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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

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

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

api_keys

cloudauthz

cloudauthzs

create_time

custos_auth

data_manager_histories

default_permissions

disk_usage

form_values_id

galaxy_sessions

groups

histories_shared_by_others

id

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

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', JSONType(), 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

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

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

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

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

exit_code

job_messages

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.

set_final_state(final_state)

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()

remappable()

Check whether job is remappable when rerun

any_output_dataset_collection_instances_deleted = <ColumnProperty at 0x7fb1cff96450; no key>

any_output_dataset_deleted = <ColumnProperty at 0x7fb1cff96350; no key>

container

create_time

data_manager_association

dynamic_tool_id

external_output_metadata

galaxy_session

galaxy_version

history

history_dataset_collection_associations

history_id

id

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', JSONType(), table=<job>), Column('job_messages', JSONType(), 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', JSONType(), 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

update_time

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

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', JSONType(), 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

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

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

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

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

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

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

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

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

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

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

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

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.

id

implicit_collection_jobs

implicit_collection_jobs_id

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

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', JSONType(), 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

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

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

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

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

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', JSONType(), 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

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', JSONType(), 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

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

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', JSONType(), 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

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

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.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

name

deleted

purged

importing

genome_build

published

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>, 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)

update_time

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

job_export_history_archive

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('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

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', JSONType(), 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

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

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)

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

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)

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

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

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, 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

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

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

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

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

name

has_cycles

has_errors

steps

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

stored_workflow_id

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', JSONType(), table=<workflow>), Column('creator_metadata', JSONType(), 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

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', JSONType(), 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

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', JSONType(), table=<workflow_step_input>), Column('value_from_type', TEXT(), table=<workflow_step_input>), Column('default_value', JSONType(), 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

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

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

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

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

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

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

workflow_id

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

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'

property is_new

add_output(output_name, output_object)

property jobs

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

Return item dictionary.

__init__()

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

action

create_time

id

implicit_collection_jobs

implicit_collection_jobs_id

job

job_id

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', JSONType(), table=<workflow_invocation_step>), schema=None)

update_time

workflow_invocation

workflow_invocation_id

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

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

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', JSONType(), 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

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

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

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', JSONType(), 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

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

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

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', JSONType(), 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

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

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

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

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', JSONType(), table=<form_definition>), Column('type', TrimmedString(length=255), table=<form_definition>), Column('layout', JSONType(), 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

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

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', JSONType(), 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

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

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

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

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

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

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', JSONType(), 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

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', JSONType(), table=<cloudauthz>), Column('authn_id', Integer(), ForeignKey('oidc_user_authnz_tokens.id'), table=<cloudauthz>), Column('tokens', JSONType(), 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

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

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

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

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

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', JSONType(), 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