
    • MockSetExternalTool
      • MockSetExternalTool.regenerate_imported_metadata_if_needed()
  • galaxy.model.unittest_utils.store_fixtures module
    • now()
    • one_ld_library_model_store_dict()
    • one_ld_library_deferred_model_store_dict()
    • one_hda_model_store_dict()
    • history_model_store_dict()
    • deferred_hda_model_store_dict()
    • deferred_hda_model_store_dict_bam()
• galaxy.model.view package
  • HistoryDatasetCollectionJobStateSummary
    • HistoryDatasetCollectionJobStateSummary.name
    • HistoryDatasetCollectionJobStateSummary.aggregate_state_query
    • HistoryDatasetCollectionJobStateSummary.pkeys
    • HistoryDatasetCollectionJobStateSummary.__init__()
    • HistoryDatasetCollectionJobStateSummary.all_jobs
    • HistoryDatasetCollectionJobStateSummary.deleted
    • HistoryDatasetCollectionJobStateSummary.deleted_new
    • HistoryDatasetCollectionJobStateSummary.error
    • HistoryDatasetCollectionJobStateSummary.failed
    • HistoryDatasetCollectionJobStateSummary.hdca_id
    • HistoryDatasetCollectionJobStateSummary.new
    • HistoryDatasetCollectionJobStateSummary.ok
    • HistoryDatasetCollectionJobStateSummary.paused
    • HistoryDatasetCollectionJobStateSummary.queued
    • HistoryDatasetCollectionJobStateSummary.resubmitted
    • HistoryDatasetCollectionJobStateSummary.running
    • HistoryDatasetCollectionJobStateSummary.skipped
    • HistoryDatasetCollectionJobStateSummary.upload
    • HistoryDatasetCollectionJobStateSummary.waiting
  • Submodules
  • galaxy.model.view.utils module
    • View
    • CreateView
      • CreateView.__init__()
    • DropView
      • DropView.__init__()
    • compile_create_view()
    • compile_drop_view()
    • is_view_model()
    • install_views()

Submodules

galaxy.model.base module

Shared model and mapping code between Galaxy and Tool Shed, trying to generalize to generic database connections.

class galaxy.model.base.ModelMapping(model_modules, engine)

Bases: Bunch

__init__(model_modules, engine)

request_scopefunc()

Return a value that is used as dictionary key for sqlalchemy’s ScopedRegistry.

This ensures that threads or request contexts will receive a single identical session from the ScopedRegistry.

static set_request_id(request_id)

unset_request_id(request_id)

property context: scoped_session

property Session

For backward compat., deprecated.

class galaxy.model.base.SharedModelMapping(model_modules, engine)

Bases: ModelMapping

Model mapping containing references to classes shared between Galaxy and ToolShed.

Generally things can be more strongly typed when importing models directly, but we need a way to do app.model.<CLASS> for common code shared by the tool shed and Galaxy.

User: Type

GalaxySession: Type

APIKeys: Type

PasswordResetToken: Type

galaxy.model.base.versioned_objects_strict(iter)

galaxy.model.base.versioned_objects(iter)

galaxy.model.base.versioned_session(session)

galaxy.model.custom_types module

class galaxy.model.custom_types.SafeJsonEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)

Bases: JSONEncoder

default(obj)

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

class galaxy.model.custom_types.GalaxyLargeBinary(length=None)

Bases: LargeBinary

result_processor(dialect, coltype)

Return a conversion function for processing result row values.

Returns a callable which will receive a result row column value as the sole positional argument and will return a value to return to the user.

If processing is not necessary, the method should return None.

Note

This method is only called relative to a dialect specific type object, which is often private to a dialect in use and is not the same type object as the public facing one, which means it’s not feasible to subclass a types.TypeEngine class in order to provide an alternate _types.TypeEngine.result_processor() method, unless subclassing the _types.UserDefinedType class explicitly.

To provide alternate behavior for _types.TypeEngine.result_processor(), implement a _types.TypeDecorator class and provide an implementation of _types.TypeDecorator.process_result_value().

See also

types_typedecorator

Parameters

• dialect – Dialect instance in use.

• coltype – DBAPI coltype argument received in cursor.description.

class galaxy.model.custom_types.JSONType(*args, **kwargs)

Bases: TypeDecorator

Represents an immutable structure as a json-encoded string.

If default is, for example, a dict, then a NULL value in the database will be exposed as an empty dict.

impl

alias of GalaxyLargeBinary

cache_ok = True

Indicate if statements using this ExternalType are “safe to cache”.

The default value None will emit a warning and then not allow caching of a statement which includes this type. Set to False to disable statements using this type from being cached at all without a warning. When set to True, the object’s class and selected elements from its state will be used as part of the cache key. For example, using a TypeDecorator:

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

    def __init__(self, choices):
        self.choices = tuple(choices)
        self.internal_only = True

The cache key for the above type would be equivalent to:

>>> MyType(["a", "b", "c"])._static_cache_key
(<class '__main__.MyType'>, ('choices', ('a', 'b', 'c')))

The caching scheme will extract attributes from the type that correspond to the names of parameters in the __init__() method. Above, the “choices” attribute becomes part of the cache key but “internal_only” does not, because there is no parameter named “internal_only”.

The requirements for cacheable elements is that they are hashable and also that they indicate the same SQL rendered for expressions using this type every time for a given cache value.

To accommodate for datatypes that refer to unhashable structures such as dictionaries, sets and lists, these objects can be made “cacheable” by assigning hashable structures to the attributes whose names correspond with the names of the arguments. For example, a datatype which accepts a dictionary of lookup values may publish this as a sorted series of tuples. Given a previously un-cacheable type as:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    this is the non-cacheable version, as "self.lookup" is not
    hashable.

    '''

    def __init__(self, lookup):
        self.lookup = lookup

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self.lookup" ...

Where “lookup” is a dictionary. The type will not be able to generate a cache key:

>>> type_ = LookupType({"a": 10, "b": 20})
>>> type_._static_cache_key
<stdin>:1: SAWarning: UserDefinedType LookupType({'a': 10, 'b': 20}) will not
produce a cache key because the ``cache_ok`` flag is not set to True.
Set this flag to True if this type object's state is safe to use
in a cache key, or False to disable this warning.
symbol('no_cache')

If we did set up such a cache key, it wouldn’t be usable. We would get a tuple structure that contains a dictionary inside of it, which cannot itself be used as a key in a “cache dictionary” such as SQLAlchemy’s statement cache, since Python dictionaries aren’t hashable:

>>> # set cache_ok = True
>>> type_.cache_ok = True

>>> # this is the cache key it would generate
>>> key = type_._static_cache_key
>>> key
(<class '__main__.LookupType'>, ('lookup', {'a': 10, 'b': 20}))

>>> # however this key is not hashable, will fail when used with
>>> # SQLAlchemy statement cache
>>> some_cache = {key: "some sql value"}
Traceback (most recent call last): File "<stdin>", line 1,
in <module> TypeError: unhashable type: 'dict'

The type may be made cacheable by assigning a sorted tuple of tuples to the “.lookup” attribute:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    The dictionary is stored both as itself in a private variable,
    and published in a public variable as a sorted tuple of tuples,
    which is hashable and will also return the same value for any
    two equivalent dictionaries.  Note it assumes the keys and
    values of the dictionary are themselves hashable.

    '''

    cache_ok = True

    def __init__(self, lookup):
        self._lookup = lookup

        # assume keys/values of "lookup" are hashable; otherwise
        # they would also need to be converted in some way here
        self.lookup = tuple(
            (key, lookup[key]) for key in sorted(lookup)
        )

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self._lookup" ...

Where above, the cache key for LookupType({"a": 10, "b": 20}) will be:

>>> LookupType({"a": 10, "b": 20})._static_cache_key
(<class '__main__.LookupType'>, ('lookup', (('a', 10), ('b', 20))))

New in version 1.4.14: - added the cache_ok flag to allow some configurability of caching for TypeDecorator classes.

New in version 1.4.28: - added the ExternalType mixin which generalizes the cache_ok flag to both the TypeDecorator and UserDefinedType classes.

See also

sql_caching

process_bind_param(value, dialect)

Receive a bound parameter value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for incoming data values. This method is called at statement execution time and is passed the literal Python data value which is to be associated with a bound parameter in the statement.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for data values being received in result rows coming from the database. This method is called at result fetching time and is passed the literal Python data value that’s extracted from a database result row.

The operation could be anything desired to perform custom behavior, such as transforming or deserializing data.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

load_dialect_impl(dialect)

Return a TypeEngine object corresponding to a dialect.

This is an end-user override hook that can be used to provide differing types depending on the given dialect. It is used by the TypeDecorator implementation of type_engine() to help determine what type should ultimately be returned for a given TypeDecorator.

By default returns self.impl.

copy_value(value)

compare_values(x, y)

Given two values, compare them for equality.

By default this calls upon TypeEngine.compare_values() of the underlying “impl”, which in turn usually uses the Python equals operator ==.

This function is used by the ORM to compare an original-loaded value with an intercepted “changed” value, to determine if a net change has occurred.

class galaxy.model.custom_types.MutableJSONType(*args, **kwargs)

Bases: JSONType

Associated with MutationObj

class galaxy.model.custom_types.MutationObj(*args, **kwds)

Bases: Mutable

Mutable JSONType for SQLAlchemy from original gist: https://gist.github.com/dbarnett/1730610

Using minor changes from this fork of the gist: https://gist.github.com/miracle2k/52a031cced285ba9b8cd

And other minor changes to make it work for us.

classmethod coerce(key, value)

Given a value, coerce it into the target type.

Can be overridden by custom subclasses to coerce incoming data into a particular type.

By default, raises ValueError.

This method is called in different scenarios depending on if the parent class is of type Mutable or of type MutableComposite. In the case of the former, it is called for both attribute-set operations as well as during ORM loading operations. For the latter, it is only called during attribute-set operations; the mechanics of the composite() construct handle coercion during load operations.

Parameters

• key – string name of the ORM-mapped attribute being set.

• value – the incoming value.

Returns

the method should return the coerced value, or raise ValueError if the coercion cannot be completed.

class galaxy.model.custom_types.MutationDict(*args, **kwds)

Bases: MutationObj, dict

classmethod coerce(key, value)

Convert plain dictionary to MutationDict

pop(k[, d]) → v, remove specified key and return the corresponding value.

If key is not found, d is returned if given, otherwise KeyError is raised

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

class galaxy.model.custom_types.MutationList(*args, **kwds)

Bases: MutationObj, list

classmethod coerce(key, value)

Convert plain list to MutationList

append(value)

Append object to the end of the list.

insert(idx, value)

Insert object before index.

extend(values)

Extend list by appending elements from the iterable.

pop(*args, **kw)

Remove and return item at index (default last).

Raises IndexError if list is empty or index is out of range.

remove(value)

Remove first occurrence of value.

Raises ValueError if the value is not present.

galaxy.model.custom_types.total_size(o, handlers=None, verbose=False)

Returns the approximate memory footprint an object and all of its contents.

Automatically finds the contents of the following builtin containers and their subclasses: tuple, list, deque, dict, set and frozenset. To search other containers, add handlers to iterate over their contents:

handlers = {SomeContainerClass: iter,

OtherContainerClass: OtherContainerClass.get_elements}

Recipe from: https://code.activestate.com/recipes/577504-compute-memory-footprint-of-an-object-and-its-cont/

class galaxy.model.custom_types.MetadataType(*args, **kwargs)

Bases: JSONType

Backward compatible metadata type. Can read pickles or JSON, but always writes in JSON.

cache_ok = True

Indicate if statements using this ExternalType are “safe to cache”.

The default value None will emit a warning and then not allow caching of a statement which includes this type. Set to False to disable statements using this type from being cached at all without a warning. When set to True, the object’s class and selected elements from its state will be used as part of the cache key. For example, using a TypeDecorator:

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

    def __init__(self, choices):
        self.choices = tuple(choices)
        self.internal_only = True

The cache key for the above type would be equivalent to:

>>> MyType(["a", "b", "c"])._static_cache_key
(<class '__main__.MyType'>, ('choices', ('a', 'b', 'c')))

The caching scheme will extract attributes from the type that correspond to the names of parameters in the __init__() method. Above, the “choices” attribute becomes part of the cache key but “internal_only” does not, because there is no parameter named “internal_only”.

The requirements for cacheable elements is that they are hashable and also that they indicate the same SQL rendered for expressions using this type every time for a given cache value.

To accommodate for datatypes that refer to unhashable structures such as dictionaries, sets and lists, these objects can be made “cacheable” by assigning hashable structures to the attributes whose names correspond with the names of the arguments. For example, a datatype which accepts a dictionary of lookup values may publish this as a sorted series of tuples. Given a previously un-cacheable type as:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    this is the non-cacheable version, as "self.lookup" is not
    hashable.

    '''

    def __init__(self, lookup):
        self.lookup = lookup

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self.lookup" ...

Where “lookup” is a dictionary. The type will not be able to generate a cache key:

>>> type_ = LookupType({"a": 10, "b": 20})
>>> type_._static_cache_key
<stdin>:1: SAWarning: UserDefinedType LookupType({'a': 10, 'b': 20}) will not
produce a cache key because the ``cache_ok`` flag is not set to True.
Set this flag to True if this type object's state is safe to use
in a cache key, or False to disable this warning.
symbol('no_cache')

If we did set up such a cache key, it wouldn’t be usable. We would get a tuple structure that contains a dictionary inside of it, which cannot itself be used as a key in a “cache dictionary” such as SQLAlchemy’s statement cache, since Python dictionaries aren’t hashable:

>>> # set cache_ok = True
>>> type_.cache_ok = True

>>> # this is the cache key it would generate
>>> key = type_._static_cache_key
>>> key
(<class '__main__.LookupType'>, ('lookup', {'a': 10, 'b': 20}))

>>> # however this key is not hashable, will fail when used with
>>> # SQLAlchemy statement cache
>>> some_cache = {key: "some sql value"}
Traceback (most recent call last): File "<stdin>", line 1,
in <module> TypeError: unhashable type: 'dict'

The type may be made cacheable by assigning a sorted tuple of tuples to the “.lookup” attribute:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    The dictionary is stored both as itself in a private variable,
    and published in a public variable as a sorted tuple of tuples,
    which is hashable and will also return the same value for any
    two equivalent dictionaries.  Note it assumes the keys and
    values of the dictionary are themselves hashable.

    '''

    cache_ok = True

    def __init__(self, lookup):
        self._lookup = lookup

        # assume keys/values of "lookup" are hashable; otherwise
        # they would also need to be converted in some way here
        self.lookup = tuple(
            (key, lookup[key]) for key in sorted(lookup)
        )

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self._lookup" ...

Where above, the cache key for LookupType({"a": 10, "b": 20}) will be:

>>> LookupType({"a": 10, "b": 20})._static_cache_key
(<class '__main__.LookupType'>, ('lookup', (('a', 10), ('b', 20))))

New in version 1.4.14: - added the cache_ok flag to allow some configurability of caching for TypeDecorator classes.

New in version 1.4.28: - added the ExternalType mixin which generalizes the cache_ok flag to both the TypeDecorator and UserDefinedType classes.

See also

sql_caching

process_bind_param(value, dialect)

Receive a bound parameter value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for incoming data values. This method is called at statement execution time and is passed the literal Python data value which is to be associated with a bound parameter in the statement.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for data values being received in result rows coming from the database. This method is called at result fetching time and is passed the literal Python data value that’s extracted from a database result row.

The operation could be anything desired to perform custom behavior, such as transforming or deserializing data.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

class galaxy.model.custom_types.UUIDType(*args, **kwargs)

Bases: TypeDecorator

Platform-independent UUID type.

Based on http://docs.sqlalchemy.org/en/rel_0_8/core/types.html#backend-agnostic-guid-type Changed to remove sqlalchemy 0.8 specific code

CHAR(32), storing as stringified hex values.

impl

alias of CHAR

cache_ok = True

Indicate if statements using this ExternalType are “safe to cache”.

The default value None will emit a warning and then not allow caching of a statement which includes this type. Set to False to disable statements using this type from being cached at all without a warning. When set to True, the object’s class and selected elements from its state will be used as part of the cache key. For example, using a TypeDecorator:

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

    def __init__(self, choices):
        self.choices = tuple(choices)
        self.internal_only = True

The cache key for the above type would be equivalent to:

>>> MyType(["a", "b", "c"])._static_cache_key
(<class '__main__.MyType'>, ('choices', ('a', 'b', 'c')))

The caching scheme will extract attributes from the type that correspond to the names of parameters in the __init__() method. Above, the “choices” attribute becomes part of the cache key but “internal_only” does not, because there is no parameter named “internal_only”.

The requirements for cacheable elements is that they are hashable and also that they indicate the same SQL rendered for expressions using this type every time for a given cache value.

To accommodate for datatypes that refer to unhashable structures such as dictionaries, sets and lists, these objects can be made “cacheable” by assigning hashable structures to the attributes whose names correspond with the names of the arguments. For example, a datatype which accepts a dictionary of lookup values may publish this as a sorted series of tuples. Given a previously un-cacheable type as:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    this is the non-cacheable version, as "self.lookup" is not
    hashable.

    '''

    def __init__(self, lookup):
        self.lookup = lookup

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self.lookup" ...

Where “lookup” is a dictionary. The type will not be able to generate a cache key:

>>> type_ = LookupType({"a": 10, "b": 20})
>>> type_._static_cache_key
<stdin>:1: SAWarning: UserDefinedType LookupType({'a': 10, 'b': 20}) will not
produce a cache key because the ``cache_ok`` flag is not set to True.
Set this flag to True if this type object's state is safe to use
in a cache key, or False to disable this warning.
symbol('no_cache')

If we did set up such a cache key, it wouldn’t be usable. We would get a tuple structure that contains a dictionary inside of it, which cannot itself be used as a key in a “cache dictionary” such as SQLAlchemy’s statement cache, since Python dictionaries aren’t hashable:

>>> # set cache_ok = True
>>> type_.cache_ok = True

>>> # this is the cache key it would generate
>>> key = type_._static_cache_key
>>> key
(<class '__main__.LookupType'>, ('lookup', {'a': 10, 'b': 20}))

>>> # however this key is not hashable, will fail when used with
>>> # SQLAlchemy statement cache
>>> some_cache = {key: "some sql value"}
Traceback (most recent call last): File "<stdin>", line 1,
in <module> TypeError: unhashable type: 'dict'

The type may be made cacheable by assigning a sorted tuple of tuples to the “.lookup” attribute:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    The dictionary is stored both as itself in a private variable,
    and published in a public variable as a sorted tuple of tuples,
    which is hashable and will also return the same value for any
    two equivalent dictionaries.  Note it assumes the keys and
    values of the dictionary are themselves hashable.

    '''

    cache_ok = True

    def __init__(self, lookup):
        self._lookup = lookup

        # assume keys/values of "lookup" are hashable; otherwise
        # they would also need to be converted in some way here
        self.lookup = tuple(
            (key, lookup[key]) for key in sorted(lookup)
        )

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self._lookup" ...

Where above, the cache key for LookupType({"a": 10, "b": 20}) will be:

>>> LookupType({"a": 10, "b": 20})._static_cache_key
(<class '__main__.LookupType'>, ('lookup', (('a', 10), ('b', 20))))

New in version 1.4.14: - added the cache_ok flag to allow some configurability of caching for TypeDecorator classes.

New in version 1.4.28: - added the ExternalType mixin which generalizes the cache_ok flag to both the TypeDecorator and UserDefinedType classes.

See also

sql_caching

load_dialect_impl(dialect)

Return a TypeEngine object corresponding to a dialect.

This is an end-user override hook that can be used to provide differing types depending on the given dialect. It is used by the TypeDecorator implementation of type_engine() to help determine what type should ultimately be returned for a given TypeDecorator.

By default returns self.impl.

process_bind_param(value, dialect)

Receive a bound parameter value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for incoming data values. This method is called at statement execution time and is passed the literal Python data value which is to be associated with a bound parameter in the statement.

The operation could be anything desired to perform custom behavior, such as transforming or serializing data. This could also be used as a hook for validating logic.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Custom subclasses of _types.TypeDecorator should override this method to provide custom behaviors for data values being received in result rows coming from the database. This method is called at result fetching time and is passed the literal Python data value that’s extracted from a database result row.

The operation could be anything desired to perform custom behavior, such as transforming or deserializing data.

Parameters

• value – Data to operate upon, of any type expected by this method in the subclass. Can be None.

• dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

class galaxy.model.custom_types.TrimmedString(*args, **kwargs)

Bases: TypeDecorator

impl

alias of String

cache_ok = True

Indicate if statements using this ExternalType are “safe to cache”.

The default value None will emit a warning and then not allow caching of a statement which includes this type. Set to False to disable statements using this type from being cached at all without a warning. When set to True, the object’s class and selected elements from its state will be used as part of the cache key. For example, using a TypeDecorator:

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

    def __init__(self, choices):
        self.choices = tuple(choices)
        self.internal_only = True

The cache key for the above type would be equivalent to:

>>> MyType(["a", "b", "c"])._static_cache_key
(<class '__main__.MyType'>, ('choices', ('a', 'b', 'c')))

The caching scheme will extract attributes from the type that correspond to the names of parameters in the __init__() method. Above, the “choices” attribute becomes part of the cache key but “internal_only” does not, because there is no parameter named “internal_only”.

The requirements for cacheable elements is that they are hashable and also that they indicate the same SQL rendered for expressions using this type every time for a given cache value.

To accommodate for datatypes that refer to unhashable structures such as dictionaries, sets and lists, these objects can be made “cacheable” by assigning hashable structures to the attributes whose names correspond with the names of the arguments. For example, a datatype which accepts a dictionary of lookup values may publish this as a sorted series of tuples. Given a previously un-cacheable type as:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    this is the non-cacheable version, as "self.lookup" is not
    hashable.

    '''

    def __init__(self, lookup):
        self.lookup = lookup

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self.lookup" ...

Where “lookup” is a dictionary. The type will not be able to generate a cache key:

>>> type_ = LookupType({"a": 10, "b": 20})
>>> type_._static_cache_key
<stdin>:1: SAWarning: UserDefinedType LookupType({'a': 10, 'b': 20}) will not
produce a cache key because the ``cache_ok`` flag is not set to True.
Set this flag to True if this type object's state is safe to use
in a cache key, or False to disable this warning.
symbol('no_cache')

If we did set up such a cache key, it wouldn’t be usable. We would get a tuple structure that contains a dictionary inside of it, which cannot itself be used as a key in a “cache dictionary” such as SQLAlchemy’s statement cache, since Python dictionaries aren’t hashable:

>>> # set cache_ok = True
>>> type_.cache_ok = True

>>> # this is the cache key it would generate
>>> key = type_._static_cache_key
>>> key
(<class '__main__.LookupType'>, ('lookup', {'a': 10, 'b': 20}))

>>> # however this key is not hashable, will fail when used with
>>> # SQLAlchemy statement cache
>>> some_cache = {key: "some sql value"}
Traceback (most recent call last): File "<stdin>", line 1,
in <module> TypeError: unhashable type: 'dict'

The type may be made cacheable by assigning a sorted tuple of tuples to the “.lookup” attribute:

class LookupType(UserDefinedType):
    '''a custom type that accepts a dictionary as a parameter.

    The dictionary is stored both as itself in a private variable,
    and published in a public variable as a sorted tuple of tuples,
    which is hashable and will also return the same value for any
    two equivalent dictionaries.  Note it assumes the keys and
    values of the dictionary are themselves hashable.

    '''

    cache_ok = True

    def __init__(self, lookup):
        self._lookup = lookup

        # assume keys/values of "lookup" are hashable; otherwise
        # they would also need to be converted in some way here
        self.lookup = tuple(
            (key, lookup[key]) for key in sorted(lookup)
        )

    def get_col_spec(self, **kw):
        return "VARCHAR(255)"

    def bind_processor(self, dialect):
        # ...  works with "self._lookup" ...

Where above, the cache key for LookupType({"a": 10, "b": 20}) will be:

>>> LookupType({"a": 10, "b": 20})._static_cache_key
(<class '__main__.LookupType'>, ('lookup', (('a', 10), ('b', 20))))

New in version 1.4.14: - added the cache_ok flag to allow some configurability of caching for TypeDecorator classes.

New in version 1.4.28: - added the ExternalType mixin which generalizes the cache_ok flag to both the TypeDecorator and UserDefinedType classes.

See also

sql_caching

process_bind_param(value, dialect)

Automatically truncate string values

galaxy.model.database_heartbeat module

galaxy.model.database_heartbeat.now()

Return a new datetime representing UTC day and time.

class galaxy.model.database_heartbeat.DatabaseHeartbeat(application_stack, heartbeat_interval=60)

Bases: object

__init__(application_stack, heartbeat_interval=60)

property sa_session

property server_name

start()

shutdown()

get_active_processes(last_seen_seconds=None)

Return all processes seen in last_seen_seconds seconds.

add_change_callback(callback)

property is_config_watcher

property worker_process

update_watcher_designation()

send_database_heartbeat()

galaxy.model.database_utils module

galaxy.model.database_utils.database_exists(db_url, database=None)

Check if database exists; connect with db_url.

If database is None, use the database name from db_url.

galaxy.model.database_utils.create_database(db_url, database=None, encoding='utf8', template=None)

Create database; connect with db_url.

If database is None, use the database name from db_url.

galaxy.model.database_utils.sqlalchemy_engine(url)

class galaxy.model.database_utils.DatabaseManager(db_url, database)

Bases: object

static make_manager(db_url, database)

__init__(db_url, database)

class galaxy.model.database_utils.PosgresDatabaseManager(db_url, database)

Bases: DatabaseManager

exists()

create(encoding, template)

class galaxy.model.database_utils.SqliteDatabaseManager(db_url, database)

Bases: DatabaseManager

exists()

create(*args)

class galaxy.model.database_utils.MySQLDatabaseManager(db_url, database)

Bases: DatabaseManager

exists()

create(encoding, *arg)

galaxy.model.database_utils.is_one_database(db1_url: str, db2_url: Optional[str])

Check if the arguments refer to one database. This will be true if only one argument is passed, or if the urls are the same. URLs are strings, so sameness is determined via string comparison.

galaxy.model.deferred module

class galaxy.model.deferred.TransientDatasetPaths(external_filename, external_extra_files_path, metadata_files_dir)

Bases: tuple

property external_filename

Alias for field number 0

property external_extra_files_path

Alias for field number 1

property metadata_files_dir

Alias for field number 2

class galaxy.model.deferred.TransientPathMapper

Bases: object

abstract transient_paths_for(old_dataset: Dataset) → TransientDatasetPaths

Map dataset to transient paths for detached HDAs.

Decide external_filename and external_extra_files_path that the supplied dataset’s materialized dataset should have its files written to.

class galaxy.model.deferred.SimpleTransientPathMapper(staging_directory: str)

Bases: TransientPathMapper

__init__(staging_directory: str)

transient_paths_for(old_dataset: Dataset) → TransientDatasetPaths

Map dataset to transient paths for detached HDAs.

Decide external_filename and external_extra_files_path that the supplied dataset’s materialized dataset should have its files written to.

class galaxy.model.deferred.DatasetInstanceMaterializer(attached: bool, object_store_populator: Optional[ObjectStorePopulator] = None, transient_path_mapper: Optional[TransientPathMapper] = None, file_sources: Optional[ConfiguredFileSources] = None, sa_session: Optional[scoped_session] = None)

Bases: object

This class is responsible for ensuring dataset instances are not deferred.

__init__(attached: bool, object_store_populator: Optional[ObjectStorePopulator] = None, transient_path_mapper: Optional[TransientPathMapper] = None, file_sources: Optional[ConfiguredFileSources] = None, sa_session: Optional[scoped_session] = None)

Constructor for DatasetInstanceMaterializer.

If attached is true, these objects should be created in a supplied object store. If not, this class produces transient HDAs with external_filename and external_extra_files_path set.

ensure_materialized(dataset_instance: Union[HistoryDatasetAssociation, LibraryDatasetDatasetAssociation], target_history: Optional[History] = None) → HistoryDatasetAssociation

Create a new detached dataset instance from the supplied instance.

There will be times we want it usable as is without an objectstore and times we want to place it in an objectstore.

galaxy.model.deferred.materialize_collection_input(collection_input: Union[HistoryDatasetCollectionAssociation, DatasetCollectionElement], materializer: DatasetInstanceMaterializer) → Union[HistoryDatasetCollectionAssociation, DatasetCollectionElement]

galaxy.model.deferred.materialize_collection_instance(hdca: HistoryDatasetCollectionAssociation, materializer: DatasetInstanceMaterializer) → HistoryDatasetCollectionAssociation

galaxy.model.deferred.materializer_factory(attached: bool, object_store: Optional[ObjectStore] = None, object_store_populator: Optional[ObjectStorePopulator] = None, transient_path_mapper: Optional[TransientPathMapper] = None, transient_directory: Optional[str] = None, file_sources: Optional[ConfiguredFileSources] = None, sa_session: Optional[scoped_session] = None) → DatasetInstanceMaterializer

galaxy.model.index_filter_util module

Utility functions used to adapt galaxy.util.search to Galaxy model index queries.

galaxy.model.index_filter_util.text_column_filter(column, term: FilteredTerm)

galaxy.model.index_filter_util.raw_text_column_filter(columns: List[Union[BinaryExpression, InstrumentedAttribute]], term: RawTextTerm)

galaxy.model.index_filter_util.tag_filter(assocation_model_class, term_text, quoted: bool = False)

galaxy.model.index_filter_util.append_user_filter(query, model_class, term: FilteredTerm)

galaxy.model.item_attrs module

galaxy.model.item_attrs.get_foreign_key(source_class, target_class)

Returns foreign key in source class that references target class.

class galaxy.model.item_attrs.UsesAnnotations

Bases: object

Mixin for getting and setting item annotations.

get_item_annotation_str(db_session, user, item)

get_item_annotation_obj(db_session, user, item)

add_item_annotation(db_session, user, item, annotation)

delete_item_annotation(db_session, user, item)

copy_item_annotation(db_session, source_user, source_item, target_user, target_item)

Copy an annotation from a user/item source to a user/item target.

class galaxy.model.item_attrs.UsesItemRatings

Bases: object

Mixin for getting and setting item ratings.

Class makes two assumptions: (1) item-rating association table is named <item_class>RatingAssocation (2) item-rating association table has a column with a foreign key referencing item table that contains the item’s id.

get_ave_item_rating_data(db_session, item, webapp_model=None)

Returns the average rating for an item.

rate_item(db_session, user, item, rating, webapp_model=None)

Rate an item. Return type is <item_class>RatingAssociation.

get_user_item_rating(db_session, user, item, webapp_model=None)

Returns user’s rating for an item. Return type is <item_class>RatingAssociation.

galaxy.model.mapping module

class galaxy.model.mapping.GalaxyModelMapping(model_modules, engine)

Bases: SharedModelMapping

security_agent: GalaxyRBACAgent

thread_local_log: Optional[_local]

User: Type

GalaxySession: Type

galaxy.model.mapping.init(file_path, url, engine_options=None, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True, slow_query_log_threshold=0, thread_local_log: Optional[_local] = None, log_query_counts=False) → GalaxyModelMapping

galaxy.model.mapping.create_additional_database_objects(engine)

galaxy.model.mapping.configure_model_mapping(file_path: str, object_store, use_pbkdf2, engine, map_install_models, thread_local_log) → GalaxyModelMapping

galaxy.model.mapping.init_models_from_config(config: GalaxyAppConfiguration, map_install_models=False, object_store=None, trace_logger=None)

galaxy.model.metadata module

Galaxy Metadata

class galaxy.model.metadata.Statement(target)

Bases: object

This class inserts its target into a list in the surrounding class. the data.Data class has a metaclass which executes these statements. This is how we shove the metadata element spec into the class.

__init__(target)

classmethod process(element)

galaxy.model.metadata.MetadataElement = <galaxy.model.metadata.Statement object>

MetadataParameter sub-classes.

class galaxy.model.metadata.MetadataCollection(parent: Union[DatasetInstance, NoneDataset], session: Optional[Union[galaxy_scoped_session, SessionlessContext]] = None)

Bases: Mapping

MetadataCollection is not a collection at all, but rather a proxy to the real metadata which is stored as a Dictionary. This class handles processing the metadata elements when they are set and retrieved, returning default values in cases when metadata is not set.

__init__(parent: Union[DatasetInstance, NoneDataset], session: Optional[Union[galaxy_scoped_session, SessionlessContext]] = None) → None

get_parent()

set_parent(parent)

property parent

property spec

remove_key(name)

element_is_set(name) → bool

check if the meta data with the given name is set, i.e.

• if the such a metadata actually exists and

• if its value differs from no_value

Parameters

name – the name of the metadata element

Returns

True if the value differes from the no_value False if its equal of if no metadata with the name is specified

get_metadata_parameter(name, **kwd)

make_dict_copy(to_copy)

Makes a deep copy of input iterable to_copy according to self.spec

property requires_dataset_id

from_JSON_dict(filename=None, path_rewriter=None, json_dict=None)

to_JSON_dict(filename=None)

class galaxy.model.metadata.MetadataSpecCollection(*args, **kwds)

Bases: OrderedDict

A simple extension of OrderedDict which allows cleaner access to items and allows the values to be iterated over directly as if it were a list. append() is also implemented for simplicity and does not “append”.

__init__(*args, **kwds)

append(item)

class galaxy.model.metadata.MetadataParameter(spec)

Bases: object

__init__(spec)

get_field(value=None, context=None, other_values=None, **kwd)

to_string(value)

to_safe_string(value)

make_copy(value, target_context: MetadataCollection, source_context)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

validate(value)

Throw an exception if the value is invalid.

unwrap(form_value)

Turns a value into its storable form.

wrap(value, session)

Turns a value into its usable form.

from_external_value(value, parent)

Turns a value read from an external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

class galaxy.model.metadata.MetadataElementSpec(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

Bases: object

Defines a metadata element and adds it to the metadata_spec (which is a MetadataSpecCollection) of datatype.

__init__(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

get(name, default=None)

wrap(value, session)

Turns a stored value into its usable form.

unwrap(value)

Turns an incoming value into its storable form.

class galaxy.model.metadata.SelectParameter(spec)

Bases: MetadataParameter

__init__(spec)

to_string(value)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

wrap(value, session)

Turns a value into its usable form.

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

class galaxy.model.metadata.DBKeyParameter(spec)

Bases: SelectParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

make_copy(value, target_context: MetadataCollection, source_context)

class galaxy.model.metadata.RangeParameter(spec)

Bases: SelectParameter

__init__(spec)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

class galaxy.model.metadata.ColumnParameter(spec)

Bases: RangeParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

class galaxy.model.metadata.ColumnTypesParameter(spec)

Bases: MetadataParameter

to_string(value)

class galaxy.model.metadata.ListParameter(spec)

Bases: MetadataParameter

to_string(value)

class galaxy.model.metadata.DictParameter(spec)

Bases: MetadataParameter

to_string(value)

to_safe_string(value)

class galaxy.model.metadata.PythonObjectParameter(spec)

Bases: MetadataParameter

to_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

class galaxy.model.metadata.FileParameter(spec)

Bases: MetadataParameter

to_string(value)

to_safe_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

wrap(value, session)

Turns a value into its usable form.

make_copy(value, target_context: MetadataCollection, source_context)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

from_external_value(value, parent, path_rewriter=None)

Turns a value read from a external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

new_file(dataset=None, metadata_tmp_files_dir=None, **kwds)

class galaxy.model.metadata.MetadataTempFile(metadata_tmp_files_dir=None, **kwds)

Bases: object

__init__(metadata_tmp_files_dir=None, **kwds)

tmp_dir = 'database/tmp'

property file_name

to_JSON()

classmethod from_JSON(json_dict)

classmethod is_JSONified_value(value)

classmethod cleanup_from_JSON_dict_filename(filename)

galaxy.model.none_like module

Objects with No values

class galaxy.model.none_like.RecursiveNone

Bases: object

class galaxy.model.none_like.NoneDataset(datatypes_registry=None, ext='data', dbkey='?')

Bases: RecursiveNone

__init__(datatypes_registry=None, ext='data', dbkey='?')

missing_meta()

galaxy.model.scoped_session module

These classes are used for registering different scoped_session objects with the DI framework. This type distinction is necessary because we need to store scoped_session objects that produce sessions that may have different binds (i.e., if the tool_shed_install model uses a different database).

class galaxy.model.scoped_session.galaxy_scoped_session(session_factory, scopefunc=None)

Bases: scoped_session

scoped_session used for galaxy model.

class galaxy.model.scoped_session.install_model_scoped_session(session_factory, scopefunc=None)

Bases: scoped_session

scoped_session used for tool_shed_install model.

galaxy.model.search module

The GQL (Galaxy Query Language) search engine parsers a simple ‘SQL-Like’ query syntax to obtain items from the Galaxy installations. Rather then allow/force the user to do queries on the Galaxy schema, it uses a small set of ‘Views’ which are simple table representations of complex galaxy ideas. So while a history and its tags may exist in seperate tables in the real schema, in GQL they exist in the same view

Example Queries:

select name, id, file_size from hda

select name from hda

select name, model_class from ldda

select * from history

select * from workflow

select id, name from history where name=’Unnamed history’

select * from history where name=’Unnamed history’

class galaxy.model.search.ViewField(name, sqlalchemy_field=None, handler=None, post_filter=None, id_decode=False)

Bases: object

A ViewField defines a field in a view that filter operations can be applied to These filter operations are either handled with standard sqlalchemy filter calls, or passed to specialized handlers (such as when a table join would be needed to do the filtering)

Parameters:

sqlalchemy_field - Simple filtering using existing table columns, the argument is an sqlalchemy column

that the right hand value will be compared against

handler - Requires more specialized code to do filtering, usually requires a table join in order to

process the conditional

post_filter - Unable to do simple sqlalchemy based table filtering, filter is applied to loaded object

Thus methods avalible to the object can be used for filtering. example: a library folder must climb its chain of parents to find out which library it belongs to

__init__(name, sqlalchemy_field=None, handler=None, post_filter=None, id_decode=False)

class galaxy.model.search.ViewQueryBaseClass

Bases: object

FIELDS: Dict[str, ViewField] = {}

VIEW_NAME = 'undefined'

__init__()

decode_query_ids(trans, conditional)

filter(left, operator, right)

search(trans)

get_results(force_query=False)

galaxy.model.search.library_extended_metadata_filter(view, left, operator, right)

galaxy.model.search.ldda_parent_library_filter(item, left, operator, right)

class galaxy.model.search.LibraryDatasetDatasetView

Bases: ViewQueryBaseClass

VIEW_NAME = 'library_dataset_dataset'

FIELDS: Dict[str, ViewField] = {'data_type': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'extended_metadata': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'parent_library_id': <galaxy.model.search.ViewField object>}

search(trans)

class galaxy.model.search.LibraryView

Bases: ViewQueryBaseClass

VIEW_NAME = 'library'

FIELDS: Dict[str, ViewField] = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.library_folder_parent_library_id_filter(item, left, operator, right)

galaxy.model.search.library_path_filter(item, left, operator, right)

class galaxy.model.search.LibraryFolderView

Bases: ViewQueryBaseClass

VIEW_NAME = 'library_folder'

FIELDS: Dict[str, ViewField] = {'id': <galaxy.model.search.ViewField object>, 'library_path': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'parent_id': <galaxy.model.search.ViewField object>, 'parent_library_id': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.library_dataset_name_filter(item, left, operator, right)

class galaxy.model.search.LibraryDatasetView

Bases: ViewQueryBaseClass

VIEW_NAME = 'library_dataset'

FIELDS: Dict[str, ViewField] = {'folder_id': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>}

search(trans)

class galaxy.model.search.ToolView

Bases: ViewQueryBaseClass

VIEW_NAME = 'tool'

FIELDS: Dict[str, ViewField] = {'id': <galaxy.model.search.ViewField object>, 'tool_id': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.history_dataset_handle_tag(view, left, operator, right)

galaxy.model.search.history_dataset_extended_metadata_filter(view, left, operator, right)

class galaxy.model.search.HistoryDatasetView

Bases: ViewQueryBaseClass

DOMAIN = 'history_dataset'

FIELDS: Dict[str, ViewField] = {'copied_from_hda_id': <galaxy.model.search.ViewField object>, 'copied_from_ldda_id': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'extended_metadata': <galaxy.model.search.ViewField object>, 'history_id': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.history_handle_tag(view, left, operator, right)

galaxy.model.search.history_handle_annotation(view, left, operator, right)

class galaxy.model.search.HistoryView

Bases: ViewQueryBaseClass

DOMAIN = 'history'

FIELDS: Dict[str, ViewField] = {'annotation': <galaxy.model.search.ViewField object>, 'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.workflow_tag_handler(view, left, operator, right)

class galaxy.model.search.WorkflowView

Bases: ViewQueryBaseClass

DOMAIN = 'workflow'

FIELDS: Dict[str, ViewField] = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'name': <galaxy.model.search.ViewField object>, 'tag': <galaxy.model.search.ViewField object>}

search(trans)

galaxy.model.search.job_param_filter(view, left, operator, right)

galaxy.model.search.job_input_hda_filter(view, left, operator, right)

galaxy.model.search.job_input_ldda_filter(view, left, operator, right)

galaxy.model.search.job_output_hda_filter(view, left, operator, right)

class galaxy.model.search.JobView

Bases: ViewQueryBaseClass

DOMAIN = 'job'

FIELDS: Dict[str, ViewField] = {'input_hda': <galaxy.model.search.ViewField object>, 'input_ldda': <galaxy.model.search.ViewField object>, 'output_hda': <galaxy.model.search.ViewField object>, 'param': <galaxy.model.search.ViewField object>, 'state': <galaxy.model.search.ViewField object>, 'tool_name': <galaxy.model.search.ViewField object>}

search(trans)

class galaxy.model.search.PageView

Bases: ViewQueryBaseClass

DOMAIN = 'page'

FIELDS: Dict[str, ViewField] = {'deleted': <galaxy.model.search.ViewField object>, 'id': <galaxy.model.search.ViewField object>, 'slug': <galaxy.model.search.ViewField object>, 'title': <galaxy.model.search.ViewField object>}

search(trans)

class galaxy.model.search.PageRevisionView

Bases: ViewQueryBaseClass

DOMAIN = 'page_revision'

FIELDS: Dict[str, ViewField] = {'id': <galaxy.model.search.ViewField object>, 'page_id': <galaxy.model.search.ViewField object>, 'title': <galaxy.model.search.ViewField object>}

search(trans)

class galaxy.model.search.GalaxyQuery(field_list, table_name, conditional)

Bases: object

This class represents a data structure of a compiled GQL query

__init__(field_list, table_name, conditional)

class galaxy.model.search.GalaxyQueryComparison(left, operator, right)

Bases: object

This class represents the data structure of the comparison arguments of a compiled GQL query (ie where name=’Untitled History’)

__init__(left, operator, right)

class galaxy.model.search.GalaxyQueryAnd(left, right)

Bases: object

This class represents the data structure of the comparison arguments of a compiled GQL query (ie where name=’Untitled History’)

__init__(left, right)

exception galaxy.model.search.GalaxyParseError

Bases: Exception

class galaxy.model.search.SearchQuery(view, query)

Bases: object

__init__(view, query)

decode_query_ids(trans)

process(trans)

item_to_api_value(item)

class galaxy.model.search.GalaxySearchEngine

Bases: object

Primary class for searching. Parses GQL (Galaxy Query Language) queries and returns a ‘SearchQuery’ class

__init__()

query(query_text)

galaxy.model.security module

class galaxy.model.security.GalaxyRBACAgent(model, permitted_actions=None)

Bases: RBACAgent

__init__(model, permitted_actions=None)

property sa_session

Returns a SQLAlchemy session

sort_by_attr(seq, attr)

Sort the sequence of objects by object’s attribute Arguments: seq - the list or any sequence (including immutable one) of objects to sort. attr - the name of attribute to sort by

get_all_roles(trans, cntrller)

get_roles_for_action(item, action)

Return a list containing the roles associated with given action on given item where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation, LibraryDataset, Dataset.

get_valid_roles(trans, item, query=None, page=None, page_limit=None, is_library_access=False)

This method retrieves the list of possible roles that user can select in the item permissions form. Admins can select any role so the results are paginated in order to save the bandwidth and to speed things up. Standard users can select their own private role, any of their sharing roles and any public role (not private and not sharing).

get_legitimate_roles(trans, item, cntrller)

Return a sorted list of legitimate roles that can be associated with a permission on item where item is a Library or a Dataset. The cntrller param is the controller from which the request is sent. We cannot use trans.user_is_admin because the controller is what is important since admin users do not necessarily have permission to do things on items outside of the admin view.

If cntrller is from the admin side ( e.g., library_admin ):

• if item is public, all roles, including private roles, are legitimate.

• if item is restricted, legitimate roles are derived from the users and groups associated with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or LIBRARY_MANAGE ) on item. Legitimate roles will include private roles.

If cntrller is not from the admin side ( e.g., root, library ):

• if item is public, all non-private roles, except for the current user’s private role, are legitimate.

• if item is restricted, legitimate roles are derived from the users and groups associated with each role that is associated with the access permission on item. Private roles, except for the current user’s private role, will be excluded.

ok_to_display(user, role)

Method for checking if: - a role is private and is the current user’s private role - a role is a sharing role and belongs to the current user

allow_action(roles, action, item)

Method for checking a permission for the current user ( based on roles ) to perform a specific action on an item, which must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation

get_actions_for_items(trans, action, permission_items)

allow_action_on_libitems(trans, user_roles, action, items)

This should be the equivalent of allow_action defined on multiple items. It is meant to specifically replace allow_action for multiple LibraryDatasets, but it could be reproduced or modified for allow_action’s permitted classes - Dataset, Library, LibraryFolder, and LDDAs.

dataset_access_mapping(trans, user_roles, datasets)

For the given list of datasets, return a mapping of the datasets’ ids to whether they can be accessed by the user or not. The datasets input is expected to be a simple list of Dataset objects.

dataset_permission_map_for_access(trans, user_roles, libitems)

For a given list of library items (e.g., Datasets), return a map of the datasets’ ids to whether they can have permission to use that action (e.g., “access” or “modify”) on the dataset. The libitems input is expected to be a simple list of library items, such as Datasets or LibraryDatasets. NB: This is currently only usable for Datasets; it was intended to be used for any library item.

item_permission_map_for_modify(trans, user_roles, libitems)

item_permission_map_for_manage(trans, user_roles, libitems)

item_permission_map_for_add(trans, user_roles, libitems)

can_access_dataset(user_roles, dataset: Dataset)

can_access_datasets(user_roles, action_tuples)

can_access_collection(user_roles: List[Role], collection: DatasetCollection)

can_manage_dataset(roles, dataset)

can_access_library(roles, library)

get_accessible_libraries(trans, user)

Return all data libraries that the received user can access

has_accessible_folders(trans, folder, user, roles, search_downward=True)

has_accessible_library_datasets(trans, folder, user, roles, search_downward=True)

can_access_library_item(roles, item, user)

can_add_library_item(roles, item)

can_modify_library_item(roles, item)

can_manage_library_item(roles, item)

get_item_actions(action, item)

guess_derived_permissions_for_datasets(datasets=None)

Returns a dict of { action : [ role, role, … ] } for the output dataset based upon provided datasets

guess_derived_permissions(all_input_permissions)

Returns a dict of { action : [ role_id, role_id, … ] } for the output dataset based upon input dataset permissions.

all_input_permissions should be of the form {action_name: set(role_ids)}

associate_components(**kwd)

associate_user_group(user, group)

associate_user_role(user, role)

associate_group_role(group, role)

associate_action_dataset_role(action, dataset, role)

create_user_role(user, app)

create_private_user_role(user)

get_private_user_role(user, auto_create=False)

get_role(name, type=None)

create_role(name, description, in_users, in_groups, create_group_for_role=False, type=None)

get_sharing_roles(user)

user_set_default_permissions(user, permissions=None, history=False, dataset=False, bypass_manage_permission=False, default_access_private=False)

user_get_default_permissions(user)

history_set_default_permissions(history, permissions=None, dataset=False, bypass_manage_permission=False)

history_get_default_permissions(history)

set_all_dataset_permissions(dataset, permissions=None, new=False, flush=True)

Set new full permissions on a dataset, eliminating all current permissions. Permission looks like: { Action : [ Role, Role ] }

set_dataset_permission(dataset, permission=None)

Set a specific permission on a dataset, leaving all other current permissions on the dataset alone. Permission looks like: { Action.action : [ Role, Role ] }

get_permissions(item)

Return a dictionary containing the actions and associated roles on item where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation, LibraryDataset, Dataset. The dictionary looks like: { Action : [ Role, Role ] }.

copy_dataset_permissions(src, dst)

privately_share_dataset(dataset, users=None)

set_all_library_permissions(trans, library_item, permissions=None)

set_library_item_permission(library_item, permission=None)

Set a specific permission on a library item, leaving all other current permissions on the item alone. Permission looks like: { Action.action : [ Role, Role ] }

library_is_public(library, contents=False)

library_is_unrestricted(library)

make_library_public(library, contents=False)

folder_is_public(folder)

folder_is_unrestricted(folder)

make_folder_public(folder)

dataset_is_public(dataset: Dataset)

A dataset is considered public if there are no “access” actions associated with it. Any other actions ( ‘manage permissions’, ‘edit metadata’ ) are irrelevant. Accessing dataset.actions will cause a query to be emitted.

dataset_is_unrestricted(trans, dataset)

Different implementation of the method above with signature: def dataset_is_public( self, dataset )

dataset_is_private_to_user(trans, dataset)

If the Dataset object has exactly one access role and that is the current user’s private role then we consider the dataset private.

datasets_are_public(trans, datasets)

Given a transaction object and a list of Datasets, return a mapping from Dataset ids to whether the Dataset is public or not. All Dataset ids should be returned in the mapping’s keys.

make_dataset_public(dataset)

derive_roles_from_access(trans, item_id, cntrller, library=False, **kwd)

copy_library_permissions(trans, source_library_item, target_library_item, user=None)

get_permitted_libraries(trans, user, actions)

This method is historical (it is not currently used), but may be useful again at some point. It returns a dictionary whose keys are library objects and whose values are a comma-separated string of folder ids. This method works with the show_library_item() method below, and it returns libraries for which the received user has permission to perform the received actions. Here is an example call to this method to return all libraries for which the received user has LIBRARY_ADD permission:

libraries = trans.app.security_agent.get_permitted_libraries( trans, user,
    [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )

show_library_item(user, roles, library_item, actions_to_check, hidden_folder_ids='')

This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with the string, True is returned if the current user has permission to perform any 1 of actions_to_check on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets this criteria, if it exists. This method does not necessarily scan the entire library as it returns when it finds the first library_item that allows user to perform any one action in actions_to_check.

get_showable_folders(user, roles, library_item, actions_to_check, hidden_folder_ids=None, showable_folders=None)

This method must be sent an instance of Library(), all the folders of which are scanned to determine if user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should contain a list of folder IDs which was generated when the library was previously scanned using the same actions_to_check. A list of showable folders is generated. This method scans the entire library.

set_entity_user_associations(users=None, roles=None, groups=None, delete_existing_assocs=True)

set_entity_group_associations(groups=None, users=None, roles=None, delete_existing_assocs=True)

set_entity_role_associations(roles=None, users=None, groups=None, delete_existing_assocs=True)

get_component_associations(**kwd)

check_folder_contents(user, roles, folder, hidden_folder_ids='')

This method must always be sent an instance of LibraryFolder(). Recursive execution produces a comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with the string, True is returned if the current user has permission to access folder. Otherwise, cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. This method does not necessarily scan the entire library as it returns when it finds the first folder that is accessible to user.

class galaxy.model.security.HostAgent(model, permitted_actions=None)

Bases: RBACAgent

A simple security agent which allows access to datasets based on host. This exists so that externals sites such as UCSC can gain access to datasets which have permissions which would normally prevent such access.

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

__init__(model, permitted_actions=None)

property sa_session

Returns a SQLAlchemy session

allow_action(addr, action, **kwd)

set_dataset_permissions(hda, user, site)

galaxy.model.tags module

class galaxy.model.tags.ItemTagAssocInfo(item_class, tag_assoc_class, item_id_col)

Bases: object

__init__(item_class, tag_assoc_class, item_id_col)

class galaxy.model.tags.TagHandler(sa_session: galaxy_scoped_session)

Bases: object

Manages CRUD operations related to tagging objects.

__init__(sa_session: galaxy_scoped_session) → None

create_tag_handler_session()

add_tags_from_list(user, item, new_tags_list, flush=True)

remove_tags_from_list(user, item, tag_to_remove_list, flush=True)

set_tags_from_list(user, item, new_tags_list, flush=True)

get_tag_assoc_class(item_class)

Returns tag association class for item class.

get_id_col_in_item_tag_assoc_table(item_class)

Returns item id column in class’ item-tag association table.

get_community_tags(item=None, limit=None)

Returns community tags for an item.

get_tool_tags()

remove_item_tag(user, item, tag_name)

Remove a tag from an item.

delete_item_tags(user, item)

Delete tags from an item.

item_has_tag(user, item, tag)

Returns true if item is has a given tag.

apply_item_tag(user, item, name, value=None, flush=True)

apply_item_tags(user, item, tags_str, flush=True)

Apply tags to an item.

get_tags_str(tags)

Build a string from an item’s tags.

get_tag_by_id(tag_id)

Get a Tag object from a tag id.

get_tag_by_name(tag_name)

Get a Tag object from a tag name (string).

parse_tags(tag_str)

Return a list of tag tuples (name, value) pairs derived from a string.

>>> th = TagHandler("bridge_of_death")
>>> assert th.parse_tags("#ARTHUR") == [('name', 'ARTHUR')]
>>> tags = th.parse_tags("name:Lancelot of Camelot;#Holy Grail;blue")
>>> assert tags == [('name', 'LancelotofCamelot'), ('name', 'HolyGrail'), ('blue', None)]

parse_tags_list(tags_list: List[str]) → List[Tuple[str, Optional[str]]]

Return a list of tag tuples (name, value) pairs derived from a list. Method scrubs tag names and values as well.

>>> th = TagHandler("bridge_of_death")
>>> tags = th.parse_tags_list(["name:Lancelot of Camelot", "#Holy Grail", "blue"])
>>> assert tags == [('name', 'LancelotofCamelot'), ('name', 'HolyGrail'), ('blue', None)]

class galaxy.model.tags.GalaxyTagHandler(sa_session: galaxy_scoped_session)

Bases: TagHandler

__init__(sa_session: galaxy_scoped_session)

class galaxy.model.tags.GalaxyTagHandlerSession(sa_session)

Bases: GalaxyTagHandler

Like GalaxyTagHandler, but avoids one flush per created tag.

__init__(sa_session)

class galaxy.model.tags.GalaxySessionlessTagHandler(sa_session)

Bases: GalaxyTagHandlerSession

get_tag_by_name(tag_name)

Get a Tag object from a tag name (string).

class galaxy.model.tags.CommunityTagHandler(sa_session)

Bases: TagHandler

__init__(sa_session)