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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)

exception galaxy.model.ConverterDependencyException(value)

Bases: Exception

__init__(value)

galaxy.model.set_datatypes_registry(d_registry)

Set up datatypes_registry

class galaxy.model.HasTags

Bases: object

dict_collection_visible_keys = ['tags']

dict_element_visible_keys = ['tags']

to_dict(*args, **kwargs)

make_tag_string_list()

copy_tags_from(target_user, source)

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)

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

seconds_since_updated

seconds_since_created

class galaxy.model.WorkerProcess(server_name, hostname)

Bases: galaxy.model.UsesCreateAndUpdateTime

__init__(server_name, hostname)

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)

metrics

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

log_str()

stdout

stderr

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

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

use_pbkdf2 = True

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)

email

password

external

deleted

purged

active

activation_token

username

last_password_change

histories

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.

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)

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()

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)

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

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)

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)

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

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

__init__(plugin, metric_name, metric_value)

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)

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)

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)

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.

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

terminal_states = ['ok', 'error', 'deleted']

non_ready_states = ['new', 'resubmitted', 'upload', 'waiting', 'queued', 'running']

job states where the job hasn’t finished and the model may still change

__init__()

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

running

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)

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_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)

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.

command_version

update_output_states()

any_output_dataset_collection_instances_deleted

any_output_dataset_deleted

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.

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

__init__(job, working_directory, prepare_files_cmd)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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

__init__(id=None, populated_state=None)

id

populated_state

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__()

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)

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)

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)

job

history_dataset_association

library_dataset_dataset_association

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)

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

Bases: galaxy.model.RepresentById

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

job

history

dataset

compressed

history_attrs_filename

fda

temp_directory

up_to_date

Return False, if a new export should be generated for corresponding history.

ready

preparing

export_name

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)

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)

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, 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, info=None, configured=False, deleted=False)

job

name

token

tool_port

host

port

protocol

entry_url

info

configured

deleted

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('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)

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

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

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

state

plugin

params

get_check_interval()

set_check_interval(seconds)

check_interval

get_last_check()

set_last_check(seconds)

last_check

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)

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)

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)

id

name

deleted

purged

importing

genome_build

published

user

datasets

galaxy_sessions

tags

init_on_load()

stage_addition(items)

empty

add_pending_datasets(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.

has_possible_members

activatable_datasets

serialize(id_encoder, serialization_options)

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

latest_export

unhide_datasets()

resume_paused_jobs()

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.

disk_nice_size

Returns human readable size of history on disk.

active_dataset_and_roles_query

active_datasets_and_roles

active_visible_datasets_and_roles

active_visible_dataset_collections

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.HistoryUserShareAssociation

Bases: galaxy.model.RepresentById

__init__()

history

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)

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)

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

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

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

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)

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)

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='=')

name

description

bytes

operation

get_amount()

set_amount(amount)

amount

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']

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

__init__(type, quota)

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)

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)

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)

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)

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)

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)

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)

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)

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

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

non_ready_states = ('new', 'upload', 'queued', 'running', 'setting_metadata')

ready_states = ('failed_metadata', 'paused', 'empty', 'discarded', 'error', 'ok')

valid_input_states = ('setting_metadata', 'failed_metadata', 'queued', 'new', 'upload', 'empty', 'paused', 'ok', 'running')

terminal_states = ('ok', 'empty', 'error', 'discarded', 'failed_metadata')

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

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)

state

deleted

purged

purgable

external_filename

file_size

sources

hashes

is_new

in_ready_state()

get_file_name()

set_file_name(filename)

file_name

get_extra_files_path()

create_extra_files_path()

set_extra_files_path(extra_files_path)

extra_files_path

extra_files_path_exists()

store_by

extra_files_path_name_from(object_store)

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()

user_can_purge

full_delete()

Remove the file and extra files, marks deleted and purged

get_access_roles(trans)

get_manage_permissions_roles(trans)

has_manage_permissions_roles(trans)

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

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

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

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

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

__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)

peek

update()

ext

get_dataset_state()

raw_set_dataset_state(state)

set_dataset_state(state)

state

get_file_name()

set_file_name(filename)

file_name

link_to(path)

extra_files_path

extra_files_path_exists()

datatype

get_metadata()

set_metadata_requires_flush

set_metadata(bunch)

metadata

metadata_file_types

get_dbkey()

set_dbkey(value)

dbkey

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)

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()

is_ok

is_pending

Return true if the dataset is neither ready nor in error

source_library_dataset

source_dataset_chain

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(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)

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(trans)

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)

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)

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)

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)

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)

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(trans)

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)

name

description

item_count

order_id

genome_build

folders

datasets

add_library_dataset(library_dataset, genome_build=None)

add_folder(folder)

activatable_library_datasets

serialize(id_encoder, serialization_options)

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

library_path

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)

folder

order_id

library_dataset_dataset_association

get_info()

set_info(info)

info

get_name()

set_name(name)

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)

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(trans)

get_manage_permissions_roles(trans)

has_manage_permissions_roles(trans)

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)

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)

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)

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)

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)

library_dataset_dataset_association

template

info

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)

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']

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

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

id

collection_type

populated_state

element_count

dataset_states_and_extensions_summary

populated_optimized

populated

dataset_action_tuples

waiting_for_elements

mark_as_populated()

handle_population_failed(message)

finalize(collection_type_description)

dataset_instances

dataset_elements

first_dataset_element

state

validate()

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

replace_failed_elements(replacements)

set_from_dict(new_data)

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)

state

populated

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)

id

hid

history

name

visible

copied_from_history_dataset_collection_association

implicit_output_name

implicit_input_collections

history_content_type

content_type = 'dataset_collection'

type_id

job_source_type

job_source_id

to_hda_representative(multiple=False)

serialize(id_encoder, serialization_options, for_link=False)

to_dict(view='collection')

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.

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)

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)

hda

ldda

child_collection

id

collection

element_index

element_identifier

element_type

is_collection

element_object

dataset_instance

dataset

first_dataset_instance()

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)

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)

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)

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)

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__()

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

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)

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)

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

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)

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)

steps_by_id

step_by_index(order_index)

input_steps

workflow_outputs

workflow_output_for(output_label)

workflow_output_labels

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.

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

id

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('uuid', UUIDType(), table=<workflow>), schema=None)

update_time

class galaxy.model.WorkflowStep

Bases: galaxy.model.RepresentById

__init__()

id

type

tool_id

tool_inputs

tool_errors

dynamic_tool

position

inputs

config

label

uuid

workflow_outputs

tool_uuid

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)

input_connections

unique_workflow_outputs

content_id

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()

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)

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__()

output_step_id

output_name

input_step_input_id

non_data_connection

input_name

input_step

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)

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.RepresentById

__init__()

stored_workflow

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__()

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']

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

non_terminal_states = ['new', 'ready']

__init__()

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)

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)

output_associations

input_associations

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

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

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']

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

is_new

add_output(output_name, output_object)

jobs

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

__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']

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

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

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)

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)

history_dataset

library_dataset

name

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'>]

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

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)

name

desc

fields

form_definition_current

type

layout

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

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)

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)

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)

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)

server_url

handle

secret

issued

lifetime

assoc_type

save()

classmethod store(server_url, association)

classmethod get(*args, **kwargs)

classmethod remove(ids_to_delete)

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)

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)

server_url

timestamp

salt

save()

classmethod use(server_url, timestamp, salt)

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)

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)

provider

uid

user_id

extra_data

lifetime

assoc_type

get_id_token(strategy)

set_extra_data(extra_data=None)

save()

classmethod username_max_length()

classmethod user_model()

classmethod changed(user)

classmethod user_query()

classmethod user_exists(*args, **kwargs)

classmethod get_username(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)

classmethod get_users_by_email(email)

classmethod get_social_auth(provider, uid)

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

classmethod create_social_auth(user, uid, provider)

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)

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='')

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__()

id

user

title

slug

latest_revision_id

revisions

importable

published

to_dict(view='element')

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__()

title

content

content_format

to_dict(view='element')

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.RepresentById

__init__()

page

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)

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)

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.RepresentById

__init__()

visualization

user

id

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

user_id

visualization_id

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

Bases: galaxy.model.RepresentById

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

terminal_states = ['error', 'done']

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

state

path

info

pid

socket

params

create_time

id

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

transfer_job

update_time

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

Bases: galaxy.model.RepresentById

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

id

type

parent_id

name

children

parent

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

tagged_histories

tagged_history_dataset_associations

tagged_history_dataset_collections

tagged_library_dataset_collections

tagged_library_dataset_dataset_associations

tagged_pages

tagged_tools

tagged_visualizations

tagged_workflow_steps

tagged_workflows

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

Bases: galaxy.util.dictifiable.Dictifiable

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

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

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

copy(cls=None)

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

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

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

histories

history_id

id

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

history_dataset_association_id

history_tag_associations

id

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

history_tag_associations

id

library_dataset_dataset_association_id

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

id

page_id

pages

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

id

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

tag

tag_id

user

user_id

user_tname

user_value

value

workflow_step_id

workflow_steps

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

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

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

id

stored_workflow_id

stored_workflows

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

id

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

tag

tag_id

user

user_id

user_tname

user_value

value

visualization_id

visualizations

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

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

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

dataset_collections

history_dataset_collection_id

id

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

dataset_collections

id

library_dataset_collection_id

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

tag

tag_id

user

user_id

user_tname

user_value

value

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

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

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

id

user

tool_id

tag_id

user_tname

value

user_value

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

tag

user_id

class galaxy.model.HistoryAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

histories

history

history_id

id

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

user

user_id

class galaxy.model.HistoryDatasetAssociationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

hda

hdas

history_dataset_association_id

id

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

user

user_id

class galaxy.model.StoredWorkflowAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

id

stored_workflow

stored_workflow_id

stored_workflows

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

user

user_id

class galaxy.model.WorkflowStepAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

id

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

user

user_id

workflow_step

workflow_step_id

workflow_steps

class galaxy.model.PageAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

id

page

page_id

pages

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

user

user_id

class galaxy.model.VisualizationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

id

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

user

user_id

visualization

visualization_id

visualizations

class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

dataset_collections

history_dataset_collection

history_dataset_collection_id

id

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

user

user_id

class galaxy.model.LibraryDatasetCollectionAnnotationAssociation

Bases: galaxy.model.RepresentById

__init__()

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

annotation

dataset_collections

id

library_dataset_collection

library_dataset_collection_id

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

user

user_id

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

Bases: object

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

set_item(item)

Set association’s item.

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

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

set_item(history)

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

histories

history

history_id

id

rating

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

user

user_id

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

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

set_item(history_dataset_association)

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

hda

hdas

history_dataset_association_id

id

rating

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

user

user_id

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

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

set_item(stored_workflow)

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

id

rating

stored_workflow

stored_workflow_id

stored_workflows

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

user

user_id

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

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

set_item(page)

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

id

page

page_id

pages

rating

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

user

user_id

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

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

set_item(visualization)

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

id

rating

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

user

user_id

visualizaiton

visualization_id

visualizations

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

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

set_item(dataset_collection)

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

dataset_collections

history_dataset_collection

history_dataset_collection_id

id

rating

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

user

user_id

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

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

set_item(dataset_collection)

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

dataset_collections

id

libary_dataset_collection

library_dataset_collection_id

rating

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

user

user_id

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

Bases: galaxy.model.RepresentById

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

id

history

user

create_time

history_id

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

update_time

user_id

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

Bases: galaxy.model.RepresentById

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

create_time

job_id

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

update_time

id

job

data_manager_id

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

Bases: galaxy.model.RepresentById

id

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

user

user_id

__init__(name=None, value=None)

name

value

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

Bases: galaxy.model.RepresentById

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

user

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

id

create_time

user_id

session_id

action

params

context

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

Bases: galaxy.model.RepresentById

create_time

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

user

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

id

user_id

key

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

Subpackages

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

Submodules

galaxy.model.base module

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

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

Bases: galaxy.util.bunch.Bunch

__init__(model_modules, engine)

Session

For backward compat., deprecated.

galaxy.model.base.versioned_objects(iter)

galaxy.model.base.versioned_session(session)

galaxy.model.custom_types module

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

Bases: json.encoder.JSONEncoder

default(obj)

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

Bases: sqlalchemy.sql.sqltypes.LargeBinary

result_processor(dialect, coltype)

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

Bases: sqlalchemy.sql.type_api.TypeDecorator

Represents an immutable structure as a json-encoded string.

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

impl

alias of GalaxyLargeBinary

process_bind_param(value, dialect)

process_result_value(value, dialect)

load_dialect_impl(dialect)

copy_value(value)

compare_values(x, y)

class galaxy.model.custom_types.MutationObj

Bases: sqlalchemy.ext.mutable.Mutable

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

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

And other minor changes to make it work for us.

classmethod coerce(key, value)

class galaxy.model.custom_types.MutationDict

Bases: galaxy.model.custom_types.MutationObj, dict

classmethod coerce(key, value)

Convert plain dictionary to MutationDict

class galaxy.model.custom_types.MutationList

Bases: galaxy.model.custom_types.MutationObj, list

classmethod coerce(key, value)

Convert plain list to MutationList

append(value)

insert(idx, value)

extend(values)

pop(*args, **kw)

remove(value)

galaxy.model.custom_types.total_size(o, handlers={}, verbose=False)

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

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

handlers = {SomeContainerClass: iter,

OtherContainerClass: OtherContainerClass.get_elements}

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

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

Bases: galaxy.model.custom_types.JSONType

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

process_bind_param(value, dialect)

process_result_value(value, dialect)

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

Bases: sqlalchemy.sql.type_api.TypeDecorator

Platform-independent UUID type.

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

CHAR(32), storing as stringified hex values.

impl

alias of sqlalchemy.sql.sqltypes.CHAR

load_dialect_impl(dialect)

process_bind_param(value, dialect)

process_result_value(value, dialect)

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

Bases: sqlalchemy.sql.type_api.TypeDecorator

impl

alias of sqlalchemy.sql.sqltypes.String

process_bind_param(value, dialect)

Automatically truncate string values

galaxy.model.database_heartbeat module

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

Bases: object

__init__(application_stack, heartbeat_interval=60)

sa_session

server_name

start()

shutdown()

get_active_processes(last_seen_seconds=None)

Return all processes seen in last_seen_seconds seconds.

add_change_callback(callback)

is_config_watcher

worker_process

update_watcher_designation()

send_database_heartbeat()

galaxy.model.database_heartbeat.now()

Return a new datetime representing UTC day and time.

galaxy.model.item_attrs module

class galaxy.model.item_attrs.UsesItemRatings

Bases: object

Mixin for getting and setting item ratings.

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

get_ave_item_rating_data(db_session, item, webapp_model=None)

Returns the average rating for an item.

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

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

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

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

class galaxy.model.item_attrs.UsesAnnotations

Bases: object

Mixin for getting and setting item annotations.

get_item_annotation_str(db_session, user, item)

get_item_annotation_obj(db_session, user, item)

add_item_annotation(db_session, user, item, annotation)

delete_item_annotation(db_session, user, item)

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

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

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

Returns foreign key in source class that references target class.

galaxy.model.mapping module

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

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

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

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

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

galaxy.model.mapping.db_next_hid(self)

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

Return type:int Returns:the next history id

galaxy.model.mapping.init(file_path, url, engine_options=None, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True, slow_query_log_threshold=0, thread_local_log=None, log_query_counts=False)

Connect mappings to the database

galaxy.model.mapping.now()

Return a new datetime representing UTC day and time.

galaxy.model.metadata module

Galaxy Metadata

class galaxy.model.metadata.Statement(target)

Bases: object

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

__init__(target)

classmethod process(element)

class galaxy.model.metadata.MetadataCollection(parent)

Bases: object

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

__init__(parent)

get_parent()

set_parent(parent)

parent

spec

get(key, default=None)

items()

remove_key(name)

element_is_set(name)

check if the meta data with the given name is set, i.e. - if the such a metadata actually exists and - if its value differs from no_value

param name the name of the metadata element return True if the value differes from the no_value

False if its equal of if no metadata with the name is specified

get_metadata_parameter(name, **kwd)

make_dict_copy(to_copy)

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

requires_dataset_id

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

to_JSON_dict(filename=None)

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

Bases: collections.OrderedDict

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

__init__(*args, **kwds)

append(item)

class galaxy.model.metadata.MetadataParameter(spec)

Bases: object

__init__(spec)

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

to_string(value)

to_safe_string(value)

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

classmethod marshal(value)

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

validate(value)

Throw an exception if the value is invalid.

unwrap(form_value)

Turns a value into its storable form.

wrap(value, session)

Turns a value into its usable form.

from_external_value(value, parent)

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

to_external_value(value)

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

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

Bases: object

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

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

get(name, default=None)

wrap(value, session)

Turns a stored value into its usable form.

unwrap(value)

Turns an incoming value into its storable form.

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

MetadataParameter sub-classes.

class galaxy.model.metadata.SelectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

__init__(spec)

to_string(value)

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

wrap(value, session)

classmethod marshal(value)

class galaxy.model.metadata.DBKeyParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

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

class galaxy.model.metadata.RangeParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

__init__(spec)

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

classmethod marshal(value)

class galaxy.model.metadata.ColumnParameter(spec)

Bases: galaxy.model.metadata.RangeParameter

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

class galaxy.model.metadata.ColumnTypesParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.ListParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.model.metadata.DictParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

class galaxy.model.metadata.PythonObjectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

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

classmethod marshal(value)

class galaxy.model.metadata.FileParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

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

wrap(value, session)

make_copy(value, target_context, source_context)

classmethod marshal(value)

from_external_value(value, parent, path_rewriter=None)

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

to_external_value(value)

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

new_file(dataset=None, **kwds)

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

Bases: object

tmp_dir = 'database/tmp'

__init__(**kwds)

file_name

to_JSON()

classmethod from_JSON(json_dict)

classmethod is_JSONified_value(value)

classmethod cleanup_from_JSON_dict_filename(filename)

galaxy.model.none_like module

Objects with No values

class galaxy.model.none_like.RecursiveNone

Bases: object

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

Bases: galaxy.model.none_like.RecursiveNone

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

missing_meta()

galaxy.model.search module

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

Example Queries:

select name, id, file_size from hda

select name from hda

select name, model_class from ldda

select * from history

select * from workflow

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

select * from history where name=’Unnamed history’

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

Bases: object

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

Parameters:

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

that the right hand value will be compared against

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

process the conditional

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

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

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

class galaxy.model.search.ViewQueryBaseClass

Bases: object

FIELDS = {}

VIEW_NAME = 'undefined'

__init__()

decode_query_ids(trans, conditional)

filter(left, operator, right)

search(trans)

get_results(force_query=False)

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

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

class galaxy.model.search.LibraryDatasetDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset_dataset'

FIELDS = {'data_type': <galaxy.model.search.ViewField object at 0x7f5318381208>, 'deleted': <galaxy.model.search.ViewField object at 0x7f5318210d30>, 'extended_metadata': <galaxy.model.search.ViewField object at 0x7f5318210160>, 'id': <galaxy.model.search.ViewField object at 0x7f5318210780>, 'name': <galaxy.model.search.ViewField object at 0x7f5318210278>, 'parent_library_id': <galaxy.model.search.ViewField object at 0x7f53182a77b8>}

search(trans)

class galaxy.model.search.LibraryView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7f53181d79b0>, 'id': <galaxy.model.search.ViewField object at 0x7f53183816a0>, 'name': <galaxy.model.search.ViewField object at 0x7f5318381198>}

search(trans)

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

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

class galaxy.model.search.LibraryFolderView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_folder'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7f53181d7a20>, 'library_path': <galaxy.model.search.ViewField object at 0x7f53181d7ac8>, 'name': <galaxy.model.search.ViewField object at 0x7f53181d79e8>, 'parent_id': <galaxy.model.search.ViewField object at 0x7f53181d7a58>, 'parent_library_id': <galaxy.model.search.ViewField object at 0x7f53181d7a90>}

search(trans)

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

class galaxy.model.search.LibraryDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'library_dataset'

FIELDS = {'folder_id': <galaxy.model.search.ViewField object at 0x7f53181d7b70>, 'id': <galaxy.model.search.ViewField object at 0x7f53181d7b38>, 'name': <galaxy.model.search.ViewField object at 0x7f53181d7b00>}

search(trans)

class galaxy.model.search.ToolView

Bases: galaxy.model.search.ViewQueryBaseClass

VIEW_NAME = 'tool'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7f53181d7be0>, 'tool_id': <galaxy.model.search.ViewField object at 0x7f53181d7ba8>}

search(trans)

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

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

class galaxy.model.search.HistoryDatasetView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history_dataset'

FIELDS = {'copied_from_hda_id': <galaxy.model.search.ViewField object at 0x7f53181d7d30>, 'copied_from_ldda_id': <galaxy.model.search.ViewField object at 0x7f53181d7cf8>, 'deleted': <galaxy.model.search.ViewField object at 0x7f53181d7d68>, 'extended_metadata': <galaxy.model.search.ViewField object at 0x7f53181d7da0>, 'history_id': <galaxy.model.search.ViewField object at 0x7f53181d7c88>, 'id': <galaxy.model.search.ViewField object at 0x7f53181d7c50>, 'name': <galaxy.model.search.ViewField object at 0x7f53181d7c18>, 'tag': <galaxy.model.search.ViewField object at 0x7f53181d7cc0>}

search(trans)

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

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

class galaxy.model.search.HistoryView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'history'

FIELDS = {'annotation': <galaxy.model.search.ViewField object at 0x7f53181d7e80>, 'deleted': <galaxy.model.search.ViewField object at 0x7f53181d7eb8>, 'id': <galaxy.model.search.ViewField object at 0x7f53181d7e10>, 'name': <galaxy.model.search.ViewField object at 0x7f53181d7dd8>, 'tag': <galaxy.model.search.ViewField object at 0x7f53181d7e48>}

search(trans)

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

class galaxy.model.search.WorkflowView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'workflow'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7f53181d7fd0>, 'id': <galaxy.model.search.ViewField object at 0x7f53181d7f60>, 'name': <galaxy.model.search.ViewField object at 0x7f53181d7f28>, 'tag': <galaxy.model.search.ViewField object at 0x7f53181d7f98>}

search(trans)

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

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

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

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

class galaxy.model.search.JobView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'job'

FIELDS = {'input_hda': <galaxy.model.search.ViewField object at 0x7f53181de160>, 'input_ldda': <galaxy.model.search.ViewField object at 0x7f53181de128>, 'output_hda': <galaxy.model.search.ViewField object at 0x7f53181de198>, 'param': <galaxy.model.search.ViewField object at 0x7f53181de0f0>, 'state': <galaxy.model.search.ViewField object at 0x7f53181de0b8>, 'tool_name': <galaxy.model.search.ViewField object at 0x7f53181de080>}

search(trans)

class galaxy.model.search.PageView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page'

FIELDS = {'deleted': <galaxy.model.search.ViewField object at 0x7f53181de2b0>, 'id': <galaxy.model.search.ViewField object at 0x7f53181de208>, 'slug': <galaxy.model.search.ViewField object at 0x7f53181de240>, 'title': <galaxy.model.search.ViewField object at 0x7f53181de278>}

search(trans)

class galaxy.model.search.PageRevisionView

Bases: galaxy.model.search.ViewQueryBaseClass

DOMAIN = 'page_revision'

FIELDS = {'id': <galaxy.model.search.ViewField object at 0x7f53181de320>, 'page_id': <galaxy.model.search.ViewField object at 0x7f53181de390>, 'title': <galaxy.model.search.ViewField object at 0x7f53181de358>}

search(trans)

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

Bases: object

This class represents a data structure of a compiled GQL query

__init__(field_list, table_name, conditional)

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

Bases: object

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

__init__(left, operator, right)

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

Bases: object

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

__init__(left, right)

exception galaxy.model.search.GalaxyParseError

Bases: Exception

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

Bases: object

__init__(view, query)

decode_query_ids(trans)

process(trans)

item_to_api_value(item)

class galaxy.model.search.GalaxySearchEngine

Bases: object

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

__init__()

query(query_text)

galaxy.model.security module

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

Bases: galaxy.security.RBACAgent

__init__(model, permitted_actions=None)

sa_session

Returns a SQLAlchemy session

sort_by_attr(seq, attr)

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

get_all_roles(trans, cntrller)

get_roles_for_action(item, action)

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

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

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

get_legitimate_roles(trans, item, cntrller)

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

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

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

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

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

ok_to_display(user, role)

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

allow_action(roles, action, item)

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

get_actions_for_items(trans, action, permission_items)

allow_action_on_libitems(trans, user_roles, action, items)

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

dataset_access_mapping(trans, user_roles, datasets)

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

dataset_permission_map_for_access(trans, user_roles, libitems)

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

item_permission_map_for_modify(trans, user_roles, libitems)

item_permission_map_for_manage(trans, user_roles, libitems)

item_permission_map_for_add(trans, user_roles, libitems)

can_access_dataset(user_roles, dataset)

can_access_datasets(user_roles, action_tuples)

can_manage_dataset(roles, dataset)

can_access_library(roles, library)

get_accessible_libraries(trans, user)

Return all data libraries that the received user can access

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

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

can_access_library_item(roles, item, user)

can_add_library_item(roles, item)

can_modify_library_item(roles, item)

can_manage_library_item(roles, item)

get_item_actions(action, item)

guess_derived_permissions_for_datasets(datasets=[])

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

guess_derived_permissions(all_input_permissions)

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

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

associate_components(**kwd)

associate_user_group(user, group)

associate_user_role(user, role)

associate_group_role(group, role)

associate_action_dataset_role(action, dataset, role)

create_user_role(user, app)

create_private_user_role(user)

get_private_user_role(user, auto_create=False)

get_role(name, type=None)

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

get_sharing_roles(user)

user_set_default_permissions(user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private=False)

user_get_default_permissions(user)

history_set_default_permissions(history, permissions={}, dataset=False, bypass_manage_permission=False)

history_get_default_permissions(history)

set_all_dataset_permissions(dataset, permissions={}, new=False, flush=True)

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

set_dataset_permission(dataset, permission={})

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

get_permissions(item)

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

copy_dataset_permissions(src, dst)

privately_share_dataset(dataset, users=[])

set_all_library_permissions(trans, library_item, permissions={})

set_library_item_permission(library_item, permission={})

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

library_is_public(library, contents=False)

library_is_unrestricted(library)

make_library_public(library, contents=False)

folder_is_public(folder)

folder_is_unrestricted(folder)

make_folder_public(folder)

dataset_is_public(dataset)

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

dataset_is_unrestricted(trans, dataset)

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

dataset_is_private_to_user(trans, dataset)

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

datasets_are_public(trans, datasets)

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

make_dataset_public(dataset)

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

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

get_permitted_libraries(trans, user, actions)

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

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

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

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

get_showable_folders(user, roles, library_item, actions_to_check, hidden_folder_ids=[], showable_folders=[])

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

set_entity_user_associations(users=[], roles=[], groups=[], delete_existing_assocs=True)

set_entity_group_associations(groups=[], users=[], roles=[], delete_existing_assocs=True)

set_entity_role_associations(roles=[], users=[], groups=[], delete_existing_assocs=True)

get_component_associations(**kwd)

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

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

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

Bases: galaxy.security.RBACAgent

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

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

__init__(model, permitted_actions=None)

sa_session

Returns a SQLAlchemy session

allow_action(addr, action, **kwd)

set_dataset_permissions(hda, user, site)

galaxy.model.tags module

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

Bases: object

__init__(item_class, tag_assoc_class, item_id_col)

class galaxy.model.tags.TagHandler(sa_session)

Bases: object

Manages CRUD operations related to tagging objects.

__init__(sa_session)

create_tag_handler_session()

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

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

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

get_tag_assoc_class(item_class)

Returns tag association class for item class.

get_id_col_in_item_tag_assoc_table(item_class)

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

get_community_tags(item=None, limit=None)

Returns community tags for an item.

get_tool_tags()

remove_item_tag(user, item, tag_name)

Remove a tag from an item.

delete_item_tags(user, item)

Delete tags from an item.

item_has_tag(user, item, tag)

Returns true if item is has a given tag.

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

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

Apply tags to an item.

get_tags_str(tags)

Build a string from an item’s tags.

get_tag_by_id(tag_id)

Get a Tag object from a tag id.

get_tag_by_name(tag_name)

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

parse_tags(tag_str)

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

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

parse_tags_list(tags_list)

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

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

class galaxy.model.tags.GalaxyTagHandler(sa_session)

Bases: galaxy.model.tags.TagHandler

__init__(sa_session)

class galaxy.model.tags.GalaxyTagHandlerSession(sa_session)

Bases: galaxy.model.tags.GalaxyTagHandler

Like GalaxyTagHandler, but avoids one flush per created tag.

__init__(sa_session)

class galaxy.model.tags.CommunityTagHandler(sa_session)

Bases: galaxy.model.tags.TagHandler

__init__(sa_session)

galaxy.model.triggers module

Database trigger installation and removal

galaxy.model.triggers.install_timestamp_triggers(engine)

Install update_time propagation triggers for history data tables

galaxy.model.triggers.drop_timestamp_triggers(engine)

Remove update_time propagation triggers for historydata tables

galaxy.model.triggers.execute_statements(engine, statements)

galaxy.model.triggers.get_timestamp_install_sql(variant)

Generate a list of sql statements for insalllation of timetamp triggers

galaxy.model.triggers.get_timestamp_drop_sql(variant)

generate a list of statements to drop the timestammp update triggers

galaxy.model.triggers.build_pg_timestamp_fn(fn_name, table_name, local_key='id', source_key='id', stamp_column='update_time')

Generates a postgres history update timestamp function

galaxy.model.triggers.build_pg_trigger(table_name, fn_name)

assigns a postgres trigger to indicated table, calling user-defined function

galaxy.model.triggers.build_timestamp_trigger(operation, source_table, target_table, source_key='id', target_key='id', when='BEFORE')

creates a non-postgres update_time trigger

galaxy.model.triggers.build_drop_trigger(operation, source_table, when='BEFORE')

drops a non-postgres trigger by name

galaxy.model.triggers.get_trigger_name(operation, source_table, when='BEFORE')

non-postgres trigger name