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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)

class galaxy.model.RepresentById

Bases: object

id: int

exception galaxy.model.NoConverterException(value)

Bases: Exception

__init__(value)

Initialize self. See help(type(self)) for accurate signature.

exception galaxy.model.ConverterDependencyException(value)

Bases: Exception

__init__(value)

Initialize self. See help(type(self)) for accurate signature.

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']

to_dict(*args, **kwargs)

make_tag_string_list()

copy_tags_from(target_user, source)

property auto_propagated_tags

class galaxy.model.SerializationOptions(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)

Bases: object

__init__(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)

Initialize self. See help(type(self)) for accurate signature.

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.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

property seconds_since_updated

property seconds_since_created

class galaxy.model.WorkerProcess(server_name, hostname)

Bases: galaxy.model.UsesCreateAndUpdateTime, object

__init__(server_name, hostname)

Initialize self. See help(type(self)) for accurate signature.

server_name

hostname

pid

id

table = Table('worker_process', MetaData(bind=None), Column('id', Integer(), table=<worker_process>, primary_key=True, nullable=False), Column('server_name', String(length=255), table=<worker_process>), Column('hostname', String(length=255), table=<worker_process>), Column('pid', Integer(), table=<worker_process>), Column('update_time', DateTime(), table=<worker_process>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)

update_time

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: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

use_pbkdf2 = True

bootstrap_admin_user = False

api_keys: List[galaxy.model.APIKeys]

Data for a Galaxy user or admin and relations to their histories, credentials, and roles.

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)

Initialize self. See help(type(self)) for accurate signature.

email

password

external

deleted

purged

active

activation_token

username

last_password_change

histories

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()

active_histories

addresses

cloudauthz

cloudauthzs

create_time

custos_auth

data_manager_histories

default_permissions

disk_usage

form_values_id

galaxy_sessions

groups

histories_shared_by_others

id: int

non_private_roles

pages_shared_by_others

preferences = ColumnAssociationProxyInstance(AssociationProxy('_preferences', 'value'))

quotas

reset_tokens

roles

social_auth

stored_workflow_menu_entries

stored_workflows

table = Table('galaxy_user', MetaData(bind=None), Column('id', Integer(), table=<galaxy_user>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('email', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('username', TrimmedString(length=255), table=<galaxy_user>), Column('password', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('last_password_change', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function datetime.utcnow>)), Column('external', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<galaxy_user>), Column('deleted', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_user>), Column('active', Boolean(), table=<galaxy_user>, nullable=False, default=ColumnDefault(True)), Column('activation_token', TrimmedString(length=64), table=<galaxy_user>), schema=None)

update_time

values

visualizations_shared_by_others

workflows_shared_by_others

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

Bases: object

__init__(user, token=None)

Initialize self. See help(type(self)) for accurate signature.

token

user

expiration_time

table = Table('password_reset_token', MetaData(bind=None), 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)

user_id

class galaxy.model.DynamicTool(tool_format=None, tool_id=None, tool_version=None, tool_path=None, tool_directory=None, uuid=None, active=True, hidden=True, value=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_collection_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')

dict_element_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')

__init__(tool_format=None, tool_id=None, tool_version=None, tool_path=None, tool_directory=None, uuid=None, active=True, hidden=True, value=None)

Initialize self. See help(type(self)) for accurate signature.

tool_format

tool_id

tool_version

tool_path

tool_directory

active

hidden

value

uuid

create_time

id: int

table = Table('dynamic_tool', MetaData(bind=None), 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)

update_time

workflow_steps

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

Bases: object

__init__(plugin, metric_name, metric_value)

Initialize self. See help(type(self)) for accurate signature.

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

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

__init__(plugin, metric_name, metric_value)

Initialize self. See help(type(self)) for accurate signature.

id: int

job

job_id

metric_name

metric_value

plugin

table = Table('job_metric_text', MetaData(bind=None), 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: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

__init__(plugin, metric_name, metric_value)

Initialize self. See help(type(self)) for accurate signature.

id: int

job

job_id

metric_name

metric_value

plugin

table = Table('job_metric_numeric', MetaData(bind=None), 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: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

__init__(plugin, metric_name, metric_value)

Initialize self. See help(type(self)) for accurate signature.

id: int

metric_name

metric_value

plugin

table = Table('task_metric_text', MetaData(bind=None), 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)

task

task_id

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

Bases: galaxy.model.BaseJobMetric, galaxy.model.RepresentById

__init__(plugin, metric_name, metric_value)

Initialize self. See help(type(self)) for accurate signature.

id: int

metric_name

metric_value

plugin

table = Table('task_metric_numeric', MetaData(bind=None), 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)

task

task_id

class galaxy.model.Job

Bases: galaxy.model.JobLike, galaxy.model.UsesCreateAndUpdateTime, galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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']

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

class states(value)

Bases: str, enum.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'

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__()

Initialize self. See help(type(self)) for accurate signature.

session_id

user_id

tool_id

tool_version

copied_from_job_id

command_line

dependencies

param_filename

parameters

input_datasets

output_datasets

input_dataset_collections

input_dataset_collection_elements

output_dataset_collection_instances

output_dataset_collections

input_library_datasets

output_library_datasets

state

info

job_runner_name

job_runner_external_id

destination_id

destination_params

post_job_actions

state_history

imported

handler

create_time

exit_code

history_id

job_messages

update_time

property running

property finished

io_dicts(exclude_implicit_outputs=False)

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)

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)

serialize(id_encoder, serialization_options)

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

any_output_dataset_collection_instances_deleted = <ColumnProperty at 0x7faa41d40b50; no key>

any_output_dataset_deleted = <ColumnProperty at 0x7faa41d40a50; no key>

container

data_manager_association

dynamic_tool_id

external_output_metadata

galaxy_session

galaxy_version

history

history_dataset_collection_associations

id: int

implicit_collection_jobs_association

interactivetool_entry_points

job

job_stderr

job_stdout

library_folder

library_folder_id

numeric_metrics

object_store_id

params

runner_name

table = Table('job', MetaData(bind=None), 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)

tasks

text_metrics

tool_stderr

tool_stdout

traceback

user

workflow_invocation_step

class galaxy.model.Task(job, working_directory, prepare_files_cmd)

Bases: galaxy.model.JobLike, galaxy.model.RepresentById

A task represents a single component of a job.

class states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

WAITING = 'waiting'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

ERROR = 'error'

DELETED = 'deleted'

__init__(job, working_directory, prepare_files_cmd)

Initialize self. See help(type(self)) for accurate signature.

command_line

state

info

working_directory

task_runner_name

task_runner_external_id

job

exit_code

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)

create_time

execution_time

id: int

job_id

job_messages

job_stderr

job_stdout

numeric_metrics

param_filename

runner_name

table = Table('task', MetaData(bind=None), 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)

text_metrics

tool_stderr

tool_stdout

traceback

update_time

class galaxy.model.JobParameter(name, value)

Bases: galaxy.model.RepresentById

__init__(name, value)

Initialize self. See help(type(self)) for accurate signature.

name

value

copy()

id: int

job_id

table = Table('job_parameter', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset)

Initialize self. See help(type(self)) for accurate signature.

name

dataset

dataset_version

dataset_id

id: int

job

job_id

table = Table('job_to_input_dataset', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset)

Initialize self. See help(type(self)) for accurate signature.

name

dataset

dataset_id

id: int

job

job_id

table = Table('job_to_output_dataset', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset_collection)

Initialize self. See help(type(self)) for accurate signature.

name

dataset_collection

dataset_collection_id

id: int

job

job_id

table = Table('job_to_input_dataset_collection', MetaData(bind=None), 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', Unicode(length=255), table=<job_to_input_dataset_collection>), schema=None)

class galaxy.model.JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element)

Bases: galaxy.model.RepresentById

__init__(name, dataset_collection_element)

Initialize self. See help(type(self)) for accurate signature.

name

dataset_collection_element

dataset_collection_element_id

id: int

job

job_id

table = Table('job_to_input_dataset_collection_element', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset_collection_instance)

Initialize self. See help(type(self)) for accurate signature.

name

dataset_collection_instance

dataset_collection_id

id: int

job

job_id

table = Table('job_to_output_dataset_collection', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset_collection)

Initialize self. See help(type(self)) for accurate signature.

name

dataset_collection

dataset_collection_id

id: int

job

job_id

table = Table('job_to_implicit_output_dataset_collection', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(name, dataset)

Initialize self. See help(type(self)) for accurate signature.

name

dataset

id: int

job

job_id

ldda_id

table = Table('job_to_input_library_dataset', MetaData(bind=None), 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', String(length=255), table=<job_to_input_library_dataset>), schema=None)

class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)

Bases: galaxy.model.RepresentById

__init__(name, dataset)

Initialize self. See help(type(self)) for accurate signature.

name

dataset

id: int

job

job_id

ldda_id

table = Table('job_to_output_library_dataset', MetaData(bind=None), 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', String(length=255), table=<job_to_output_library_dataset>), schema=None)

class galaxy.model.JobStateHistory(job)

Bases: galaxy.model.RepresentById

__init__(job)

Initialize self. See help(type(self)) for accurate signature.

job

state

info

create_time

id: int

job_id

table = Table('job_state_history', MetaData(bind=None), 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('update_time', DateTime(), table=<job_state_history>, onupdate=ColumnDefault(<function datetime.utcnow>), 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)

update_time

class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)

Bases: galaxy.model.RepresentById

__init__(name, input_dataset_collection)

Initialize self. See help(type(self)) for accurate signature.

name

input_dataset_collection

dataset_collection

dataset_collection_id

id: int

input_dataset_collection_id

table = Table('implicitly_created_dataset_collection_inputs', MetaData(bind=None), 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(id=None, populated_state=None)

Bases: galaxy.model.RepresentById

class populated_states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

OK = 'ok'

FAILED = 'failed'

__init__(id=None, populated_state=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

populated_state

property job_list

serialize(id_encoder, serialization_options)

history_dataset_collection_associations

jobs

table = Table('implicit_collection_jobs', MetaData(bind=None), 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)

workflow_invocation_step

class galaxy.model.ImplicitCollectionJobsJobAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

implicit_collection_jobs_id

id: int

implicit_collection_jobs

job

job_id

order_index

table = Table('implicit_collection_jobs_job_association', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(action_type, workflow_step=None, output_name=None, action_arguments=None)

Initialize self. See help(type(self)) for accurate signature.

action_type

output_name

action_arguments

workflow_step

id: int

table = Table('post_job_action', MetaData(bind=None), 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)

workflow_step_id

class galaxy.model.PostJobActionAssociation(pja, job=None, job_id=None)

Bases: galaxy.model.RepresentById

__init__(pja, job=None, job_id=None)

Initialize self. See help(type(self)) for accurate signature.

job

job_id

post_job_action

id: int

post_job_action_id

table = Table('post_job_action_association', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(job=None, dataset=None)

Initialize self. See help(type(self)) for accurate signature.

job

history_dataset_association

library_dataset_dataset_association

property dataset

filename_in

filename_kwds

filename_out

filename_override_metadata

filename_results_code

history_dataset_association_id

id: int

is_valid

job_id

job_runner_external_pid

library_dataset_dataset_association_id

table = Table('job_external_output_metadata', MetaData(bind=None), 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)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.model.JobExportHistoryArchive(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)

Bases: galaxy.model.RepresentById

ATTRS_FILENAME_HISTORY = 'history_attrs.txt'

__init__(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)

Initialize self. See help(type(self)) for accurate signature.

job

history

dataset

compressed

history_attrs_filename

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()

dataset_id

history_id

id: int

job_id

table = Table('job_export_history_archive', MetaData(bind=None), 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(job=None, history=None, archive_dir=None)

Bases: galaxy.model.RepresentById

__init__(job=None, history=None, archive_dir=None)

Initialize self. See help(type(self)) for accurate signature.

job

history

archive_dir

history_id

id: int

job_id

table = Table('job_import_history_archive', MetaData(bind=None), 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.JobContainerAssociation(job=None, container_type=None, container_name=None, container_info=None)

Bases: galaxy.model.RepresentById

__init__(job=None, container_type=None, container_name=None, container_info=None)

Initialize self. See help(type(self)) for accurate signature.

job

container_type

container_name

container_info

created_time

id: int

job_id

modified_time

table = Table('job_container_association', MetaData(bind=None), 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(job=None, name=None, token=None, tool_port=None, host=None, port=None, protocol=None, entry_url=None, requires_domain=True, info=None, configured=False, deleted=False)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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

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

__init__(job=None, name=None, token=None, tool_port=None, host=None, port=None, protocol=None, entry_url=None, requires_domain=True, info=None, configured=False, deleted=False)

Initialize self. See help(type(self)) for accurate signature.

job

name

token

tool_port

host

port

protocol

entry_url

requires_domain

info

configured

deleted

property active

created_time

id: int

job_id

modified_time

table = Table('interactivetool_entry_point', MetaData(bind=None), 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(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)

Bases: galaxy.model.RepresentById

__init__(job=None, params=None, dataset=None, deferred_job=None, transfer_job=None, fasta_path=None, created_time=None, modified_time=None, dbkey=None, user=None, indexer=None)

Initialize self. See help(type(self)) for accurate signature.

job

dataset

fasta_path

user

indexer

created_time

modified_time

deferred

transfer

dataset_id

deferred_job_id

id: int

job_id

table = Table('genome_index_tool_data', MetaData(bind=None), 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('deferred_job_id', Integer(), ForeignKey('deferred_job.id'), table=<genome_index_tool_data>), Column('transfer_job_id', Integer(), ForeignKey('transfer_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)

transfer_job_id

user_id

class galaxy.model.DeferredJob(state=None, plugin=None, params=None)

Bases: galaxy.model.RepresentById

class states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

WAITING = 'waiting'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

ERROR = 'error'

__init__(state=None, plugin=None, params=None)

Initialize self. See help(type(self)) for accurate signature.

state

plugin

params

get_check_interval()

set_check_interval(seconds)

property check_interval

get_last_check()

set_last_check(seconds)

property last_check

property is_check_time

create_time

deferred_job

id: int

table = Table('deferred_job', MetaData(bind=None), Column('id', Integer(), table=<deferred_job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<deferred_job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<deferred_job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<deferred_job>), Column('plugin', String(length=128), table=<deferred_job>), Column('params', MutableJSONType(), table=<deferred_job>), schema=None)

update_time

class galaxy.model.Group(name=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_collection_visible_keys = ['id', 'name']

dict_element_visible_keys = ['id', 'name']

__init__(name=None)

Initialize self. See help(type(self)) for accurate signature.

name

deleted

create_time

id: int

members

quotas

roles

table = Table('galaxy_group', MetaData(bind=None), 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)

update_time

users

class galaxy.model.UserGroupAssociation(user, group)

Bases: galaxy.model.RepresentById

__init__(user, group)

Initialize self. See help(type(self)) for accurate signature.

user

group

create_time

group_id

id: int

table = Table('user_group_association', MetaData(bind=None), 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)

update_time

user_id

galaxy.model.is_hda(d)

class galaxy.model.HistoryAudit(history, update_time)

Bases: galaxy.model.RepresentById

__init__(history, update_time)

Initialize self. See help(type(self)) for accurate signature.

classmethod prune(sa_session)

table = Table('history_audit', MetaData(bind=None), 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)

id: int

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

Bases: galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName, galaxy.model.RepresentById

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)

Initialize self. See help(type(self)) for accurate signature.

id: int

name

deleted

purged

importing

genome_build

published

update_time

user

datasets

galaxy_sessions

tags

init_on_load()

stage_addition(items)

property empty

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.

property has_possible_members

property activatable_datasets

serialize(id_encoder, serialization_options)

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.

active_dataset_collections

active_datasets

annotations

average_rating

create_time

dataset_collections

default_permissions

exports

hid_counter

importable

jobs

ratings

slug

table = Table('history', MetaData(bind=None), 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>, key='_update_time', 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)

user_id

users_shared_with

users_shared_with_count

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

visible_dataset_collections

visible_datasets

workflow_invocations

class galaxy.model.UserShareAssociation

Bases: galaxy.model.RepresentById

user: Optional[galaxy.model.User]

class galaxy.model.HistoryUserShareAssociation

Bases: galaxy.model.UserShareAssociation

__init__()

Initialize self. See help(type(self)) for accurate signature.

history

user: Optional[galaxy.model.User]

history_id

id: int

table = Table('history_user_share_association', MetaData(bind=None), 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)

user_id

class galaxy.model.UserRoleAssociation(user, role)

Bases: galaxy.model.RepresentById

__init__(user, role)

Initialize self. See help(type(self)) for accurate signature.

user

role

create_time

id: int

non_private_roles

role_id

table = Table('user_role_association', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.GroupRoleAssociation(group, role)

Bases: galaxy.model.RepresentById

__init__(group, role)

Initialize self. See help(type(self)) for accurate signature.

group

role

create_time

group_id

id: int

role_id

table = Table('group_role_association', MetaData(bind=None), 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)

update_time

class galaxy.model.Role(name='', description='', type='system', deleted=False)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_collection_visible_keys = ['id', 'name']

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

private_id = None

class types(value)

Bases: str, enum.Enum

An enumeration.

PRIVATE = 'private'

SYSTEM = 'system'

USER = 'user'

ADMIN = 'admin'

SHARING = 'sharing'

__init__(name='', description='', type='system', deleted=False)

Initialize self. See help(type(self)) for accurate signature.

name

description

type

deleted

create_time

dataset_actions

groups

id: int

library_actions

library_dataset_actions

library_dataset_dataset_actions

library_folder_actions

table = Table('role', MetaData(bind=None), 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)

update_time

users

class galaxy.model.UserQuotaAssociation(user, quota)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_element_visible_keys = ['user']

__init__(user, quota)

Initialize self. See help(type(self)) for accurate signature.

user

quota

create_time

id: int

quota_id

table = Table('user_quota_association', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.GroupQuotaAssociation(group, quota)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_element_visible_keys = ['group']

__init__(group, quota)

Initialize self. See help(type(self)) for accurate signature.

group

quota

create_time

group_id

id: int

quota_id

table = Table('group_quota_association', MetaData(bind=None), 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)

update_time

class galaxy.model.Quota(name='', description='', amount=0, operation='=')

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_collection_visible_keys = ['id', 'name']

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

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

__init__(name='', description='', amount=0, operation='=')

Initialize self. See help(type(self)) for accurate signature.

name

description

bytes

operation

get_amount()

set_amount(amount)

property amount

property display_amount

create_time

default

deleted

groups

id: int

table = Table('quota', MetaData(bind=None), 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)

update_time

users

class galaxy.model.DefaultQuotaAssociation(type, quota)

Bases: galaxy.model.Quota, galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

dict_element_visible_keys = ['type']

class types(value)

Bases: str, enum.Enum

An enumeration.

UNREGISTERED = 'unregistered'

REGISTERED = 'registered'

__init__(type, quota)

Initialize self. See help(type(self)) for accurate signature.

type

quota

create_time

id: int

quota_id

table = Table('default_quota_association', MetaData(bind=None), 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)

update_time

class galaxy.model.DatasetPermissions(action, dataset, role=None, role_id=None)

Bases: galaxy.model.RepresentById

__init__(action, dataset, role=None, role_id=None)

Initialize self. See help(type(self)) for accurate signature.

action

dataset

role

role_id

create_time

dataset_id

id: int

table = Table('dataset_permissions', MetaData(bind=None), 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)

update_time

class galaxy.model.LibraryPermissions(action, library_item, role)

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

Initialize self. See help(type(self)) for accurate signature.

action

library

role

create_time

id: int

library_id

role_id

table = Table('library_permissions', MetaData(bind=None), 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)

update_time

class galaxy.model.LibraryFolderPermissions(action, library_item, role)

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

Initialize self. See help(type(self)) for accurate signature.

action

folder

role

create_time

id: int

library_folder_id

role_id

table = Table('library_folder_permissions', MetaData(bind=None), 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)

update_time

class galaxy.model.LibraryDatasetPermissions(action, library_item, role)

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

Initialize self. See help(type(self)) for accurate signature.

action

library_dataset

role

create_time

id: int

library_dataset_id

role_id

table = Table('library_dataset_permissions', MetaData(bind=None), 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)

update_time

class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)

Bases: galaxy.model.RepresentById

__init__(action, library_item, role)

Initialize self. See help(type(self)) for accurate signature.

action

library_dataset_dataset_association

role

create_time

id: int

library_dataset_dataset_association_id

role_id

table = Table('library_dataset_dataset_association_permissions', MetaData(bind=None), 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)

update_time

class galaxy.model.DefaultUserPermissions(user, action, role)

Bases: galaxy.model.RepresentById

__init__(user, action, role)

Initialize self. See help(type(self)) for accurate signature.

user

action

role

id: int

role_id

table = Table('default_user_permissions', MetaData(bind=None), 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)

user_id

class galaxy.model.DefaultHistoryPermissions(history, action, role)

Bases: galaxy.model.RepresentById

__init__(history, action, role)

Initialize self. See help(type(self)) for accurate signature.

history

action

role

history_id

id: int

role_id

table = Table('default_history_permissions', MetaData(bind=None), 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(id, uuid)

Bases: object

__init__(id, uuid)

Initialize self. See help(type(self)) for accurate signature.

flush()

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

Bases: galaxy.model.StorableObject, galaxy.model.RepresentById, object

class states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

UPLOAD = 'upload'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

EMPTY = 'empty'

ERROR = 'error'

DISCARDED = 'discarded'

PAUSED = 'paused'

SETTING_METADATA = 'setting_metadata'

FAILED_METADATA = 'failed_metadata'

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

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

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

class conversion_messages(value)

Bases: str, enum.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 = None

engine = None

__init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)

Initialize self. See help(type(self)) for accurate signature.

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)

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)

serialize(id_encoder, serialization_options)

actions

active_history_associations

active_library_associations

create_time

created_from_basename

genome_index_tool_data

history_associations

id: int

job

job_export_history_archive

job_id

library_associations

object_store_id

purged_history_associations

table = Table('dataset', MetaData(bind=None), 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)

total_size

update_time

uuid

class galaxy.model.DatasetSource

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset

dataset_id

extra_files_path

hashes

id: int

source_uri

table = Table('dataset_source', MetaData(bind=None), 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)

transform

class galaxy.model.DatasetSourceHash

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset_source_id

hash_function

hash_value

id: int

source

table = Table('dataset_source_hash', MetaData(bind=None), 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

Bases: galaxy.model.RepresentById

serialize(id_encoder, serialization_options)

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset

dataset_id

extra_files_path

hash_function

hash_value

id: int

table = Table('dataset_hash', MetaData(bind=None), 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)

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, creating_job_id=None)

Bases: object

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

class states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

UPLOAD = 'upload'

QUEUED = 'queued'

RUNNING = 'running'

OK = 'ok'

EMPTY = 'empty'

ERROR = 'error'

DISCARDED = 'discarded'

PAUSED = 'paused'

SETTING_METADATA = 'setting_metadata'

FAILED_METADATA = 'failed_metadata'

classmethod values()

class conversion_messages(value)

Bases: str, enum.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>

class validated_states(value)

Bases: str, enum.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, creating_job_id=None)

Initialize self. See help(type(self)) for accurate signature.

property peek

update()

property ext

get_dataset_state()

raw_set_dataset_state(state)

set_dataset_state(state)

property state

get_file_name()

set_file_name(filename)

property file_name

link_to(path)

property extra_files_path

extra_files_path_exists()

property datatype

get_metadata()

property set_metadata_requires_flush

set_metadata(bunch)

property metadata

property metadata_file_types

get_dbkey()

set_dbkey(value)

property dbkey

ok_to_edit_metadata()

change_datatype(new_ext)

get_size(nice_size=False)

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

get_raw_data()

Returns the full data. To stream it open the file_name and read/write as needed

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, **kwd)

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_visualizations()

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.

serialize(id_encoder, serialization_options, for_link=False)

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: galaxy.model.DatasetInstance, galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.HasName, galaxy.model.RepresentById

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

copy_from(other_hda)

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.

serialize(id_encoder, serialization_options, for_link=False)

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

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

name

parent_id

purged

ratings

table = Table('history_dataset_association', MetaData(bind=None), 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('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

tool_version

update_time

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: galaxy.model.RepresentById

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

Initialize self. See help(type(self)) for accurate signature.

history_dataset_association_id

name

update_time

version

extension

extended_metadata_id

id: int

table = Table('history_dataset_association_history', MetaData(bind=None), 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>, key='_metadata'), 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: galaxy.model.RepresentById

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

Initialize self. See help(type(self)) for accurate signature.

history_dataset_association

user

site

create_time

history_dataset_association_id

id: int

table = Table('history_dataset_association_display_at_authorization', MetaData(bind=None), 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)

update_time

user_id

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

Bases: galaxy.model.RepresentById

__init__(hda, subset, location)

Initialize self. See help(type(self)) for accurate signature.

hda

subset

location

history_dataset_association_id

history_dataset_association_subset_id

id: int

table = Table('history_dataset_association_subset', MetaData(bind=None), 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: galaxy.util.dictifiable.Dictifiable, galaxy.model.HasName, galaxy.model.RepresentById

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)

Initialize self. See help(type(self)) for accurate signature.

name

description

synopsis

root_folder

serialize(id_encoder, serialization_options)

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

We prepend an F to folders.

get_active_folders(folder, folders=None)

get_access_roles(security_agent)

actions

create_time

deleted

id: int

info_association

purged

root_folder_id

table = Table('library', MetaData(bind=None), 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)

update_time

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

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.HasName, galaxy.model.RepresentById

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)

Initialize self. See help(type(self)) for accurate signature.

name

description

item_count

order_id

genome_build

folders

datasets

add_library_dataset(library_dataset, genome_build=None)

add_folder(folder)

property activatable_library_datasets

serialize(id_encoder, serialization_options)

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

Return item dictionary.

property library_path

property parent_library

actions

active_datasets

active_folders

create_time

dataset_collections

deleted

id: int

info_association

library_root

parent

parent_id

purged

table = Table('library_folder', MetaData(bind=None), 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)

update_time

class galaxy.model.LibraryDataset(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)

Bases: galaxy.model.RepresentById

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')]

__init__(folder=None, order_id=None, name=None, info=None, library_dataset_dataset_association=None, **kwd)

Initialize self. See help(type(self)) for accurate signature.

folder

order_id

library_dataset_dataset_association

get_info()

set_info(info)

property info

get_name()

set_name(name)

property name

display_name()

serialize(id_encoder, serialization_options)

to_dict(view='collection')

actions

create_time

deleted

expired_datasets

folder_id

id: int

library_dataset_dataset_association_id

purged

table = Table('library_dataset', MetaData(bind=None), 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>, key='_name'), Column('info', TrimmedString(length=255), table=<library_dataset>, key='_info'), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)

update_time

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: galaxy.model.DatasetInstance, galaxy.model.HasName, galaxy.model.RepresentById

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

Initialize self. See help(type(self)) for accurate signature.

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)

serialize(id_encoder, serialization_options, for_link=False)

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

dataset

dataset_id

deleted

dependent_jobs

designation

extended_metadata

extended_metadata_id

extension

id: int

implicitly_converted_datasets

implicitly_converted_parent_datasets

info

info_association

library_dataset_id

message

name

parent_id

table = Table('library_dataset_dataset_association', MetaData(bind=None), 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('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

user_id

validated_state

validated_state_message

visible

class galaxy.model.ExtendedMetadata(data)

Bases: galaxy.model.RepresentById

__init__(data)

Initialize self. See help(type(self)) for accurate signature.

data

children

id: int

table = Table('extended_metadata', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(extended_metadata, path, value)

Initialize self. See help(type(self)) for accurate signature.

extended_metadata

path

value

extended_metadata_id

id: int

parent

table = Table('extended_metadata_index', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(library, form_definition, info, inheritable=False)

Initialize self. See help(type(self)) for accurate signature.

library

template

info

inheritable

deleted

form_definition_id

form_values_id

id: int

library_id

table = Table('library_info_association', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(folder, form_definition, info, inheritable=False)

Initialize self. See help(type(self)) for accurate signature.

folder

template

info

inheritable

deleted

form_definition_id

form_values_id

id: int

library_folder_id

table = Table('library_folder_info_association', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(library_dataset_dataset_association, form_definition, info)

Initialize self. See help(type(self)) for accurate signature.

library_dataset_dataset_association

template

info

property inheritable

deleted

form_definition_id

form_values_id

id: int

library_dataset_dataset_association_id

table = Table('library_dataset_dataset_info_association', MetaData(bind=None), 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: galaxy.model.RepresentById

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

Initialize self. See help(type(self)) for accurate signature.

id: int

dataset

dataset_ldda

parent_hda

parent_ldda

type

deleted

metadata_safe

clear(purge=False, delete_dataset=True)

create_time

hda_id

hda_parent_id

ldda_id

ldda_parent_id

table = Table('implicitly_converted_dataset_association', MetaData(bind=None), 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)

update_time

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

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.RepresentById

dict_collection_visible_keys = ['id', 'collection_type']

dict_element_visible_keys = ['id', 'collection_type']

class populated_states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

OK = 'ok'

FAILED = 'failed'

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

Initialize self. See help(type(self)) for accurate signature.

id: int

collection_type

populated_state

element_count

property dataset_states_and_extensions_summary

property populated_optimized

property populated

property dataset_action_tuples

property waiting_for_elements

mark_as_populated()

handle_population_failed(message)

finalize(collection_type_description)

property dataset_instances

property dataset_elements

property first_dataset_element

property state

validate()

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

replace_failed_elements(replacements)

set_from_dict(new_data)

property has_subcollections

serialize(id_encoder, serialization_options)

create_time

elements

output_dataset_collections

populated_state_message

table = Table('dataset_collection', MetaData(bind=None), 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)

update_time

class galaxy.model.DatasetCollectionInstance(collection=None, deleted=False)

Bases: galaxy.model.HasName

__init__(collection=None, deleted=False)

Initialize self. See help(type(self)) for accurate signature.

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.

class galaxy.model.HistoryDatasetCollectionAssociation(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=None)

Bases: galaxy.model.DatasetCollectionInstance, galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.RepresentById

Associates a DatasetCollection with a History.

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

__init__(id=None, hid=None, collection=None, history=None, name=None, deleted=False, visible=True, copied_from_history_dataset_collection_association=None, implicit_output_name=None, implicit_input_collections=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

hid

history

name

visible

copied_from_history_dataset_collection_association

implicit_output_name

implicit_input_collections

property history_content_type

content_type = 'dataset_collection'

type_id

property job_source_type

property job_source_id

to_hda_representative(multiple=False)

serialize(id_encoder, serialization_options, for_link=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)

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

annotations

collection

collection_id

copied_from_history_dataset_collection_association_id

copied_to_history_dataset_collection_associations

create_time

creating_job_associations

deleted

hidden_dataset_instances

history_id

implicit_collection_jobs

implicit_collection_jobs_id

job

job_id

job_state_summary

output_dataset_collection_instances

ratings

table = Table('history_dataset_collection_association', MetaData(bind=None), 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)

tags

update_time

class galaxy.model.LibraryDatasetCollectionAssociation(id=None, collection=None, name=None, deleted=False, folder=None)

Bases: galaxy.model.DatasetCollectionInstance, galaxy.model.RepresentById

Associates a DatasetCollection with a library folder.

editable_keys = ('name', 'deleted')

__init__(id=None, collection=None, name=None, deleted=False, folder=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

folder

name

to_dict(view='collection')

annotations

collection

collection_id

deleted

folder_id

ratings

table = Table('library_dataset_collection_association', MetaData(bind=None), 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)

tags

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

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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

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)

Initialize self. See help(type(self)) for accurate signature.

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

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

serialize(id_encoder, serialization_options)

child_collection_id

dataset_collection_id

hda_id

ldda_id

table = Table('dataset_collection_element', MetaData(bind=None), 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(message=None, history=None, user=None, galaxy_session=None)

Bases: galaxy.model.RepresentById

__init__(message=None, history=None, user=None, galaxy_session=None)

Initialize self. See help(type(self)) for accurate signature.

history

galaxy_session

user

tool_id

message

create_time

history_id

id: int

session_id

table = Table('event', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.GalaxySession(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)

Bases: galaxy.model.RepresentById

__init__(id=None, user=None, remote_host=None, remote_addr=None, referer=None, current_history=None, session_key=None, is_valid=False, prev_session_id=None, last_action=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

user

remote_host

remote_addr

referer

current_history

session_key

is_valid

prev_session_id

histories

last_action

add_history(history, association=None)

get_disk_usage()

set_disk_usage(bytes)

property total_disk_usage

create_time

current_history_id

disk_usage

table = Table('galaxy_session', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)

Bases: galaxy.model.RepresentById

__init__(galaxy_session, history)

Initialize self. See help(type(self)) for accurate signature.

galaxy_session

history

create_time

history_id

id: int

session_id

table = Table('galaxy_session_to_history', MetaData(bind=None), 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__()

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.HasTags, galaxy.util.dictifiable.Dictifiable, galaxy.model.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

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

dict_element_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', '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)

Initialize self. See help(type(self)) for accurate signature.

id: int

user

name

slug

create_time

update_time

published

latest_workflow_id

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.

annotations

average_rating

deleted

from_path

importable

owner_tags

ratings

table = Table('stored_workflow', MetaData(bind=None), 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)

tags

user_id

users_shared_with

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

class galaxy.model.Workflow(uuid=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.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

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)

Initialize self. See help(type(self)) for accurate signature.

id: int

name

has_cycles

has_errors

steps

stored_workflow_id

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)

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()

create_time

creator_metadata

license

parent_workflow_id

parent_workflow_steps

reports_config

step_count

stored_workflow

table = Table('workflow', MetaData(bind=None), 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', MutableJSONType(), table=<workflow>), Column('creator_metadata', MutableJSONType(), table=<workflow>), Column('license', TEXT(), table=<workflow>), Column('uuid', UUIDType(), table=<workflow>), schema=None)

update_time

class galaxy.model.WorkflowStep

Bases: galaxy.model.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.

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

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

id: int

type

tool_id

tool_inputs

tool_errors

dynamic_tool

position

inputs

config

label

uuid

workflow_outputs

property tool_uuid

property input_type

property input_default_value

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()

annotations

create_time

dynamic_tool_id

order_index

output_connections

parent_workflow_input_connections

post_job_actions

subworkflow

subworkflow_id

table = Table('workflow_step', MetaData(bind=None), 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('uuid', UUIDType(), table=<workflow_step>), Column('label', Unicode(length=255), table=<workflow_step>), schema=None)

tags

tool_version

update_time

workflow

workflow_id

class galaxy.model.WorkflowStepInput(workflow_step)

Bases: galaxy.model.RepresentById

default_merge_type = None

default_scatter_type = None

__init__(workflow_step)

Initialize self. See help(type(self)) for accurate signature.

workflow_step

name

default_value

default_value_set

merge_type

scatter_type

copy(copied_step)

connections

id: int

runtime_value

table = Table('workflow_step_input', MetaData(bind=None), 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)

value_from

value_from_type

workflow_step_id

class galaxy.model.WorkflowStepConnection

Bases: galaxy.model.RepresentById

NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'

__init__()

Initialize self. See help(type(self)) for accurate signature.

output_step_id

output_name

input_step_input_id

property non_data_connection

property input_name

property input_step

property input_step_id

copy()

id: int

input_step_input

input_subworkflow_step

input_subworkflow_step_id

output_step

table = Table('workflow_step_connection', MetaData(bind=None), 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: galaxy.model.RepresentById

__init__(workflow_step, output_name=None, label=None, uuid=None)

Initialize self. See help(type(self)) for accurate signature.

workflow_step

output_name

label

uuid

copy(copied_step)

id: int

table = Table('workflow_output', MetaData(bind=None), 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)

workflow_step_id

class galaxy.model.StoredWorkflowUserShareAssociation

Bases: galaxy.model.UserShareAssociation

__init__()

Initialize self. See help(type(self)) for accurate signature.

stored_workflow

user: Optional[galaxy.model.User]

id: int

stored_workflow_id

table = Table('stored_workflow_user_share_connection', MetaData(bind=None), 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)

user_id

class galaxy.model.StoredWorkflowMenuEntry

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

stored_workflow

user

order_index

id: int

stored_workflow_id

table = Table('stored_workflow_menu_entry', MetaData(bind=None), 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)

user_id

class galaxy.model.WorkflowInvocation

Bases: galaxy.model.UsesCreateAndUpdateTime, galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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.Enum

An enumeration.

NEW = 'new'

READY = 'ready'

SCHEDULED = 'scheduled'

CANCELLED = 'cancelled'

FAILED = 'failed'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

subworkflow_invocations

step_states

steps

workflow_id

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)

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)

property resource_parameters

has_input_for_step(step_id)

set_handler(handler)

log_str()

create_time

handler

history

history_id

id: int

input_dataset_collections

input_datasets

input_parameters

input_step_parameters

output_dataset_collections

output_datasets

output_values

parent_workflow_invocation_association

scheduler

state

table = Table('workflow_invocation', MetaData(bind=None), 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)

update()

update_time

uuid

workflow

class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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__()

Initialize self. See help(type(self)) for accurate signature.

id: int

parent_workflow_invocation

subworkflow_invocation

subworkflow_invocation_id

table = Table('workflow_invocation_to_subworkflow_invocation_association', MetaData(bind=None), 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)

workflow_invocation_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowInvocationStep

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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.Enum

An enumeration.

NEW = 'new'

READY = 'ready'

SCHEDULED = 'scheduled'

__init__()

Initialize self. See help(type(self)) for accurate signature.

implicit_collection_jobs_id

job_id

workflow_invocation_id

property is_new

add_output(output_name, output_object)

property jobs

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

Return item dictionary.

action

create_time

id: int

implicit_collection_jobs

job

output_dataset_collections

output_datasets

output_value

state

subworkflow_invocation_id

table = Table('workflow_invocation_step', MetaData(bind=None), 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)

update_time

workflow_invocation

workflow_step

workflow_step_id

class galaxy.model.WorkflowRequestInputParameter(name=None, value=None, type=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Workflow-related parameters not tied to steps or inputs.

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

class types(value)

Bases: str, enum.Enum

An enumeration.

REPLACEMENT_PARAMETERS = 'replacements'

STEP_PARAMETERS = 'step'

META_PARAMETERS = 'meta'

RESOURCE_PARAMETERS = 'resource'

__init__(name=None, value=None, type=None)

Initialize self. See help(type(self)) for accurate signature.

name

value

type

id: int

table = Table('workflow_request_input_parameters', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

class galaxy.model.WorkflowRequestStepState(workflow_step=None, name=None, value=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Workflow step value parameters.

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

__init__(workflow_step=None, name=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

workflow_step

value

id: int

table = Table('workflow_request_step_states', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_step_id

class galaxy.model.WorkflowRequestToInputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Workflow step input dataset parameters.

history_content_type = 'dataset'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset

dataset_id

id: int

name

table = Table('workflow_request_to_input_dataset', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Workflow step input dataset collection parameters.

history_content_type = 'dataset_collection'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset_collection

dataset_collection_id

id: int

name

table = Table('workflow_request_to_input_collection_dataset', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowRequestInputStepParameter

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Workflow step parameter inputs.

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

id: int

parameter_value

table = Table('workflow_request_input_step_parameter', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowInvocationOutputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Represents links to output datasets for the workflow.

history_content_type = 'dataset'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset

dataset_id

id: int

table = Table('workflow_invocation_output_dataset_association', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_output

workflow_output_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Represents links to output dataset collections for the workflow.

history_content_type = 'dataset_collection'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset_collection

dataset_collection_id

id: int

table = Table('workflow_invocation_output_dataset_collection_association', MetaData(bind=None), 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)

workflow_invocation

workflow_invocation_id

workflow_output

workflow_output_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowInvocationOutputValue

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Represents a link to a specified or computed workflow parameter.

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

id: int

table = Table('workflow_invocation_output_value', MetaData(bind=None), 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)

value

workflow_invocation

workflow_invocation_id

workflow_invocation_step

workflow_output

workflow_output_id

workflow_step

workflow_step_id

class galaxy.model.WorkflowInvocationStepOutputDatasetAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Represents links to output datasets for the workflow.

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset

dataset_id

id: int

output_name

table = Table('workflow_invocation_step_output_dataset_association', MetaData(bind=None), 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)

workflow_invocation_step

workflow_invocation_step_id

class galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

Represents links to output dataset collections for the workflow.

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

dataset_collection

dataset_collection_id

id: int

output_name

table = Table('workflow_invocation_step_output_dataset_collection_association', MetaData(bind=None), 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)

workflow_invocation_step

workflow_invocation_step_id

workflow_step_id

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

Bases: galaxy.model.StorableObject, galaxy.model.RepresentById

__init__(dataset=None, name=None, uuid=None)

Initialize self. See help(type(self)) for accurate signature.

history_dataset

library_dataset

name

property file_name

serialize(id_encoder, serialization_options)

create_time

deleted

hda_id

id: int

lda_id

object_store_id

purged

table = Table('metadata_file', MetaData(bind=None), 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)

update_time

uuid

class galaxy.model.FormDefinition(name=None, desc=None, fields=None, form_definition_current=None, form_type=None, layout=None)

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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.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']

__init__(name=None, desc=None, fields=None, form_definition_current=None, form_type=None, layout=None)

Initialize self. See help(type(self)) for accurate signature.

name

desc

fields

form_definition_current

type

layout

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

Return item dictionary.

grid_fields(grid_index)

create_time

current

form_definition_current_id

id: int

table = Table('form_definition', MetaData(bind=None), 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)

update_time

class galaxy.model.FormDefinitionCurrent(form_definition=None)

Bases: galaxy.model.RepresentById

__init__(form_definition=None)

Initialize self. See help(type(self)) for accurate signature.

latest_form

create_time

deleted

forms

id: int

latest_form_id

table = Table('form_definition_current', MetaData(bind=None), 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)

update_time

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

Bases: galaxy.model.RepresentById

__init__(form_def=None, content=None)

Initialize self. See help(type(self)) for accurate signature.

form_definition

content

create_time

form_definition_id

id: int

table = Table('form_values', MetaData(bind=None), 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)

update_time

class galaxy.model.UserAddress(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)

Bases: galaxy.model.RepresentById

__init__(user=None, desc=None, name=None, institution=None, address=None, city=None, state=None, postal_code=None, country=None, phone=None)

Initialize self. See help(type(self)) for accurate signature.

user

desc

name

institution

address

city

state

postal_code

country

phone

to_dict(trans)

create_time

deleted

id: int

purged

table = Table('user_address', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.PSAAssociation(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)

Bases: social_core.storage.AssociationMixin, galaxy.model.RepresentById

sa_session = None

__init__(server_url=None, handle=None, secret=None, issued=None, lifetime=None, assoc_type=None)

Initialize self. See help(type(self)) for accurate signature.

server_url

handle

secret

issued

lifetime

assoc_type

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

id: int

table = Table('psa_association', MetaData(bind=None), 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: social_core.storage.CodeMixin, galaxy.model.RepresentById

sa_session = None

__init__(email, code)

Initialize self. See help(type(self)) for accurate signature.

email

code

save()

classmethod get_code(code)

id: int

table = Table('psa_code', MetaData(bind=None), 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: social_core.storage.NonceMixin, galaxy.model.RepresentById

sa_session = None

__init__(server_url, timestamp, salt)

Initialize self. See help(type(self)) for accurate signature.

server_url

timestamp

salt

save()

classmethod use(server_url, timestamp, salt)

Create a Nonce instance

id: int

table = Table('psa_nonce', MetaData(bind=None), 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: social_core.storage.PartialMixin, galaxy.model.RepresentById

sa_session = None

__init__(token, data, next_step, backend)

Initialize self. See help(type(self)) for accurate signature.

token

data

next_step

backend

save()

classmethod load(token)

classmethod destroy(token)

id: int

table = Table('psa_partial', MetaData(bind=None), 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: social_core.storage.UserMixin, galaxy.model.RepresentById

sa_session = None

__init__(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)

Initialize self. See help(type(self)) for accurate signature.

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

cloudauthz

id: int

table = Table('oidc_user_authnz_tokens', MetaData(bind=None), 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)

user

class galaxy.model.CustosAuthnzToken(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)

Bases: galaxy.model.RepresentById

__init__(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)

Initialize self. See help(type(self)) for accurate signature.

id: int

user

external_user_id

provider

access_token

id_token

refresh_token

expiration_time

refresh_expiration_time

table = Table('custos_authnz_token', MetaData(bind=None), 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)

user_id

class galaxy.model.CloudAuthz(user_id, provider, config, authn_id, description='')

Bases: object

__init__(user_id, provider, config, authn_id, description='')

Initialize self. See help(type(self)) for accurate signature.

id

user_id

provider

config

authn_id

tokens

last_update

last_activity

description

equals(user_id, provider, authn_id, config)

authn

create_time

table = Table('cloudauthz', MetaData(bind=None), 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)

user

class galaxy.model.Page

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

id: int

user

title

slug

latest_revision_id

revisions

importable

published

to_dict(view='element')

Return item dictionary.

property username

annotations

average_rating

create_time

deleted

latest_revision

ratings

table = Table('page', MetaData(bind=None), 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)

tags

update_time

user_id

users_shared_with

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

class galaxy.model.PageRevision

Bases: galaxy.util.dictifiable.Dictifiable, galaxy.model.RepresentById

DEFAULT_CONTENT_FORMAT = 'html'

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

__init__()

Initialize self. See help(type(self)) for accurate signature.

title

content

content_format

to_dict(view='element')

Return item dictionary.

create_time

id: int

page

page_id

table = Table('page_revision', MetaData(bind=None), 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)

update_time

class galaxy.model.PageUserShareAssociation

Bases: galaxy.model.UserShareAssociation

__init__()

Initialize self. See help(type(self)) for accurate signature.

page

user: Optional[galaxy.model.User]

id: int

page_id

table = Table('page_user_share_association', MetaData(bind=None), 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)

user_id

class galaxy.model.Visualization(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)

Bases: galaxy.model.RepresentById

__init__(id=None, user=None, type=None, title=None, dbkey=None, slug=None, latest_revision=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

user

type

title

dbkey

slug

latest_revision

revisions

copy(user=None, title=None)

Provide copy of visualization with only its latest revision.

annotations

average_rating

create_time

deleted

importable

latest_revision_id

published

ratings

table = Table('visualization', MetaData(bind=None), 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)

tags

update_time

user_id

users_shared_with

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

class galaxy.model.VisualizationRevision(visualization=None, title=None, dbkey=None, config=None)

Bases: galaxy.model.RepresentById

__init__(visualization=None, title=None, dbkey=None, config=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

visualization

title

dbkey

config

copy(visualization=None)

Returns a copy of this object.

create_time

table = Table('visualization_revision', MetaData(bind=None), 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)

update_time

visualization_id

class galaxy.model.VisualizationUserShareAssociation

Bases: galaxy.model.UserShareAssociation

__init__()

Initialize self. See help(type(self)) for accurate signature.

visualization

user: Optional[galaxy.model.User]

id: int

table = Table('visualization_user_share_association', MetaData(bind=None), 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)

user_id

visualization_id

class galaxy.model.TransferJob(state=None, path=None, info=None, pid=None, socket=None, params=None)

Bases: galaxy.model.RepresentById

class states(value)

Bases: str, enum.Enum

An enumeration.

NEW = 'new'

UNKNOWN = 'unknown'

PROGRESS = 'progress'

RUNNING = 'running'

ERROR = 'error'

DONE = 'done'

terminal_states = [<states.ERROR: 'error'>, <states.DONE: 'done'>]

__init__(state=None, path=None, info=None, pid=None, socket=None, params=None)

Initialize self. See help(type(self)) for accurate signature.

state

path

info

pid

socket

params

create_time

id: int

table = Table('transfer_job', MetaData(bind=None), Column('id', Integer(), table=<transfer_job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<transfer_job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<transfer_job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<transfer_job>), Column('path', String(length=1024), table=<transfer_job>), Column('info', TEXT(), table=<transfer_job>), Column('pid', Integer(), table=<transfer_job>), Column('socket', Integer(), table=<transfer_job>), Column('params', MutableJSONType(), table=<transfer_job>), schema=None)

transfer_job

update_time

class galaxy.model.Tag(id=None, type=None, parent_id=None, name=None)

Bases: galaxy.model.RepresentById

__init__(id=None, type=None, parent_id=None, name=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

type

parent_id

name

children

parent

table = Table('tag', MetaData(bind=None), 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)

tagged_histories

tagged_history_dataset_associations

tagged_history_dataset_collections

tagged_library_dataset_collections

tagged_library_dataset_dataset_associations

tagged_pages

tagged_tools

tagged_visualizations

tagged_workflow_steps

tagged_workflows

class galaxy.model.ItemTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.util.dictifiable.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']

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

copy(cls=None)

class galaxy.model.HistoryTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

histories

history_id

id: int

table = Table('history_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<history_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.HistoryDatasetAssociationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

history_dataset_association_id

history_tag_associations

id: int

table = Table('history_dataset_association_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.LibraryDatasetDatasetAssociationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

history_tag_associations

id: int

library_dataset_dataset_association_id

table = Table('library_dataset_dataset_association_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.PageTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

page_id

pages

table = Table('page_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<page_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.WorkflowStepTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

table = Table('workflow_step_tag_association', MetaData(bind=None), 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', Unicode(length=255), table=<workflow_step_tag_association>), Column('value', Unicode(length=255), table=<workflow_step_tag_association>), Column('user_value', Unicode(length=255), table=<workflow_step_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

workflow_step_id

workflow_steps

class galaxy.model.StoredWorkflowTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

stored_workflow_id

stored_workflows

table = Table('stored_workflow_tag_association', MetaData(bind=None), 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', Unicode(length=255), table=<stored_workflow_tag_association>), Column('value', Unicode(length=255), table=<stored_workflow_tag_association>), Column('user_value', Unicode(length=255), table=<stored_workflow_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.VisualizationTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

table = Table('visualization_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<visualization_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

visualization_id

visualizations

class galaxy.model.HistoryDatasetCollectionTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

dataset_collections

history_dataset_collection_id

id: int

table = Table('history_dataset_collection_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.LibraryDatasetCollectionTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

dataset_collections

id: int

library_dataset_collection_id

table = Table('library_dataset_collection_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), schema=None)

tag

tag_id

user

user_id

user_tname

user_value

value

class galaxy.model.ToolTagAssociation(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)

Bases: galaxy.model.ItemTagAssociation, galaxy.model.RepresentById

__init__(id=None, user=None, tool_id=None, tag_id=None, user_tname=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

user

tool_id

tag_id

user_tname

value

user_value

table = Table('tool_tag_association', MetaData(bind=None), 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>), Column('user_value', TrimmedString(length=255), table=<tool_tag_association>), schema=None)

tag

user_id

class galaxy.model.HistoryAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

histories

history

history_id

id: int

table = Table('history_annotation_association', MetaData(bind=None), 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

user_id

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

hda

hdas

history_dataset_association_id

id: int

table = Table('history_dataset_association_annotation_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.StoredWorkflowAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

id: int

stored_workflow

stored_workflow_id

stored_workflows

table = Table('stored_workflow_annotation_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.WorkflowStepAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

id: int

table = Table('workflow_step_annotation_association', MetaData(bind=None), 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)

user

user_id

workflow_step

workflow_step_id

workflow_steps

class galaxy.model.PageAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

id: int

page

page_id

pages

table = Table('page_annotation_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.VisualizationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

id: int

table = Table('visualization_annotation_association', MetaData(bind=None), 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)

user

user_id

visualization

visualization_id

visualizations

class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

dataset_collections

history_dataset_collection

history_dataset_collection_id

id: int

table = Table('history_dataset_collection_annotation_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

Initialize self. See help(type(self)) for accurate signature.

annotation

dataset_collections

id: int

library_dataset_collection

library_dataset_collection_id

table = Table('library_dataset_collection_annotation_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.ItemRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: object

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

set_item(item)

Set association’s item.

class galaxy.model.HistoryRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(history)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

histories

history

history_id

id: int

rating

table = Table('history_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.HistoryDatasetAssociationRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(history_dataset_association)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

hda

hdas

history_dataset_association_id

id: int

rating

table = Table('history_dataset_association_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.StoredWorkflowRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(stored_workflow)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

id: int

rating

stored_workflow

stored_workflow_id

stored_workflows

table = Table('stored_workflow_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.PageRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(page)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

id: int

page

page_id

pages

rating

table = Table('page_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.VisualizationRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(visualization)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

id: int

rating

table = Table('visualization_rating_association', MetaData(bind=None), 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)

user

user_id

visualizaiton

visualization_id

visualizations

class galaxy.model.HistoryDatasetCollectionRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(dataset_collection)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

dataset_collections

history_dataset_collection

history_dataset_collection_id

id: int

rating

table = Table('history_dataset_collection_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.LibraryDatasetCollectionRatingAssociation(id=None, user=None, item=None, rating=0)

Bases: galaxy.model.ItemRatingAssociation, galaxy.model.RepresentById

set_item(dataset_collection)

Set association’s item.

__init__(id=None, user=None, item=None, rating=0)

Initialize self. See help(type(self)) for accurate signature.

dataset_collections

id: int

libary_dataset_collection

library_dataset_collection_id

rating

table = Table('library_dataset_collection_rating_association', MetaData(bind=None), 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)

user

user_id

class galaxy.model.DataManagerHistoryAssociation(id=None, history=None, user=None)

Bases: galaxy.model.RepresentById

__init__(id=None, history=None, user=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

history

user

create_time

history_id

table = Table('data_manager_history_association', MetaData(bind=None), 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)

update_time

user_id

class galaxy.model.DataManagerJobAssociation(id=None, job=None, data_manager_id=None)

Bases: galaxy.model.RepresentById

__init__(id=None, job=None, data_manager_id=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

job

data_manager_id

create_time

job_id

table = Table('data_manager_job_association', MetaData(bind=None), 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)

update_time

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

Bases: galaxy.model.RepresentById

__init__(name=None, value=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

table = Table('user_preference', MetaData(bind=None), 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)

user

user_id

name

value

class galaxy.model.UserAction(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)

Bases: galaxy.model.RepresentById

table = Table('user_action', MetaData(bind=None), 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)

user

__init__(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

create_time

user_id

session_id

action

params

context

class galaxy.model.APIKeys(id=None, user_id=None, key=None)

Bases: galaxy.model.RepresentById

create_time

table = Table('api_keys', MetaData(bind=None), 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>), schema=None)

user

__init__(id=None, user_id=None, key=None)

Initialize self. See help(type(self)) for accurate signature.

id: int

user_id

key

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

Subpackages

• galaxy.model.dataset_collections package
  • Subpackages
    • galaxy.model.dataset_collections.types package
      • Submodules
      • galaxy.model.dataset_collections.types.list module
      • galaxy.model.dataset_collections.types.paired module
  • Submodules
  • galaxy.model.dataset_collections.builder module
  • galaxy.model.dataset_collections.matching module
  • galaxy.model.dataset_collections.registry module
  • galaxy.model.dataset_collections.structure module
  • galaxy.model.dataset_collections.subcollections module
  • galaxy.model.dataset_collections.type_description module
• galaxy.model.migrate package
  • Subpackages
    • galaxy.model.migrate.versions package
      • Submodules
      • galaxy.model.migrate.versions.0001_initial_tables module
      • galaxy.model.migrate.versions.0002_metadata_file_table module
      • galaxy.model.migrate.versions.0003_security_and_libraries module
      • galaxy.model.migrate.versions.0004_indexes_and_defaults module
      • galaxy.model.migrate.versions.0005_cleanup_datasets_fix module
      • galaxy.model.migrate.versions.0006_change_qual_datatype module
      • galaxy.model.migrate.versions.0007_sharing_histories module
      • galaxy.model.migrate.versions.0008_galaxy_forms module
      • galaxy.model.migrate.versions.0009_request_table module
      • galaxy.model.migrate.versions.0010_hda_display_at_authz_table module
      • galaxy.model.migrate.versions.0011_v0010_mysql_index_fix module
      • galaxy.model.migrate.versions.0012_user_address module
      • galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms module
      • galaxy.model.migrate.versions.0014_pages module
      • galaxy.model.migrate.versions.0015_tagging module
      • galaxy.model.migrate.versions.0016_v0015_mysql_index_fix module
      • galaxy.model.migrate.versions.0017_library_item_indexes module
      • galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags module
      • galaxy.model.migrate.versions.0019_request_library_folder module
      • galaxy.model.migrate.versions.0020_library_upload_job module
      • galaxy.model.migrate.versions.0021_user_prefs module
      • galaxy.model.migrate.versions.0022_visualization_tables module
      • galaxy.model.migrate.versions.0023_page_published_and_deleted_columns module
      • galaxy.model.migrate.versions.0024_page_slug_unique_constraint module
      • galaxy.model.migrate.versions.0025_user_info module
      • galaxy.model.migrate.versions.0026_cloud_tables module
      • galaxy.model.migrate.versions.0027_request_events module
      • galaxy.model.migrate.versions.0028_external_metadata_file_override module
      • galaxy.model.migrate.versions.0029_user_actions module
      • galaxy.model.migrate.versions.0030_history_slug_column module
      • galaxy.model.migrate.versions.0031_community_and_workflow_tags module
      • galaxy.model.migrate.versions.0032_stored_workflow_slug_column module
      • galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows module
      • galaxy.model.migrate.versions.0034_page_user_share_association module
      • galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags module
      • galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables module
      • galaxy.model.migrate.versions.0037_samples_library module
      • galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables module
      • galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table module
      • galaxy.model.migrate.versions.0040_page_annotations module
      • galaxy.model.migrate.versions.0041_workflow_invocation module
      • galaxy.model.migrate.versions.0042_workflow_invocation_fix module
      • galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating module
      • galaxy.model.migrate.versions.0044_add_notify_column_to_request_table module
      • galaxy.model.migrate.versions.0045_request_type_permissions_table module
      • galaxy.model.migrate.versions.0046_post_job_actions module
      • galaxy.model.migrate.versions.0047_job_table_user_id_column module
      • galaxy.model.migrate.versions.0048_dataset_instance_state_column module
      • galaxy.model.migrate.versions.0049_api_keys_table module
      • galaxy.model.migrate.versions.0050_drop_cloud_tables module
      • galaxy.model.migrate.versions.0051_imported_col_for_jobs_table module
      • galaxy.model.migrate.versions.0052_sample_dataset_table module
      • galaxy.model.migrate.versions.0053_item_ratings module
      • galaxy.model.migrate.versions.0054_visualization_dbkey module
      • galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs module
      • galaxy.model.migrate.versions.0056_workflow_outputs module
      • galaxy.model.migrate.versions.0057_request_notify module
      • galaxy.model.migrate.versions.0058_history_import_export module
      • galaxy.model.migrate.versions.0059_sample_dataset_file_path module
      • galaxy.model.migrate.versions.0060_history_archive_import module
      • galaxy.model.migrate.versions.0061_tasks module
      • galaxy.model.migrate.versions.0062_user_openid_table module
      • galaxy.model.migrate.versions.0063_sequencer_table module
      • galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables module
      • galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values module
      • galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables module
      • galaxy.model.migrate.versions.0067_populate_sequencer_table module
      • galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services module
      • galaxy.model.migrate.versions.0069_rename_sequencer_form_type module
      • galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table module
      • galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample module
      • galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table module
      • galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table module
      • galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table module
      • galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table module
      • galaxy.model.migrate.versions.0076_fix_form_values_data_corruption module
      • galaxy.model.migrate.versions.0077_create_tool_tag_association_table module
      • galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting module
      • galaxy.model.migrate.versions.0079_input_library_to_job_table module
      • galaxy.model.migrate.versions.0080_quota_tables module
      • galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda module
      • galaxy.model.migrate.versions.0082_add_tool_shed_repository_table module
      • galaxy.model.migrate.versions.0083_add_prepare_files_to_task module
      • galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table module
      • galaxy.model.migrate.versions.0085_add_task_info module
      • galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns module
      • galaxy.model.migrate.versions.0087_tool_id_guid_map_table module
      • galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column module
      • galaxy.model.migrate.versions.0089_add_object_store_id_columns module
      • galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns module
      • galaxy.model.migrate.versions.0091_add_tool_version_tables module
      • galaxy.model.migrate.versions.0092_add_migrate_tools_table module
      • galaxy.model.migrate.versions.0093_add_job_params_col module
      • galaxy.model.migrate.versions.0094_add_job_handler_col module
      • galaxy.model.migrate.versions.0095_hda_subsets module
      • galaxy.model.migrate.versions.0096_openid_provider module
      • galaxy.model.migrate.versions.0097_add_ctx_rev_column module
      • galaxy.model.migrate.versions.0098_genome_index_tool_data_table module
      • galaxy.model.migrate.versions.0099_add_tool_dependency_table module
      • galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column module
      • galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column module
      • galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns module
      • galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns module
      • galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters module
      • galaxy.model.migrate.versions.0105_add_cleanup_event_table module
      • galaxy.model.migrate.versions.0106_add_missing_indexes module
      • galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task module
      • galaxy.model.migrate.versions.0108_add_extended_metadata module
      • galaxy.model.migrate.versions.0109_add_repository_dependency_tables module
      • galaxy.model.migrate.versions.0110_add_dataset_uuid module
      • galaxy.model.migrate.versions.0111_add_job_destinations module
      • galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables module
      • galaxy.model.migrate.versions.0113_update_migrate_tools_table module
      • galaxy.model.migrate.versions.0114_update_migrate_tools_table_again module
      • galaxy.model.migrate.versions.0115_longer_user_password_field module
      • galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col module
      • galaxy.model.migrate.versions.0117_add_user_activation module
      • galaxy.model.migrate.versions.0118_add_hda_extended_metadata module
      • galaxy.model.migrate.versions.0119_job_metrics module
      • galaxy.model.migrate.versions.0120_dataset_collections module
      • galaxy.model.migrate.versions.0121_workflow_uuids module
      • galaxy.model.migrate.versions.0122_grow_mysql_blobs module
      • galaxy.model.migrate.versions.0123_add_workflow_request_tables module
      • galaxy.model.migrate.versions.0124_job_state_history module
      • galaxy.model.migrate.versions.0125_workflow_step_tracking module
      • galaxy.model.migrate.versions.0126_password_reset module
      • galaxy.model.migrate.versions.0127_output_collection_adjustments module
      • galaxy.model.migrate.versions.0128_session_timeout module
      • galaxy.model.migrate.versions.0129_job_external_output_metadata_validity module
      • galaxy.model.migrate.versions.0130_change_pref_datatype module
      • galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules module
      • galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user module
      • galaxy.model.migrate.versions.0133_add_dependency_column_to_job module
      • galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged module
      • galaxy.model.migrate.versions.0135_add_library_tags module
      • galaxy.model.migrate.versions.0136_collection_and_workflow_state module
      • galaxy.model.migrate.versions.0137_add_copied_from_job_id_column module
      • galaxy.model.migrate.versions.0138_add_hda_version module
      • galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table module
      • galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table module
      • galaxy.model.migrate.versions.0141_add_oidc_tables module
      • galaxy.model.migrate.versions.0142_change_numeric_metric_precision module
      • galaxy.model.migrate.versions.0143_add_cloudauthz_tables module
      • galaxy.model.migrate.versions.0144_add_cleanup_event_user_table module
      • galaxy.model.migrate.versions.0145_add_workflow_step_input module
      • galaxy.model.migrate.versions.0146_workflow_paths module
      • galaxy.model.migrate.versions.0147_job_messages module
      • galaxy.model.migrate.versions.0148_add_checksum_table module
      • galaxy.model.migrate.versions.0149_dynamic_tools module
      • galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz module
      • galaxy.model.migrate.versions.0151_add_worker_process module
      • galaxy.model.migrate.versions.0152_add_metadata_file_uuid module
      • galaxy.model.migrate.versions.0153_add_custos_authnz_token_table module
      • galaxy.model.migrate.versions.0154_created_from_basename module
      • galaxy.model.migrate.versions.0155_job_galaxy_version module
      • galaxy.model.migrate.versions.0156_add_interactivetools module
      • galaxy.model.migrate.versions.0157_rework_dataset_validation module
      • galaxy.model.migrate.versions.0158_workflow_reports module
      • galaxy.model.migrate.versions.0159_add_job_external_id_index module
      • galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again module
      • galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table module
      • galaxy.model.migrate.versions.0162_job_only_pjas module
      • galaxy.model.migrate.versions.0163_worker_process_pid module
      • galaxy.model.migrate.versions.0164_page_format module
      • galaxy.model.migrate.versions.0165_add_content_update_time module
      • galaxy.model.migrate.versions.0166_job_state_summary_view module
      • galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association module
      • galaxy.model.migrate.versions.0168_stored_workflow_hidden_col module
      • galaxy.model.migrate.versions.0169_add_missing_indexes module
      • galaxy.model.migrate.versions.0170_add_more_missing_indexes module
      • galaxy.model.migrate.versions.0171_schemaorg_metadata module
      • galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain module
      • galaxy.model.migrate.versions.util module
  • Submodules
  • galaxy.model.migrate.check module
• galaxy.model.orm package
  • Submodules
  • galaxy.model.orm.engine_factory module
  • galaxy.model.orm.now module
  • galaxy.model.orm.scripts module
• galaxy.model.store package
  • Submodules
  • galaxy.model.store.build_objects module
  • galaxy.model.store.discover module
• galaxy.model.tool_shed_install package
  • Subpackages
    • galaxy.model.tool_shed_install.migrate package
      • Submodules
      • galaxy.model.tool_shed_install.migrate.check module
  • Submodules
  • galaxy.model.tool_shed_install.mapping module
• galaxy.model.view package
  • Submodules
  • galaxy.model.view.utils module

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: galaxy.util.bunch.Bunch

__init__(model_modules, engine)

Initialize self. See help(type(self)) for accurate signature.

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

property Session

For backward compat., deprecated.

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

Bases: galaxy.model.base.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(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: json.encoder.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: sqlalchemy.sql.sqltypes.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.

Parameters

• dialect – Dialect instance in use.

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

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

Bases: sqlalchemy.sql.type_api.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 galaxy.model.custom_types.GalaxyLargeBinary

process_bind_param(value, dialect)

Receive a bound parameter value to be converted.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

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.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters

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

• dialect – the Dialect in use.

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

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.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

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: galaxy.model.custom_types.JSONType

Associated with MutationObj

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

Bases: sqlalchemy.ext.mutable.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: galaxy.model.custom_types.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: galaxy.model.custom_types.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: galaxy.model.custom_types.JSONType

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

process_bind_param(value, dialect)

Receive a bound parameter value to be converted.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

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.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters

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

• dialect – the Dialect in use.

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

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.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

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

Bases: sqlalchemy.sql.type_api.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 sqlalchemy.sql.sqltypes.CHAR

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.

Subclasses override this method to return the value that should be passed along to the underlying TypeEngine object, and from there to the DBAPI execute() method.

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.

This operation should be designed with the reverse operation in mind, which would be the process_result_value method of this class.

Parameters

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

• dialect – the Dialect in use.

process_result_value(value, dialect)

Receive a result-row column value to be converted.

Subclasses should implement this method to operate on data fetched from the database.

Subclasses override this method to return the value that should be passed back to the application, given a value that is already processed by the underlying TypeEngine object, originally from the DBAPI cursor method fetchone() or similar.

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.

This operation should be designed to be reversible by the “process_bind_param” method of this class.

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

Bases: sqlalchemy.sql.type_api.TypeDecorator

impl

alias of sqlalchemy.sql.sqltypes.String

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)

Initialize self. See help(type(self)) for accurate signature.

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.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

Details of how the data model objects are mapped onto the relational database are encapsulated here.

galaxy.model.mapping.now()

Return a new datetime representing UTC day and time.

galaxy.model.mapping.simple_mapping(model, **kwds)

galaxy.model.mapping.tag_mapping(tag_association_class, backref_name)

galaxy.model.mapping.annotation_mapping(annotation_class, **kwds)

galaxy.model.mapping.rating_mapping(rating_class, **kwds)

galaxy.model.mapping.db_next_hid(self)

Override __next_hid to generate from the database in a concurrency safe way. Loads the next history ID from the DB and returns it. It also saves the future next_id into the DB.

Return type

int

Returns

the next history id

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

Bases: galaxy.model.base.SharedModelMapping

security_agent: galaxy.model.security.GalaxyRBACAgent

thread_local_log: Optional[_thread._local]

create_tables: bool

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[_thread._local] = None, log_query_counts=False) → galaxy.model.mapping.GalaxyModelMapping

Connect mappings to the database

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)

Initialize self. See help(type(self)) for accurate signature.

classmethod process(element)

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

MetadataParameter sub-classes.

class galaxy.model.metadata.MetadataCollection(parent)

Bases: collections.abc.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)

Initialize self. See help(type(self)) for accurate signature.

get_parent()

set_parent(parent)

property parent

property spec

remove_key(name)

element_is_set(name)

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: collections.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)

Initialize self. See help(type(self)) for accurate signature.

append(item)

class galaxy.model.metadata.MetadataParameter(spec)

Bases: object

__init__(spec)

Initialize self. See help(type(self)) for accurate signature.

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

to_string(value)

to_safe_string(value)

make_copy(value, target_context=None, source_context=None)

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)

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.metadata.MetadataParameter

__init__(spec)

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.metadata.SelectParameter

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

class galaxy.model.metadata.RangeParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

__init__(spec)

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.metadata.RangeParameter

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

class galaxy.model.metadata.ColumnTypesParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.ListParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.DictParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

class galaxy.model.metadata.PythonObjectParameter(spec)

Bases: galaxy.model.metadata.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: galaxy.model.metadata.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, 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, **kwds)

class galaxy.model.metadata.MetadataTempFile(**kwds)

Bases: object

tmp_dir = 'database/tmp'

__init__(**kwds)

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.none_like.RecursiveNone

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

Initialize self. See help(type(self)) for accurate signature.

missing_meta()

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)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.model.search.ViewQueryBaseClass

Bases: object

FIELDS: Dict[str, galaxy.model.search.ViewField] = {}

VIEW_NAME = 'undefined'

__init__()

Initialize self. See help(type(self)) for accurate signature.

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: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset_dataset'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_folder'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'tool'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history_dataset'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'workflow'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'job'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page'

FIELDS: Dict[str, galaxy.model.search.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: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page_revision'

FIELDS: Dict[str, galaxy.model.search.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)

Initialize self. See help(type(self)) for accurate signature.

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)

Initialize self. See help(type(self)) for accurate signature.

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)

Initialize self. See help(type(self)) for accurate signature.

exception galaxy.model.search.GalaxyParseError

Bases: Exception

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

Bases: object

__init__(view, query)

Initialize self. See help(type(self)) for accurate signature.

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__()

Initialize self. See help(type(self)) for accurate signature.

query(query_text)

galaxy.model.security module

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

Bases: galaxy.security.RBACAgent

__init__(model, permitted_actions=None)

Initialize self. See help(type(self)) for accurate signature.

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)

can_access_datasets(user_roles, action_tuples)

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)

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: galaxy.security.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)

Initialize self. See help(type(self)) for accurate signature.

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)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.model.tags.TagHandler(sa_session: sqlalchemy.orm.scoping.scoped_session)

Bases: object

Manages CRUD operations related to tagging objects.

__init__(sa_session: sqlalchemy.orm.scoping.scoped_session) → None

Initialize self. See help(type(self)) for accurate signature.

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)

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: sqlalchemy.orm.scoping.scoped_session)

Bases: galaxy.model.tags.TagHandler

__init__(sa_session: sqlalchemy.orm.scoping.scoped_session)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.model.tags.GalaxyTagHandlerSession(sa_session)

Bases: galaxy.model.tags.GalaxyTagHandler

Like GalaxyTagHandler, but avoids one flush per created tag.

__init__(sa_session)

Initialize self. See help(type(self)) for accurate signature.

class galaxy.model.tags.CommunityTagHandler(sa_session)

Bases: galaxy.model.tags.TagHandler

__init__(sa_session)

Initialize self. See help(type(self)) for accurate signature.

galaxy.model.triggers module