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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[source]

Bases: object

exception galaxy.model.NoConverterException(value)[source]

Bases: exceptions.Exception

__init__(value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

exception galaxy.model.ConverterDependencyException(value)[source]

Bases: exceptions.Exception

__init__(value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

galaxy.model.set_datatypes_registry(d_registry)[source]

Set up datatypes_registry

class galaxy.model.HasTags[source]

Bases: object

dict_collection_visible_keys = ['tags']
dict_element_visible_keys = ['tags']
to_dict(*args, **kwargs)[source]
make_tag_string_list()[source]
copy_tags_from(target_user, source)[source]
auto_propagated_tags
class galaxy.model.SerializationOptions(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)[source]

Bases: object

__init__(for_edit, serialize_dataset_objects=None, serialize_files_handler=None, strip_metadata_files=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

attach_identifier(id_encoder, obj, ret_val)[source]
get_identifier(id_encoder, obj)[source]
get_identifier_for_id(id_encoder, obj_id)[source]
serialize_files(dataset, as_dict)[source]
class galaxy.model.HasName[source]

Bases: object

get_display_name()[source]

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[source]

Bases: object

seconds_since_updated
seconds_since_created
class galaxy.model.WorkerProcess(server_name, hostname)[source]

Bases: galaxy.model.UsesCreateAndUpdateTime

__init__(server_name, hostname)
server_name
hostname
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('update_time', DateTime(), table=<worker_process>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
galaxy.model.cached_id(galaxy_model_object)[source]

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[source]

Bases: object

MAX_NUMERIC = 9999999999999999999L
add_metric(plugin, metric_name, metric_value)[source]
metrics
set_streams(tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None)[source]
log_str()[source]
stdout
stderr
class galaxy.model.User(email=None, password=None, username=None)[source]

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)[source]

Set user password to the digest of cleartext.

set_random_password(length=16)[source]

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

check_password(cleartext)[source]

Check if cleartext matches user password when hashed.

system_user_pwent(real_system_username)[source]

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

all_roles()[source]

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

all_roles_exploiting_cache()[source]
get_disk_usage(nice_size=False)[source]

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

set_disk_usage(bytes)[source]

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)[source]
nice_total_disk_usage

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

calculate_disk_usage()[source]

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

calculate_and_set_disk_usage()[source]

Calculates and sets user disk usage.

static user_template_environment(user)[source]
>>> 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)[source]
is_active()[source]
is_authenticated()[source]
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 utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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 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)[source]

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, uuid=None, active=True, hidden=True, value=None)[source]

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, uuid=None, active=True, hidden=True, value=None)
tool_format
tool_id
tool_version
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 utcnow>)), Column('update_time', DateTime(), table=<dynamic_tool>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)
tool_directory
tool_path
update_time
workflow_steps
class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)[source]

Bases: object

__init__(plugin, metric_name, metric_value)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.JobMetricText(plugin, metric_name, metric_value)[source]

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)[source]

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)[source]

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)[source]

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[source]

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']

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
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
finished
io_dicts()[source]
get_external_output_metadata()[source]

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

get_session_id()[source]
get_user_id()[source]
get_tool_id()[source]
get_tool_version()[source]
get_command_line()[source]
get_dependencies()[source]
get_param_filename()[source]
get_parameters()[source]
get_copied_from_job_id()[source]
get_input_datasets()[source]
get_output_datasets()[source]
get_input_library_datasets()[source]
get_output_library_datasets()[source]
get_state()[source]
get_info()[source]
get_job_runner_name()[source]
get_job_runner_external_id()[source]
get_post_job_actions()[source]
get_imported()[source]
get_handler()[source]
get_params()[source]
get_user()[source]
get_tasks()[source]
get_id_tag()[source]

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

set_session_id(session_id)[source]
set_user_id(user_id)[source]
set_tool_id(tool_id)[source]
set_tool_version(tool_version)[source]
set_command_line(command_line)[source]
set_dependencies(dependencies)[source]
set_param_filename(param_filename)[source]
set_parameters(parameters)[source]
set_copied_from_job_id(job_id)[source]
set_input_datasets(input_datasets)[source]
set_output_datasets(output_datasets)[source]
set_input_library_datasets(input_library_datasets)[source]
set_output_library_datasets(output_library_datasets)[source]
set_info(info)[source]
set_runner_name(job_runner_name)[source]
get_job()[source]
set_runner_external_id(job_runner_external_id)[source]
set_post_job_actions(post_job_actions)[source]
set_imported(imported)[source]
set_handler(handler)[source]
set_params(params)[source]
add_parameter(name, value)[source]
add_input_dataset(name, dataset=None, dataset_id=None)[source]
add_output_dataset(name, dataset)[source]
add_input_dataset_collection(name, dataset_collection)[source]
add_output_dataset_collection(name, dataset_collection_instance)[source]
add_implicit_output_dataset_collection(name, dataset_collection)[source]
add_input_library_dataset(name, dataset)[source]
add_output_library_dataset(name, dataset)[source]
add_post_job_action(pja)[source]
set_state(state)[source]

Save state history

get_param_values(app, ignore_errors=False)[source]

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

raw_param_dict()[source]
check_if_output_datasets_deleted()[source]

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

mark_deleted(track_jobs_in_database=False)[source]

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

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

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

resume(flush=True)[source]
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', system_details=False)[source]

Return item dictionary.

set_final_state(final_state)[source]
get_destination_configuration(dest_params, config, key, default=None)[source]

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

any_output_dataset_collection_instances_deleted
any_output_dataset_deleted
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
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 utcnow>)), Column('update_time', DateTime(), table=<job>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]

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

get_id_tag()[source]

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()[source]
get_parameters()[source]
get_state()[source]
get_info()[source]
get_working_directory()[source]
get_task_runner_name()[source]
get_task_runner_external_id()[source]
get_job()[source]
get_prepare_input_files_cmd()[source]
get_external_output_metadata()[source]

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()[source]

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()[source]

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()[source]
set_id(id)[source]
set_command_line(command_line)[source]
set_parameters(parameters)[source]
set_state(state)[source]
set_info(info)[source]
set_working_directory(working_directory)[source]
set_task_runner_name(task_runner_name)[source]
set_job_runner_external_id(task_runner_external_id)[source]
set_task_runner_external_id(task_runner_external_id)[source]
set_job(job)[source]
set_prepare_input_files_cmd(prepare_input_files_cmd)[source]
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 utcnow>)), Column('execution_time', DateTime(), table=<task>), Column('update_time', DateTime(), table=<task>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

Bases: galaxy.model.RepresentById

__init__(name, value)
name
value
copy()[source]
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)[source]

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)[source]

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)[source]

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.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<job_state_history>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]

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)[source]
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[source]

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, output_name=None, action_arguments=None)[source]

Bases: galaxy.model.RepresentById

__init__(action_type, workflow_step, 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>, nullable=False), 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)[source]

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)[source]

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.JobExportHistoryArchive(job=None, history=None, dataset=None, compressed=False, history_attrs_filename=None)[source]

Bases: galaxy.model.RepresentById

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

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.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)[source]

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 utcnow>)), Column('modified_time', DateTime(), table=<genome_index_tool_data>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

Bases: galaxy.model.RepresentById

states = <galaxy.util.bunch.Bunch object>
__init__(state=None, plugin=None, params=None)
state
plugin
params
get_check_interval()[source]
set_check_interval(seconds)[source]
check_interval
get_last_check()[source]
set_last_check(seconds)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<deferred_job>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
user_id
galaxy.model.is_hda(d)[source]
class galaxy.model.History(id=None, name=None, user=None)[source]

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
empty
add_galaxy_session(galaxy_session, association=None)[source]
add_dataset(dataset, parent_id=None, genome_build=None, set_hid=True, quota=True)[source]
add_datasets(sa_session, datasets, parent_id=None, genome_build=None, set_hid=True, quota=True, flush=False)[source]

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

add_dataset_collection(history_dataset_collection, set_hid=True)[source]
copy(name=None, target_user=None, activatable=False, all_datasets=False)[source]

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)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

latest_export
unhide_datasets()[source]
resume_paused_jobs()[source]
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_datasets_and_roles
active_visible_datasets_and_roles
active_visible_dataset_collections
active_contents

Return all active contents ordered by hid.

contents_iter(**kwds)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<history>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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[source]

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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
user_id
class galaxy.model.GroupRoleAssociation(group, role)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
class galaxy.model.Role(name='', description='', type='system', deleted=False)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<user_quota_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
user_id
class galaxy.model.GroupQuotaAssociation(group, quota)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<group_quota_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
class galaxy.model.Quota(name='', description='', amount=0, operation='=')[source]

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()[source]
set_amount(amount)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<quota>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<default_quota_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<dataset_permissions>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<library_permissions>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<library_folder_permissions>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<library_dataset_permissions>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association_permissions>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]

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)[source]

Bases: object

__init__(id, uuid)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

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

states = <galaxy.util.bunch.Bunch object>
non_ready_states = ('new', 'upload', 'queued', 'running', 'setting_metadata')
ready_states = ('discarded', 'ok', 'failed_metadata', 'paused', 'error', 'empty')
valid_input_states = ('ok', 'failed_metadata', 'upload', 'paused', 'running', 'setting_metadata', 'new', 'queued', 'empty')
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
in_ready_state()[source]
get_file_name()[source]
set_file_name(filename)[source]
file_name
get_extra_files_path()[source]
create_extra_files_path()[source]
set_extra_files_path(extra_files_path)[source]
extra_files_path
extra_files_path_exists()[source]
get_size(nice_size=False)[source]

Returns the size of the data on disk

set_size(no_extra_files=False)[source]

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()[source]
set_total_size()[source]
has_data()[source]

Detects whether there is any data

mark_deleted()[source]
user_can_purge
full_delete()[source]

Remove the file and extra files, marks deleted and purged

get_access_roles(trans)[source]
get_manage_permissions_roles(trans)[source]
has_manage_permissions_roles(trans)[source]
serialize(id_encoder, serialization_options)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)
tags
total_size
update_time
uuid
class galaxy.model.DatasetSource[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

serialize(id_encoder, serialization_options)[source]
__init__()

x.__init__(…) initializes x; see help(type(x)) for 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)[source]
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, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)[source]

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>
__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, validation_errors=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

peek
update()[source]
ext
get_dataset_state()[source]
raw_set_dataset_state(state)[source]
set_dataset_state(state)[source]
state
get_file_name()[source]
set_file_name(filename)[source]
file_name
extra_files_path
extra_files_path_exists()[source]
datatype
get_metadata()[source]
set_metadata_requires_flush
set_metadata(bunch)[source]
metadata
metadata_file_types
get_dbkey()[source]
set_dbkey(value)[source]
dbkey
change_datatype(new_ext)[source]
get_size(nice_size=False)[source]

Returns the size of the data on disk

set_size(**kwds)[source]

Sets and gets the size of the data on disk

get_total_size()[source]
set_total_size()[source]
has_data()[source]

Detects whether there is any data

get_created_from_basename()[source]
set_created_from_basename(created_from_basename)[source]
created_from_basename
get_raw_data()[source]

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

get_mime()[source]

Returns the mime type of the data

set_peek()[source]
init_meta(copy_from=None)[source]
set_meta(**kwd)[source]
missing_meta(**kwd)[source]
as_display_type(type, **kwd)[source]
display_peek()[source]
display_name()[source]
display_info()[source]
get_converted_files_by_type(file_type)[source]
get_converted_dataset_deps(trans, target_ext)[source]

Returns dict of { “dependency” => HDA }

get_converted_dataset(trans, target_ext, target_context=None, history=None)[source]

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)[source]

Copies attributes to a new datasets, used for implicit conversions

get_metadata_dataset(dataset_ext)[source]

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)[source]
get_converter_types()[source]
can_convert_to(format)[source]
find_conversion_destination(accepted_formats, **kwd)[source]

Returns ( target_ext, existing converted dataset )

add_validation_error(validation_error)[source]
extend_validation_errors(validation_errors)[source]
mark_deleted()[source]
mark_undeleted()[source]
mark_unhidden()[source]
undeletable()[source]
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)[source]
get_visualizations()[source]
get_datasources(trans)[source]

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)[source]

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)[source]
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)[source]

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, force_flush=True, copy_hid=True, new_name=None)[source]

Create a copy of this HDA.

copy_tags_to(copy_tags=None)[source]
copy_attributes(new_dataset)[source]

Copies attributes to a new datasets, used for implicit conversions

to_library_dataset_dataset_association(trans, target_folder, replace_dataset=None, parent_id=None, user=None, roles=None, ldda_message='', element_identifier=None)[source]

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

clear_associated_files(metadata_safe=False, purge=False)[source]
get_access_roles(trans)[source]

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

quota_amount(user)[source]

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)[source]
to_dict(view='collection', expose_dataset_path=False)[source]

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

unpause_dependent_jobs(jobs=None)[source]
history_content_type
content_type = u'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 utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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('hidden_beneath_collection_instance_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_association>), schema=None)
tags
tool_version
update_time
version
visible
class galaxy.model.HistoryDatasetAssociationHistory(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)[source]

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 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association_display_at_authorization>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]

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)[source]
to_dict(view='collection', value_mapper=None)[source]

We prepend an F to folders.

get_active_folders(folder, folders=None)[source]
get_access_roles(trans)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<library>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]
add_folder(folder)[source]
activatable_library_datasets
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

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 utcnow>)), Column('update_time', DateTime(), table=<library_folder>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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
set_library_dataset_dataset_association(ldda)[source]
get_info()[source]
set_info(info)[source]
info
get_name()[source]
set_name(name)[source]
name
display_name()[source]
serialize(id_encoder, serialization_options)[source]
to_dict(view='collection')[source]
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 utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]
copy(parent_id=None, target_folder=None)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
get_access_roles(trans)[source]
get_manage_permissions_roles(trans)[source]
has_manage_permissions_roles(trans)[source]
serialize(id_encoder, serialization_options, for_link=False)[source]
to_dict(view='collection')[source]
update_parent_folder_update_times()[source]
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 utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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('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
visible
class galaxy.model.ExtendedMetadata(data)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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.ValidationError(message=None, err_type=None, attributes=None)[source]

Bases: galaxy.model.RepresentById

__init__(message=None, err_type=None, attributes=None)
message
err_type
attributes
dataset_id
id
table = Table('validation_error', MetaData(bind=None), Column('id', Integer(), table=<validation_error>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<validation_error>), Column('message', TrimmedString(length=255), table=<validation_error>), Column('err_type', TrimmedString(length=64), table=<validation_error>), Column('attributes', TEXT(), table=<validation_error>), schema=None)
class galaxy.model.DatasetToValidationErrorAssociation(dataset, validation_error)[source]

Bases: object

__init__(dataset, validation_error)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

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)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<implicitly_converted_dataset_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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()[source]
handle_population_failed(message)[source]
finalize(collection_type_description)[source]
dataset_instances
dataset_elements
first_dataset_element
state
validate()[source]
copy(destination=None, element_destination=None)[source]
replace_failed_elements(replacements)[source]
set_from_dict(new_data)[source]
has_subcollections
serialize(id_encoder, serialization_options)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<dataset_collection>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), schema=None)
update_time
class galaxy.model.DatasetCollectionInstance(collection=None, deleted=False)[source]

Bases: galaxy.model.HasName

__init__(collection=None, deleted=False)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

state
populated
dataset_instances
display_name()[source]
set_from_dict(new_data)[source]

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=[])[source]

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=[])
id
hid
history
name
visible
copied_from_history_dataset_collection_association
implicit_output_name
implicit_input_collections
history_content_type
content_type = u'dataset_collection'
type_id
job_source_type
job_source_id
to_hda_representative(multiple=False)[source]
serialize(id_encoder, serialization_options, for_link=False)[source]
to_dict(view='collection')[source]

Return item dictionary.

add_implicit_input_collection(name, history_dataset_collection)[source]
find_implicit_input_collection(name)[source]
copy(element_destination=None)[source]

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

annotations
collection
collection_id
copied_from_history_dataset_collection_association_id
copied_to_history_dataset_collection_associations
creating_job_associations
deleted
hidden_dataset_instances
history_id
implicit_collection_jobs
implicit_collection_jobs_id
job
job_id
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>), schema=None)
tags
class galaxy.model.LibraryDatasetCollectionAssociation(id=None, collection=None, name=None, deleted=False, folder=None)[source]

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')[source]
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)[source]

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()[source]
dataset_instances
copy_to_collection(collection, destination=None, element_destination=None)[source]
serialize(id_encoder, serialization_options)[source]
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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<event>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]
get_disk_usage()[source]
set_disk_usage(bytes)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 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[source]

Bases: object

__init__()[source]

x.__init__(…) initializes x; see help(type(x)) for signature

class galaxy.model.StoredWorkflow[source]

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

dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
dict_element_visible_keys = ['id', 'name', 'published', 'deleted']
__init__()
id
user
name
slug
published
latest_workflow_id
workflows
get_internal_version(version)[source]
show_in_tool_panel(user_id)[source]
copy_tags_from(target_user, source_workflow)[source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

annotations
average_rating
create_time
deleted
from_path
importable
latest_workflow
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 utcnow>)), Column('update_time', DateTime(), table=<stored_workflow>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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('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
update_time
user_id
users_shared_with
users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))
class galaxy.model.Workflow(uuid=None)[source]

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()[source]

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

to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

steps_by_id
step_by_index(order_index)[source]
input_steps
workflow_outputs
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()[source]

Copy a workflow (without user information) for a new StoredWorkflow object.

log_str()[source]
create_time
id
parent_workflow_id
parent_workflow_steps
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 utcnow>)), Column('update_time', DateTime(), table=<workflow>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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('uuid', UUIDType(), table=<workflow>), schema=None)
update_time
class galaxy.model.WorkflowStep[source]

Bases: galaxy.model.RepresentById

__init__()
id
type
tool_id
tool_inputs
tool_errors
dynamic_tool
position
inputs
config
label
uuid
workflow_outputs
tool_uuid
get_input(input_name)[source]
get_or_add_input(input_name)[source]
add_connection(input_name, output_name, output_step, input_subworkflow_step_index=None)[source]
input_connections
unique_workflow_outputs
content_id
input_connections_by_name
setup_input_connections_by_name()[source]
create_or_update_workflow_output(output_name, label, uuid)[source]
workflow_output_for(output_name)[source]
copy_to(copied_step, step_mapping)[source]
log_str()[source]
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 utcnow>)), Column('update_time', DateTime(), table=<workflow_step>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]
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[source]

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()[source]
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)[source]

Bases: galaxy.model.RepresentById

__init__(workflow_step, output_name=None, label=None, uuid=None)
workflow_step
output_name
label
uuid
copy(copied_step)[source]
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[source]

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[source]

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[source]

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

dict_collection_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']
dict_element_visible_keys = ['id', 'update_time', 'workflow_id', 'history_id', 'uuid', 'state']
states = <galaxy.util.bunch.Bunch object>
__init__()
subworkflow_invocations
step_states
steps
create_subworkflow_invocation_for_step(step)[source]
attach_subworkflow_invocation_for_step(step, subworkflow_invocation)[source]
get_subworkflow_invocation_for_step(step)[source]
get_subworkflow_invocation_association_for_step(step)[source]
active

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

cancel()[source]
fail()[source]
step_states_by_step_id()[source]
step_invocations_by_step_id()[source]
step_invocation_for_step_id(step_id)[source]
static poll_unhandled_workflow_ids(sa_session)[source]
static poll_active_workflow_ids(sa_session, scheduler=None, handler=None)[source]
add_output(workflow_output, step, output_object)[source]
to_dict(view='collection', value_mapper=None, step_details=False, legacy_job_state=False)[source]

Return item dictionary.

update()
add_input(content, step_id)[source]
resource_parameters
has_input_for_step(step_id)[source]
set_handler(handler)[source]
log_str()[source]
create_time
handler
history
history_id
id
input_dataset_collections
input_datasets
input_parameters
input_step_parameters
output_dataset_collections
output_datasets
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 utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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_time
uuid
workflow
workflow_id
class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation[source]

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__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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

dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'state', 'action']
states = <galaxy.util.bunch.Bunch object>
update()[source]
is_new
add_output(output_name, output_object)[source]
jobs
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

action
create_time
id
implicit_collection_jobs
implicit_collection_jobs_id
job
job_id
output_dataset_collections
output_datasets
state
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 utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation_step>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]

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[source]

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

Workflow step input dataset parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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

Workflow step input dataset collection parameters.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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

Represents links to output datasets for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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

Represents links to output dataset collections for the workflow.

dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
__init__()

x.__init__(…) initializes x; see help(type(x)) for 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.WorkflowInvocationStepOutputDatasetAssociation[source]

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__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

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__()

x.__init__(…) initializes x; see help(type(x)) for 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)[source]

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)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<metadata_file>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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=[], form_definition_current=None, form_type=None, layout=None)[source]

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=[], 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)[source]

Return item dictionary.

grid_fields(grid_index)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<form_definition>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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>), 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<form_definition_current>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<form_values>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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)[source]
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 utcnow>)), Column('update_time', DateTime(), table=<user_address>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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()[source]
classmethod store(server_url, association)[source]

Create an Association instance

classmethod get(*args, **kwargs)[source]

Get an Association instance

classmethod remove(ids_to_delete)[source]

Remove an Association instance

id
table = Table('psa_association', MetaData(bind=None), Column('id', Integer(), table=<psa_association>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_association>), Column('handle', VARCHAR(length=255), table=<psa_association>), Column('secret', VARCHAR(length=255), table=<psa_association>), Column('issued', Integer(), table=<psa_association>), Column('lifetime', Integer(), table=<psa_association>), Column('assoc_type', VARCHAR(length=64), table=<psa_association>), schema=None)
class galaxy.model.PSACode(email, code)[source]

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

sa_session = None
__init__(email, code)
email
code
save()[source]
classmethod get_code(code)[source]
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)[source]

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

sa_session = None
__init__(server_url, timestamp, salt)
server_url
timestamp
salt
save()[source]
classmethod use(server_url, timestamp, salt)[source]

Create a Nonce instance

id
table = Table('psa_nonce', MetaData(bind=None), Column('id', Integer(), table=<psa_nonce>, primary_key=True, nullable=False), Column('server_url', VARCHAR(length=255), table=<psa_nonce>), Column('timestamp', Integer(), table=<psa_nonce>), Column('salt', VARCHAR(length=40), table=<psa_nonce>), schema=None)
class galaxy.model.PSAPartial(token, data, next_step, backend)[source]

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

sa_session = None
__init__(token, data, next_step, backend)
token
data
next_step
backend
save()[source]
classmethod load(token)[source]
classmethod destroy(token)[source]
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)[source]

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)[source]
set_extra_data(extra_data=None)[source]
save()[source]
classmethod username_max_length()[source]

Return the max length for username

classmethod user_model()[source]

Return the user model

classmethod changed(user)[source]

The given user instance is ready to be saved

classmethod user_query()[source]
classmethod user_exists(*args, **kwargs)[source]

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

classmethod get_username(user)[source]

Return the username for given user

classmethod create_user(*args, **kwargs)[source]

Create a user instance

classmethod get_user(pk)[source]

Return user instance for given id

classmethod get_users_by_email(email)[source]

Return users instances for given email address

classmethod get_social_auth(provider, uid)[source]

Return UserSocialAuth for given provider and uid

classmethod get_social_auth_for_user(user, provider=None, id=None)[source]

Return all the UserSocialAuth instances for given user

classmethod create_social_auth(user, uid, provider)[source]

Create a UserSocialAuth instance for given user

cloudauthz
id
table = Table('oidc_user_authnz_tokens', MetaData(bind=None), Column('id', Integer(), table=<oidc_user_authnz_tokens>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<oidc_user_authnz_tokens>), Column('uid', VARCHAR(length=255), table=<oidc_user_authnz_tokens>), Column('provider', VARCHAR(length=32), table=<oidc_user_authnz_tokens>), Column('extra_data', JSONType(), table=<oidc_user_authnz_tokens>), Column('lifetime', Integer(), table=<oidc_user_authnz_tokens>), Column('assoc_type', VARCHAR(length=64), table=<oidc_user_authnz_tokens>), schema=None)
user
class galaxy.model.CustosAuthnzToken(user, external_user_id, provider, access_token, id_token, refresh_token, expiration_time, refresh_expiration_time)[source]

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='')[source]

Bases: galaxy.model.RepresentById

__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)[source]
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 utcnow>)), schema=None)
user
class galaxy.model.Page[source]

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

dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted']
__init__()
id
user
title
slug
latest_revision_id
revisions
importable
published
to_dict(view='element')[source]

Return item dictionary.

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 utcnow>)), Column('update_time', DateTime(), table=<page>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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[source]

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

dict_element_visible_keys = ['id', 'page_id', 'title', 'content']
__init__()
title
content
to_dict(view='element')[source]

Return item dictionary.

create_time
id
page
page_id
table = Table('page_revision', MetaData(bind=None), Column('id', Integer(), table=<page_revision>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<page_revision>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<page_revision>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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>), schema=None)
update_time
class galaxy.model.PageUserShareAssociation[source]

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)[source]

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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<visualization>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

Bases: galaxy.model.RepresentById

__init__(visualization=None, title=None, dbkey=None, config=None)
id
visualization
title
dbkey
config
copy(visualization=None)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<visualization_revision>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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[source]

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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<transfer_job>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

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_datasets
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)[source]

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)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

copy(cls=None)[source]
class galaxy.model.HistoryTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]

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.DatasetTagAssociation(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)[source]

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

__init__(id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None)
dataset_id
datasets
id
table = Table('dataset_tag_association', MetaData(bind=None), Column('id', Integer(), table=<dataset_tag_association>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<dataset_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<dataset_tag_association>), Column('user_tname', TrimmedString(length=255), table=<dataset_tag_association>), Column('value', TrimmedString(length=255), table=<dataset_tag_association>), Column('user_value', TrimmedString(length=255), table=<dataset_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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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)[source]

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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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[source]

Bases: galaxy.model.RepresentById

__init__()

x.__init__(…) initializes x; see help(type(x)) for 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)[source]

Bases: object

__init__(id=None, user=None, item=None, rating=0)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

set_item(item)[source]

Set association’s item.

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

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

set_item(history)[source]

Set association’s item.

__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)[source]

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

set_item(history_dataset_association)[source]

Set association’s item.

__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)[source]

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

set_item(stored_workflow)[source]

Set association’s item.

__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)[source]

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

set_item(page)[source]

Set association’s item.

__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)[source]

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

set_item(visualization)[source]

Set association’s item.

__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)[source]

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

set_item(dataset_collection)[source]

Set association’s item.

__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)[source]

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

set_item(dataset_collection)[source]

Set association’s item.

__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)[source]

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 utcnow>)), Column('update_time', DateTime(), table=<data_manager_history_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function 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)[source]

Bases: galaxy.model.RepresentById

__init__(id=None, job=None, data_manager_id=None)
id
job
data_manager_id
create_time
job_id
table = Table('data_manager_job_association', MetaData(bind=None), Column('id', Integer(), table=<data_manager_job_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<data_manager_job_association>, default=ColumnDefault(<function utcnow>)), Column('update_time', DateTime(), table=<data_manager_job_association>, onupdate=ColumnDefault(<function utcnow>), default=ColumnDefault(<function utcnow>)), Column('job_id', Integer(), ForeignKey('job.id'), table=<data_manager_job_association>), Column('data_manager_id', TEXT(), table=<data_manager_job_association>), schema=None)
update_time
class galaxy.model.UserPreference(name=None, value=None)[source]

Bases: galaxy.model.RepresentById

__init__(name=None, value=None)
id
name
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
value
class galaxy.model.UserAction(id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None)[source]

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 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)[source]

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 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)[source]

Subpackages

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)[source]

Bases: galaxy.util.bunch.Bunch

__init__(model_modules, engine)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

Session

For backward compat., deprecated.

galaxy.model.base.versioned_objects(iter)[source]
galaxy.model.base.versioned_session(session)[source]

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, encoding='utf-8', default=None)[source]

Bases: json.encoder.JSONEncoder

default(obj)[source]

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

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

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)
class galaxy.model.custom_types.GalaxyLargeBinary(length=None)[source]

Bases: sqlalchemy.sql.sqltypes.LargeBinary

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

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)[source]

Receive a bound parameter value to be converted.

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

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

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

Parameters:
  • value – Data to operate upon, of any type expected by this method in the subclass. Can be None.
  • dialect – the Dialect in use.
process_result_value(value, dialect)