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galaxy.model package

Galaxy data model classes

Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data)

galaxy.model.now()

Return a new datetime representing UTC day and time.

galaxy.model.get_uuid(uuid: UUID | str | None = None) UUID[source]
class galaxy.model.Base(**kwargs)[source]

Bases: object

metadata = MetaData()
registry = <sqlalchemy.orm.decl_api.registry object>
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

class galaxy.model.RepresentById[source]

Bases: object

id: int
exception galaxy.model.NoConverterException(value)[source]

Bases: Exception

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

Bases: Exception

__init__(value)[source]
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']
tags: List[ItemTagAssociation]
to_dict(*args, **kwargs)[source]
make_tag_string_list()[source]
copy_tags_from(target_user, source)[source]
property auto_propagated_tags
class galaxy.model.SerializeFilesHandler(*args, **kwargs)[source]

Bases: Protocol

serialize_files(dataset: DatasetInstance, as_dict: Dict[str, Any]) None[source]
__init__(*args, **kwargs)
class galaxy.model.SerializationOptions(for_edit: bool, serialize_dataset_objects: bool | None = None, serialize_files_handler: SerializeFilesHandler | None = None, strip_metadata_files: bool | None = None)[source]

Bases: object

__init__(for_edit: bool, serialize_dataset_objects: bool | None = None, serialize_files_handler: SerializeFilesHandler | None = None, strip_metadata_files: bool | None = None) None[source]
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.Serializable[source]

Bases: RepresentById

serialize(id_encoder: IdEncodingHelper, serialization_options: SerializationOptions, for_link: bool = False) Dict[str, Any][source]

Serialize model for a re-population in (potentially) another Galaxy instance.

id: int
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

update_time: DateTime
property seconds_since_updated
property seconds_since_created
update()[source]
class galaxy.model.WorkerProcess(**kwargs)[source]

Bases: Base, UsesCreateAndUpdateTime

id
server_name
hostname
pid
update_time: DateTime
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('worker_process', MetaData(), Column('id', Integer(), table=<worker_process>, primary_key=True, nullable=False), Column('server_name', String(length=255), table=<worker_process>), Column('hostname', String(length=255), table=<worker_process>), Column('pid', Integer(), table=<worker_process>), Column('update_time', DateTime(), table=<worker_process>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
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 = 9999999999999999999
add_metric(plugin, metric_name, metric_value)[source]
property metrics
set_streams(tool_stdout, tool_stderr, job_stdout=None, job_stderr=None, job_messages=None)[source]
log_str()[source]
property stdout
property stderr
galaxy.model.calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False)[source]

Standalone function so can be reused for postgres directly in pgcleanup.py.

class galaxy.model.UserQuotaBasicUsage(*, quota_source_label: str | None = None, total_disk_usage: float)[source]

Bases: BaseModel

quota_source_label: str | None
total_disk_usage: float
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'quota_source_label': FieldInfo(annotation=Union[str, NoneType], required=False), 'total_disk_usage': FieldInfo(annotation=float, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class galaxy.model.UserQuotaUsage(*, quota_source_label: str | None = None, total_disk_usage: float, quota_percent: float | None = None, quota_bytes: int | None = None, quota: str | None = None)[source]

Bases: UserQuotaBasicUsage

quota_percent: float | None
quota_bytes: int | None
quota: str | None
model_config: ClassVar[ConfigDict] = {}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'quota': FieldInfo(annotation=Union[str, NoneType], required=False), 'quota_bytes': FieldInfo(annotation=Union[int, NoneType], required=False), 'quota_percent': FieldInfo(annotation=Union[float, NoneType], required=False), 'quota_source_label': FieldInfo(annotation=Union[str, NoneType], required=False), 'total_disk_usage': FieldInfo(annotation=float, required=True)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

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

Bases: Base, Dictifiable, RepresentById

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

use_pbkdf2 = True
bootstrap_admin_user = False
id: int
create_time
update_time
last_password_change
form_values_id
preferred_object_store_id
disk_usage
activation_token
addresses
cloudauthz
custos_auth
default_permissions
groups
histories
active_histories
galaxy_sessions
quotas
quota_source_usages
social_auth
stored_workflow_menu_entries
values
api_keys: List[APIKeys]
data_manager_histories
roles
stored_workflows
all_notifications
non_private_roles
preferences: association_proxy = ColumnAssociationProxyInstance(AssociationProxy('_preferences', 'value'))
dict_collection_visible_keys = ['id', 'email', 'username', 'deleted', 'active', 'last_password_change']
dict_element_visible_keys = ['id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage', 'deleted', 'active', 'last_password_change', 'preferred_object_store_id']
__init__(email=None, password=None, username=None)

A simple constructor that allows initialization from kwargs.

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

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

email
password
external
deleted
purged
active
username
get_user_data_tables(data_table: str)[source]
property 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, quota_source_label=None)[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.

property total_disk_usage

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

adjust_total_disk_usage(amount, quota_source_label)[source]
get_oidc_tokens(provider_backend)[source]
property nice_total_disk_usage

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

calculate_disk_usage_default_source(object_store)[source]

Return byte count total of disk space used by all non-purged, non-library HDAs in non-purged histories assigned to default quota source.

calculate_and_set_disk_usage(object_store)[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]
attempt_create_private_role()[source]
dictify_usage(object_store=None) List[UserQuotaBasicUsage][source]

Include object_store to include empty/unused usage info.

dictify_usage_for(quota_source_label: str | None) UserQuotaBasicUsage[source]
quota_source_usage_for(quota_source_label: str | None) UserQuotaSourceUsage | None[source]
count_stored_workflow_user_assocs(stored_workflow) int[source]
current_galaxy_session
table = Table('galaxy_user', MetaData(), Column('id', Integer(), table=<galaxy_user>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_user>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('email', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('username', TrimmedString(length=255), table=<galaxy_user>), Column('password', TrimmedString(length=255), table=<galaxy_user>, nullable=False), Column('last_password_change', DateTime(), table=<galaxy_user>, default=ColumnDefault(<function datetime.utcnow>)), Column('external', Boolean(), table=<galaxy_user>, default=ColumnDefault(False)), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<galaxy_user>), Column('preferred_object_store_id', String(length=255), 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)
class galaxy.model.PasswordResetToken(user, token=None)[source]

Bases: Base

user_id
__init__(user, token=None)

A simple constructor that allows initialization from kwargs.

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

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

token
user
expiration_time
table = Table('password_reset_token', MetaData(), Column('token', String(length=32), table=<password_reset_token>, primary_key=True, nullable=False), Column('expiration_time', DateTime(), table=<password_reset_token>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<password_reset_token>), schema=None)
class galaxy.model.DynamicTool(active=True, hidden=True, **kwd)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
tool_id
tool_version
tool_format
tool_path
tool_directory
value
dict_collection_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
dict_element_visible_keys = ('id', 'tool_id', 'tool_format', 'tool_version', 'uuid', 'active', 'hidden')
__init__(active=True, hidden=True, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

active
hidden
uuid
table = Table('dynamic_tool', MetaData(), Column('id', Integer(), table=<dynamic_tool>, primary_key=True, nullable=False), Column('uuid', UUIDType(), table=<dynamic_tool>), Column('create_time', DateTime(), table=<dynamic_tool>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dynamic_tool>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('tool_id', Unicode(length=255), table=<dynamic_tool>), Column('tool_version', Unicode(length=255), table=<dynamic_tool>), Column('tool_format', Unicode(length=255), table=<dynamic_tool>), Column('tool_path', Unicode(length=255), table=<dynamic_tool>), Column('tool_directory', Unicode(length=255), table=<dynamic_tool>), Column('hidden', Boolean(), table=<dynamic_tool>, default=ColumnDefault(True)), Column('active', Boolean(), table=<dynamic_tool>, default=ColumnDefault(True)), Column('value', MutableJSONType(), table=<dynamic_tool>), schema=None)
class galaxy.model.BaseJobMetric(plugin, metric_name, metric_value)[source]

Bases: Base

__init__(plugin, metric_name, metric_value)[source]

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: BaseJobMetric, RepresentById

id: int
job_id
plugin
metric_name
metric_value
__init__(plugin, metric_name, metric_value)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('job_metric_text', MetaData(), Column('id', Integer(), table=<job_metric_text>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_text>), Column('plugin', Unicode(length=255), table=<job_metric_text>), Column('metric_name', Unicode(length=255), table=<job_metric_text>), Column('metric_value', Unicode(length=1023), table=<job_metric_text>), schema=None)
class galaxy.model.JobMetricNumeric(plugin, metric_name, metric_value)[source]

Bases: BaseJobMetric, RepresentById

id: int
job_id
plugin
metric_name
metric_value
__init__(plugin, metric_name, metric_value)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('job_metric_numeric', MetaData(), Column('id', Integer(), table=<job_metric_numeric>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_metric_numeric>), Column('plugin', Unicode(length=255), table=<job_metric_numeric>), Column('metric_name', Unicode(length=255), table=<job_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<job_metric_numeric>), schema=None)
class galaxy.model.TaskMetricText(plugin, metric_name, metric_value)[source]

Bases: BaseJobMetric, RepresentById

id: int
task_id
plugin
metric_name
metric_value
__init__(plugin, metric_name, metric_value)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('task_metric_text', MetaData(), Column('id', Integer(), table=<task_metric_text>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_text>), Column('plugin', Unicode(length=255), table=<task_metric_text>), Column('metric_name', Unicode(length=255), table=<task_metric_text>), Column('metric_value', Unicode(length=1023), table=<task_metric_text>), schema=None)
class galaxy.model.TaskMetricNumeric(plugin, metric_name, metric_value)[source]

Bases: BaseJobMetric, RepresentById

id: int
task_id
plugin
metric_name
metric_value
__init__(plugin, metric_name, metric_value)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('task_metric_numeric', MetaData(), Column('id', Integer(), table=<task_metric_numeric>, primary_key=True, nullable=False), Column('task_id', Integer(), ForeignKey('task.id'), table=<task_metric_numeric>), Column('plugin', Unicode(length=255), table=<task_metric_numeric>), Column('metric_name', Unicode(length=255), table=<task_metric_numeric>), Column('metric_value', Numeric(precision=26, scale=7), table=<task_metric_numeric>), schema=None)
class galaxy.model.IoDicts(inp_data, out_data, out_collections)[source]

Bases: tuple

inp_data: Dict[str, DatasetInstance | None]

Alias for field number 0

out_data: Dict[str, DatasetInstance]

Alias for field number 1

out_collections: Dict[str, DatasetCollectionInstance | DatasetCollection]

Alias for field number 2

class galaxy.model.Job[source]

Bases: Base, JobLike, UsesCreateAndUpdateTime, Dictifiable, Serializable

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

id: int
create_time
update_time: DateTime
history_id
library_folder_id
tool_id
tool_version
galaxy_version
dynamic_tool_id
info
copied_from_job_id
command_line
job_messages
param_filename
runner_name
job_stdout
job_stderr
tool_stdout
tool_stderr
exit_code
traceback
session_id
user_id
job_runner_name
job_runner_external_id
destination_id
destination_params
object_store_id
params
handler
preferred_object_store_id
object_store_id_overrides
user
galaxy_session
history
library_folder
parameters
input_datasets
input_dataset_collections
input_dataset_collection_elements
output_dataset_collection_instances
output_dataset_collections
post_job_actions
input_library_datasets
output_library_datasets
external_output_metadata
tasks
output_datasets
state_history
text_metrics
numeric_metrics
interactivetool_entry_points
implicit_collection_jobs_association
container
data_manager_association
history_dataset_collection_associations
workflow_invocation_step
any_output_dataset_collection_instances_deleted: column_property
any_output_dataset_deleted: column_property
dict_collection_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version']
dict_element_visible_keys = ['id', 'state', 'exit_code', 'update_time', 'create_time', 'galaxy_version', 'command_version', 'copied_from_job_id']
states

alias of JobState

terminal_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>]
finished_states = [<JobState.OK: 'ok'>, <JobState.ERROR: 'error'>, <JobState.DELETED: 'deleted'>, <JobState.DELETING: 'deleting'>]
non_ready_states = [<JobState.NEW: 'new'>, <JobState.RESUBMITTED: 'resubmitted'>, <JobState.UPLOAD: 'upload'>, <JobState.WAITING: 'waiting'>, <JobState.QUEUED: 'queued'>, <JobState.RUNNING: 'running'>]

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

__init__()

A simple constructor that allows initialization from kwargs.

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

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

dependencies
state
imported
property running
property finished
io_dicts(exclude_implicit_outputs=False) IoDicts[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]
get_user_email()[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_input_dataset_collection_element(name, dataset_collection_element)[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]
property all_entry_points_configured
set_state(state: JobState) bool[source]

Save state history. Returns True if state has changed, else False.

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_stopped(track_jobs_in_database=False)[source]

Mark this job as stopped

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]
requires_shareable_storage(security_agent)[source]
to_dict(view='collection', system_details=False)[source]

Return item dictionary.

update_hdca_update_time_for_job(update_time, sa_session, supports_skip_locked)[source]
set_final_state(final_state, supports_skip_locked)[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.

property command_version
update_output_states(supports_skip_locked)[source]
remappable()[source]

Check whether job is remappable when rerun

hide_outputs(flush=True)[source]
table = Table('job', MetaData(), Column('id', Integer(), table=<job>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<job>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<job>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<job>), Column('tool_id', String(length=255), table=<job>), Column('tool_version', TEXT(), table=<job>, default=ColumnDefault('1.0.0')), Column('galaxy_version', String(length=64), table=<job>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<job>), Column('state', String(length=64), table=<job>), Column('info', TrimmedString(length=255), table=<job>), Column('copied_from_job_id', Integer(), table=<job>), Column('command_line', TEXT(), table=<job>), Column('dependencies', MutableJSONType(), table=<job>), Column('job_messages', MutableJSONType(), table=<job>), Column('param_filename', String(length=1024), table=<job>), Column('runner_name', String(length=255), table=<job>), Column('job_stdout', TEXT(), table=<job>), Column('job_stderr', TEXT(), table=<job>), Column('tool_stdout', TEXT(), table=<job>), Column('tool_stderr', TEXT(), table=<job>), Column('exit_code', Integer(), table=<job>), Column('traceback', TEXT(), table=<job>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<job>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<job>), Column('job_runner_name', String(length=255), table=<job>), Column('job_runner_external_id', String(length=255), table=<job>), Column('destination_id', String(length=255), table=<job>), Column('destination_params', MutableJSONType(), table=<job>), Column('object_store_id', TrimmedString(length=255), table=<job>), Column('imported', Boolean(), table=<job>, default=ColumnDefault(False)), Column('params', TrimmedString(length=255), table=<job>), Column('handler', TrimmedString(length=255), table=<job>), Column('preferred_object_store_id', String(length=255), table=<job>), Column('object_store_id_overrides', JSONType(), table=<job>), schema=None)
class galaxy.model.Task(job, working_directory, prepare_files_cmd)[source]

Bases: Base, JobLike, RepresentById

A task represents a single component of a job.

id: int
create_time
execution_time
update_time
command_line
param_filename
runner_name
job_stdout
job_stderr
tool_stdout
tool_stderr
exit_code
job_messages
info
traceback
job_id
task_runner_name
task_runner_external_id
text_metrics
numeric_metrics
class states(value)[source]

Bases: str, Enum

An enumeration.

NEW = 'new'
WAITING = 'waiting'
QUEUED = 'queued'
RUNNING = 'running'
OK = 'ok'
ERROR = 'error'
DELETED = 'deleted'
__init__(job, working_directory, prepare_files_cmd)

A simple constructor that allows initialization from kwargs.

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

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

state
working_directory
job
prepare_input_files_cmd
get_param_values(app)[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]
table = Table('task', MetaData(), Column('id', Integer(), table=<task>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<task>, default=ColumnDefault(<function datetime.utcnow>)), Column('execution_time', DateTime(), table=<task>), Column('update_time', DateTime(), table=<task>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', String(length=64), table=<task>), Column('command_line', TEXT(), table=<task>), Column('param_filename', String(length=1024), table=<task>), Column('runner_name', String(length=255), table=<task>), Column('job_stdout', TEXT(), table=<task>), Column('job_stderr', TEXT(), table=<task>), Column('tool_stdout', TEXT(), table=<task>), Column('tool_stderr', TEXT(), table=<task>), Column('exit_code', Integer(), table=<task>), Column('job_messages', MutableJSONType(), table=<task>), Column('info', TrimmedString(length=255), table=<task>), Column('traceback', TEXT(), table=<task>), Column('job_id', Integer(), ForeignKey('job.id'), table=<task>, nullable=False), Column('working_directory', String(length=1024), table=<task>), Column('task_runner_name', String(length=255), table=<task>), Column('task_runner_external_id', String(length=255), table=<task>), Column('prepare_input_files_cmd', TEXT(), table=<task>), schema=None)
class galaxy.model.JobParameter(name, value)[source]

Bases: Base, RepresentById

id: int
job_id
__init__(name, value)

A simple constructor that allows initialization from kwargs.

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

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

name
value
copy()[source]
table = Table('job_parameter', MetaData(), Column('id', Integer(), table=<job_parameter>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_parameter>), Column('name', String(length=255), table=<job_parameter>), Column('value', TEXT(), table=<job_parameter>), schema=None)
class galaxy.model.JobToInputDatasetAssociation(name, dataset)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_id
job
__init__(name, dataset)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset
dataset_version
table = Table('job_to_input_dataset', MetaData(), Column('id', Integer(), table=<job_to_input_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_input_dataset>), Column('dataset_version', Integer(), table=<job_to_input_dataset>), Column('name', String(length=255), table=<job_to_input_dataset>), schema=None)
class galaxy.model.JobToOutputDatasetAssociation(name, dataset)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_id
job
__init__(name, dataset)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset
property item
table = Table('job_to_output_dataset', MetaData(), Column('id', Integer(), table=<job_to_output_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_to_output_dataset>), Column('name', String(length=255), table=<job_to_output_dataset>), schema=None)
class galaxy.model.JobToInputDatasetCollectionAssociation(name, dataset_collection)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_collection_id
job
__init__(name, dataset_collection)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset_collection
table = Table('job_to_input_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_input_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_input_dataset_collection>), Column('name', String(length=255), table=<job_to_input_dataset_collection>), schema=None)
class galaxy.model.JobToInputDatasetCollectionElementAssociation(name, dataset_collection_element)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_collection_element_id
job
__init__(name, dataset_collection_element)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset_collection_element
table = Table('job_to_input_dataset_collection_element', MetaData(), Column('id', Integer(), table=<job_to_input_dataset_collection_element>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_dataset_collection_element>), Column('dataset_collection_element_id', Integer(), ForeignKey('dataset_collection_element.id'), table=<job_to_input_dataset_collection_element>), Column('name', Unicode(length=255), table=<job_to_input_dataset_collection_element>), schema=None)
class galaxy.model.JobToOutputDatasetCollectionAssociation(name, dataset_collection_instance)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_collection_id
job
__init__(name, dataset_collection_instance)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset_collection_instance
property item
table = Table('job_to_output_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<job_to_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_output_dataset_collection>), schema=None)
class galaxy.model.JobToImplicitOutputDatasetCollectionAssociation(name, dataset_collection)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_collection_id
job
__init__(name, dataset_collection)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset_collection
table = Table('job_to_implicit_output_dataset_collection', MetaData(), Column('id', Integer(), table=<job_to_implicit_output_dataset_collection>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_implicit_output_dataset_collection>), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<job_to_implicit_output_dataset_collection>), Column('name', Unicode(length=255), table=<job_to_implicit_output_dataset_collection>), schema=None)
class galaxy.model.JobToInputLibraryDatasetAssociation(name, dataset)[source]

Bases: Base, RepresentById

id: int
job_id
ldda_id
job
__init__(name, dataset)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset
table = Table('job_to_input_library_dataset', MetaData(), Column('id', Integer(), table=<job_to_input_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_input_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_input_library_dataset>), Column('name', Unicode(length=255), table=<job_to_input_library_dataset>), schema=None)
class galaxy.model.JobToOutputLibraryDatasetAssociation(name, dataset)[source]

Bases: Base, RepresentById

id: int
job_id
ldda_id
job
__init__(name, dataset)

A simple constructor that allows initialization from kwargs.

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

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

name
dataset
table = Table('job_to_output_library_dataset', MetaData(), Column('id', Integer(), table=<job_to_output_library_dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_to_output_library_dataset>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_to_output_library_dataset>), Column('name', Unicode(length=255), table=<job_to_output_library_dataset>), schema=None)
class galaxy.model.JobStateHistory(job)[source]

Bases: Base, RepresentById

id: int
create_time
__init__(job)

A simple constructor that allows initialization from kwargs.

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

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

job_id
state
info
table = Table('job_state_history', MetaData(), Column('id', Integer(), table=<job_state_history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<job_state_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_state_history>), Column('state', String(length=64), table=<job_state_history>), Column('info', TrimmedString(length=255), table=<job_state_history>), schema=None)
class galaxy.model.ImplicitlyCreatedDatasetCollectionInput(name, input_dataset_collection)[source]

Bases: Base, RepresentById

id: int
dataset_collection_id
input_dataset_collection_id
__init__(name, input_dataset_collection)

A simple constructor that allows initialization from kwargs.

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

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

name
input_dataset_collection
table = Table('implicitly_created_dataset_collection_inputs', MetaData(), Column('id', Integer(), table=<implicitly_created_dataset_collection_inputs>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('input_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<implicitly_created_dataset_collection_inputs>), Column('name', Unicode(length=255), table=<implicitly_created_dataset_collection_inputs>), schema=None)
class galaxy.model.ImplicitCollectionJobs(populated_state=None)[source]

Bases: Base, Serializable

id: int
jobs
class populated_states(value)[source]

Bases: str, Enum

An enumeration.

NEW = 'new'
OK = 'ok'
FAILED = 'failed'
__init__(populated_state=None)

A simple constructor that allows initialization from kwargs.

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

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

populated_state
property job_list
table = Table('implicit_collection_jobs', MetaData(), Column('id', Integer(), table=<implicit_collection_jobs>, primary_key=True, nullable=False), Column('populated_state', TrimmedString(length=64), table=<implicit_collection_jobs>, nullable=False, default=ColumnDefault('new')), schema=None)
class galaxy.model.ImplicitCollectionJobsJobAssociation(**kwargs)[source]

Bases: Base, RepresentById

id: int
implicit_collection_jobs_id
job_id
order_index
implicit_collection_jobs
job
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('implicit_collection_jobs_job_association', MetaData(), Column('id', Integer(), table=<implicit_collection_jobs_job_association>, primary_key=True, nullable=False), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<implicit_collection_jobs_job_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<implicit_collection_jobs_job_association>), Column('order_index', Integer(), table=<implicit_collection_jobs_job_association>, nullable=False), schema=None)
class galaxy.model.PostJobAction(action_type, workflow_step=None, output_name=None, action_arguments=None)[source]

Bases: Base, RepresentById

id: int
workflow_step_id
__init__(action_type, workflow_step=None, output_name=None, action_arguments=None)

A simple constructor that allows initialization from kwargs.

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

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

action_type
output_name
action_arguments
workflow_step
table = Table('post_job_action', MetaData(), Column('id', Integer(), table=<post_job_action>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<post_job_action>), Column('action_type', String(length=255), table=<post_job_action>, nullable=False), Column('output_name', String(length=255), table=<post_job_action>), Column('action_arguments', MutableJSONType(), table=<post_job_action>), schema=None)
class galaxy.model.PostJobActionAssociation(pja, job=None, job_id=None)[source]

Bases: Base, RepresentById

id: int
post_job_action_id
__init__(pja, job=None, job_id=None)

A simple constructor that allows initialization from kwargs.

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

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

job
job_id
post_job_action
table = Table('post_job_action_association', MetaData(), Column('id', Integer(), table=<post_job_action_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<post_job_action_association>, nullable=False), Column('post_job_action_id', Integer(), ForeignKey('post_job_action.id'), table=<post_job_action_association>, nullable=False), schema=None)
class galaxy.model.JobExternalOutputMetadata(job=None, dataset=None)[source]

Bases: Base, RepresentById

id: int
job_id
history_dataset_association_id
library_dataset_dataset_association_id
is_valid
filename_in
filename_out
filename_results_code
filename_kwds
filename_override_metadata
job_runner_external_pid
__init__(job=None, dataset=None)

A simple constructor that allows initialization from kwargs.

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

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

job
history_dataset_association
library_dataset_dataset_association
property dataset
table = Table('job_external_output_metadata', MetaData(), Column('id', Integer(), table=<job_external_output_metadata>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_external_output_metadata>), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<job_external_output_metadata>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<job_external_output_metadata>), Column('is_valid', Boolean(), table=<job_external_output_metadata>, default=ColumnDefault(True)), Column('filename_in', String(length=255), table=<job_external_output_metadata>), Column('filename_out', String(length=255), table=<job_external_output_metadata>), Column('filename_results_code', String(length=255), table=<job_external_output_metadata>), Column('filename_kwds', String(length=255), table=<job_external_output_metadata>), Column('filename_override_metadata', String(length=255), table=<job_external_output_metadata>), Column('job_runner_external_pid', String(length=255), table=<job_external_output_metadata>), schema=None)
class galaxy.model.FakeDatasetAssociation(dataset=None)[source]

Bases: object

fake_dataset_association = True
__init__(dataset=None)[source]
get_file_name(sync_cache=True)[source]
class galaxy.model.JobExportHistoryArchive(compressed=False, **kwd)[source]

Bases: Base, RepresentById

id: int
job_id
history_id
dataset_id
history_attrs_filename
job
dataset
history
ATTRS_FILENAME_HISTORY = 'history_attrs.txt'
__init__(compressed=False, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

compressed
property fda
property temp_directory
property up_to_date

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

property ready
property preparing
property export_name
static create_for_history(history, job, sa_session, object_store, compressed)[source]
to_dict()[source]
table = Table('job_export_history_archive', MetaData(), Column('id', Integer(), table=<job_export_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_export_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_export_history_archive>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<job_export_history_archive>), Column('compressed', Boolean(), table=<job_export_history_archive>, default=ColumnDefault(False)), Column('history_attrs_filename', TEXT(), table=<job_export_history_archive>), schema=None)
class galaxy.model.JobImportHistoryArchive(**kwargs)[source]

Bases: Base, RepresentById

id: int
job_id
history_id
archive_dir
job
history
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('job_import_history_archive', MetaData(), Column('id', Integer(), table=<job_import_history_archive>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_import_history_archive>), Column('history_id', Integer(), ForeignKey('history.id'), table=<job_import_history_archive>), Column('archive_dir', TEXT(), table=<job_import_history_archive>), schema=None)
class galaxy.model.StoreExportAssociation(**kwargs)[source]

Bases: Base, RepresentById

id: int
task_uuid
create_time
object_type
object_id
export_metadata
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('store_export_association', MetaData(), Column('id', Integer(), table=<store_export_association>, primary_key=True, nullable=False), Column('task_uuid', UUIDType(), table=<store_export_association>), Column('create_time', DateTime(), table=<store_export_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('object_type', TrimmedString(length=32), table=<store_export_association>), Column('object_id', Integer(), table=<store_export_association>), Column('export_metadata', JSONType(), table=<store_export_association>), schema=None)
class galaxy.model.JobContainerAssociation(**kwd)[source]

Bases: Base, RepresentById

id: int
job_id
container_type
container_name
created_time
modified_time
job
__init__(**kwd)

A simple constructor that allows initialization from kwargs.

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

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

container_info
table = Table('job_container_association', MetaData(), Column('id', Integer(), table=<job_container_association>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<job_container_association>), Column('container_type', TEXT(), table=<job_container_association>), Column('container_name', TEXT(), table=<job_container_association>), Column('container_info', MutableJSONType(), table=<job_container_association>), Column('created_time', DateTime(), table=<job_container_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<job_container_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.InteractiveToolEntryPoint(requires_domain=True, requires_path_in_url=False, configured=False, deleted=False, **kwd)[source]

Bases: Base, Dictifiable, RepresentById

id: int
job_id
name
tool_port
host
port
protocol
entry_url
requires_path_in_header_named
created_time
modified_time
label
job
dict_collection_visible_keys = ['id', 'job_id', 'name', 'label', 'active', 'created_time', 'modified_time', 'output_datasets_ids']
dict_element_visible_keys = ['id', 'job_id', 'name', 'label', 'active', 'created_time', 'modified_time', 'output_datasets_ids']
__init__(requires_domain=True, requires_path_in_url=False, configured=False, deleted=False, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

requires_domain
requires_path_in_url
configured
deleted
token
info
property active
property class_id
property output_datasets_ids
table = Table('interactivetool_entry_point', MetaData(), Column('id', Integer(), table=<interactivetool_entry_point>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<interactivetool_entry_point>), Column('name', TEXT(), table=<interactivetool_entry_point>), Column('token', TEXT(), table=<interactivetool_entry_point>), Column('tool_port', Integer(), table=<interactivetool_entry_point>), Column('host', TEXT(), table=<interactivetool_entry_point>), Column('port', Integer(), table=<interactivetool_entry_point>), Column('protocol', TEXT(), table=<interactivetool_entry_point>), Column('entry_url', TEXT(), table=<interactivetool_entry_point>), Column('requires_domain', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(True)), Column('requires_path_in_url', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('requires_path_in_header_named', TEXT(), table=<interactivetool_entry_point>), Column('info', MutableJSONType(), table=<interactivetool_entry_point>), Column('configured', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<interactivetool_entry_point>, default=ColumnDefault(False)), Column('created_time', DateTime(), table=<interactivetool_entry_point>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<interactivetool_entry_point>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('label', TEXT(), table=<interactivetool_entry_point>), schema=None)
class galaxy.model.GenomeIndexToolData(**kwargs)[source]

Bases: Base, RepresentById

id: int
job_id
dataset_id
fasta_path
created_time
modified_time
indexer
user_id
job
dataset
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('genome_index_tool_data', MetaData(), Column('id', Integer(), table=<genome_index_tool_data>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<genome_index_tool_data>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<genome_index_tool_data>), Column('fasta_path', String(length=255), table=<genome_index_tool_data>), Column('created_time', DateTime(), table=<genome_index_tool_data>, default=ColumnDefault(<function datetime.utcnow>)), Column('modified_time', DateTime(), table=<genome_index_tool_data>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('indexer', String(length=64), table=<genome_index_tool_data>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<genome_index_tool_data>), schema=None)
class galaxy.model.Group(name=None)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
quotas
roles
users
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name']
__init__(name=None)

A simple constructor that allows initialization from kwargs.

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

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

name
deleted
table = Table('galaxy_group', MetaData(), Column('id', Integer(), table=<galaxy_group>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_group>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_group>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<galaxy_group>), Column('deleted', Boolean(), table=<galaxy_group>, default=ColumnDefault(False)), schema=None)
class galaxy.model.UserGroupAssociation(user, group)[source]

Bases: Base, RepresentById

id: int
user_id
group_id
create_time
update_time
__init__(user, group)

A simple constructor that allows initialization from kwargs.

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

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

user
group
table = Table('user_group_association', MetaData(), Column('id', Integer(), table=<user_group_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_group_association>), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<user_group_association>), Column('create_time', DateTime(), table=<user_group_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_group_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.Notification(source, category, variant, content)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
publication_time
expiration_time
user_notification_associations
__init__(source, category, variant, content)

A simple constructor that allows initialization from kwargs.

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

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

source
category
variant
content
table = Table('notification', MetaData(), Column('id', Integer(), table=<notification>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<notification>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('publication_time', DateTime(), table=<notification>, default=ColumnDefault(<function datetime.utcnow>)), Column('expiration_time', DateTime(), table=<notification>, default=ColumnDefault(datetime.datetime(2024, 9, 14, 18, 56, 43, 43645))), Column('source', String(length=32), table=<notification>), Column('category', String(length=64), table=<notification>), Column('variant', String(length=16), table=<notification>), Column('content', DoubleEncodedJsonType(), table=<notification>), schema=None)
class galaxy.model.UserNotificationAssociation(user, notification)[source]

Bases: Base, RepresentById

id: int
user_id
notification_id
seen_time
deleted
update_time
__init__(user, notification)

A simple constructor that allows initialization from kwargs.

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

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

user
notification
table = Table('user_notification_association', MetaData(), Column('id', Integer(), table=<user_notification_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_notification_association>), Column('notification_id', Integer(), ForeignKey('notification.id'), table=<user_notification_association>), Column('seen_time', DateTime(), table=<user_notification_association>), Column('deleted', Boolean(), table=<user_notification_association>, default=ColumnDefault(False)), Column('update_time', DateTime(), table=<user_notification_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
galaxy.model.is_hda(d)[source]
class galaxy.model.HistoryAudit(*args, **kwargs)[source]

Bases: Base, RepresentById

history_id
update_time
__init__(*args, **kwargs)

A simple constructor that allows initialization from kwargs.

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

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

classmethod prune(sa_session)[source]
table = Table('history_audit', MetaData(), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_audit>, primary_key=True, nullable=False), Column('update_time', DateTime(), table=<history_audit>, primary_key=True, nullable=False, default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.History(id=None, name=None, user=None)[source]

Bases: Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable

create_time
user_id
hid_counter
genome_build
importable
slug
preferred_object_store_id
archived
archive_export_id
datasets
exports
active_datasets
dataset_collections
active_dataset_collections
visible_datasets
visible_dataset_collections
tags: List[ItemTagAssociation]
annotations
ratings
default_permissions
users_shared_with
galaxy_sessions
workflow_invocations
jobs
update_time
users_shared_with_count: column_property
average_rating: column_property
users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))
dict_collection_visible_keys = ['id', 'name', 'published', 'deleted']
dict_element_visible_keys = ['id', 'name', 'archived', 'create_time', 'deleted', 'empty', 'genome_build', 'hid_counter', 'importable', 'preferred_object_store_id', 'purged', 'published', 'slug', 'tags', 'update_time', 'username']
default_name = 'Unnamed history'
__init__(id=None, name=None, user=None)

A simple constructor that allows initialization from kwargs.

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

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

id: int
name
deleted
purged
importing
published
user
init_on_load()[source]
stage_addition(items)[source]
property empty
property username
property count
add_pending_items(set_output_hid=True)[source]
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 and collections 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.

get_dataset_by_hid(hid)[source]
property has_possible_members
property activatable_datasets
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

property latest_export
unhide_datasets()[source]
resume_paused_jobs()[source]
property paused_jobs
disk_size

Return a query scalar that will get any history’s size in bytes by summing the ‘total_size’s of all non-purged, unique datasets within it.

property disk_nice_size

Returns human readable size of history on disk.

property active_datasets_and_roles
property active_visible_datasets_and_roles
property active_visible_dataset_collections
property active_contents

Return all active contents ordered by hid.

contents_iter(**kwds)[source]

Fetch filtered list of contents of history.

table = Table('history', MetaData(), Column('id', Integer(), table=<history>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history>), Column('name', TrimmedString(length=255), table=<history>), Column('hid_counter', Integer(), table=<history>, default=ColumnDefault(1)), Column('deleted', Boolean(), table=<history>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<history>, default=ColumnDefault(False)), Column('importing', Boolean(), table=<history>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<history>), Column('importable', Boolean(), table=<history>, default=ColumnDefault(False)), Column('slug', TEXT(), table=<history>), Column('published', Boolean(), table=<history>, default=ColumnDefault(False)), Column('preferred_object_store_id', String(length=255), table=<history>), Column('archived', Boolean(), table=<history>, default=ColumnDefault(False), server_default=DefaultClause(<sqlalchemy.sql.elements.False_ object>, for_update=False)), Column('archive_export_id', Integer(), ForeignKey('store_export_association.id'), table=<history>), schema=None)
class galaxy.model.UserShareAssociation[source]

Bases: RepresentById

user: User | None
class galaxy.model.HistoryUserShareAssociation(**kwargs)[source]

Bases: Base, UserShareAssociation

id: int
history_id
user_id
user: User | None
history
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_user_share_association', MetaData(), Column('id', Integer(), table=<history_user_share_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_user_share_association>), schema=None)
class galaxy.model.UserRoleAssociation(user, role)[source]

Bases: Base, RepresentById

id: int
user_id
role_id
create_time
update_time
__init__(user, role)

A simple constructor that allows initialization from kwargs.

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

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

user
role
table = Table('user_role_association', MetaData(), Column('id', Integer(), table=<user_role_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<user_role_association>), Column('create_time', DateTime(), table=<user_role_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.GroupRoleAssociation(group, role)[source]

Bases: Base, RepresentById

id: int
group_id
role_id
create_time
update_time
__init__(group, role)

A simple constructor that allows initialization from kwargs.

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

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

group
role
table = Table('group_role_association', MetaData(), Column('id', Integer(), table=<group_role_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_role_association>), Column('role_id', Integer(), ForeignKey('role.id'), table=<group_role_association>), Column('create_time', DateTime(), table=<group_role_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_role_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.Role(name=None, description=None, type=types.SYSTEM, deleted=False)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
dataset_actions
groups
users
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'description', 'type']
private_id = None
class types(value)[source]

Bases: str, Enum

An enumeration.

PRIVATE = 'private'
SYSTEM = 'system'
USER = 'user'
ADMIN = 'admin'
SHARING = 'sharing'
__init__(name=None, description=None, type=types.SYSTEM, deleted=False)

A simple constructor that allows initialization from kwargs.

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

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

name
description
type
deleted
table = Table('role', MetaData(), Column('id', Integer(), table=<role>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<role>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<role>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<role>), Column('description', TEXT(), table=<role>), Column('type', String(length=40), table=<role>), Column('deleted', Boolean(), table=<role>, default=ColumnDefault(False)), schema=None)
class galaxy.model.UserQuotaSourceUsage(**kwargs)[source]

Bases: Base, Dictifiable, RepresentById

dict_element_visible_keys = ['disk_usage', 'quota_source_label']
id: int
user_id
quota_source_label
disk_usage
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('user_quota_source_usage', MetaData(), Column('id', Integer(), table=<user_quota_source_usage>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_source_usage>), Column('quota_source_label', String(length=32), table=<user_quota_source_usage>), Column('disk_usage', Numeric(precision=15, scale=0), table=<user_quota_source_usage>, nullable=False, default=ColumnDefault(0)), schema=None)
class galaxy.model.UserQuotaAssociation(user, quota)[source]

Bases: Base, Dictifiable, RepresentById

id: int
user_id
quota_id
create_time
update_time
dict_element_visible_keys = ['user']
__init__(user, quota)

A simple constructor that allows initialization from kwargs.

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

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

user
quota
table = Table('user_quota_association', MetaData(), Column('id', Integer(), table=<user_quota_association>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<user_quota_association>), Column('create_time', DateTime(), table=<user_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.GroupQuotaAssociation(group, quota)[source]

Bases: Base, Dictifiable, RepresentById

id: int
group_id
quota_id
create_time
update_time
dict_element_visible_keys = ['group']
__init__(group, quota)

A simple constructor that allows initialization from kwargs.

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

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

group
quota
table = Table('group_quota_association', MetaData(), Column('id', Integer(), table=<group_quota_association>, primary_key=True, nullable=False), Column('group_id', Integer(), ForeignKey('galaxy_group.id'), table=<group_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<group_quota_association>), Column('create_time', DateTime(), table=<group_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<group_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.Quota(name=None, description=None, amount=0, operation='=', quota_source_label=None)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
deleted
default
groups
users
dict_collection_visible_keys = ['id', 'name', 'quota_source_label']
dict_element_visible_keys = ['id', 'name', 'description', 'bytes', 'operation', 'display_amount', 'default', 'users', 'groups', 'quota_source_label']
valid_operations = ('+', '-', '=')
__init__(name=None, description=None, amount=0, operation='=', quota_source_label=None)

A simple constructor that allows initialization from kwargs.

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

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

name
description
bytes
operation
quota_source_label
get_amount()[source]
set_amount(amount)[source]
property amount
property display_amount
table = Table('quota', MetaData(), Column('id', Integer(), table=<quota>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<quota>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<quota>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<quota>), Column('description', TEXT(), table=<quota>), Column('bytes', BigInteger(), table=<quota>), Column('operation', String(length=8), table=<quota>), Column('deleted', Boolean(), table=<quota>, default=ColumnDefault(False)), Column('quota_source_label', String(length=32), table=<quota>), schema=None)
class galaxy.model.DefaultQuotaAssociation(type, quota)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
quota_id
dict_element_visible_keys = ['type']
class types(value)[source]

Bases: str, Enum

An enumeration.

UNREGISTERED = 'unregistered'
REGISTERED = 'registered'
__init__(type, quota)

A simple constructor that allows initialization from kwargs.

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

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

type
quota
table = Table('default_quota_association', MetaData(), Column('id', Integer(), table=<default_quota_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<default_quota_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<default_quota_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('type', String(length=32), table=<default_quota_association>), Column('quota_id', Integer(), ForeignKey('quota.id'), table=<default_quota_association>), schema=None)
class galaxy.model.DatasetPermissions(action, dataset, role=None, role_id=None)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
dataset_id
__init__(action, dataset, role=None, role_id=None)

A simple constructor that allows initialization from kwargs.

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

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

action
dataset
role
role_id
table = Table('dataset_permissions', MetaData(), Column('id', Integer(), table=<dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<dataset_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<dataset_permissions>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<dataset_permissions>), schema=None)
class galaxy.model.LibraryPermissions(action, library_item, role)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
library_id
role_id
__init__(action, library_item, role)

A simple constructor that allows initialization from kwargs.

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

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

action
library
role
table = Table('library_permissions', MetaData(), Column('id', Integer(), table=<library_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_permissions>), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_permissions>), schema=None)
class galaxy.model.LibraryFolderPermissions(action, library_item, role)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
library_folder_id
role_id
__init__(action, library_item, role)

A simple constructor that allows initialization from kwargs.

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

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

action
folder
role
table = Table('library_folder_permissions', MetaData(), Column('id', Integer(), table=<library_folder_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_folder_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_folder_permissions>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_folder_permissions>), schema=None)
class galaxy.model.LibraryDatasetPermissions(action, library_item, role)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
library_dataset_id
role_id
__init__(action, library_item, role)

A simple constructor that allows initialization from kwargs.

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

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

action
library_dataset
role
table = Table('library_dataset_permissions', MetaData(), Column('id', Integer(), table=<library_dataset_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_permissions>), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_permissions>), schema=None)
class galaxy.model.LibraryDatasetDatasetAssociationPermissions(action, library_item, role)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
library_dataset_dataset_association_id
role_id
__init__(action, library_item, role)

A simple constructor that allows initialization from kwargs.

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

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

action
library_dataset_dataset_association
role
table = Table('library_dataset_dataset_association_permissions', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_association_permissions>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<library_dataset_dataset_association_permissions>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association_permissions>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('action', TEXT(), table=<library_dataset_dataset_association_permissions>), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<library_dataset_dataset_association_permissions>), schema=None)
class galaxy.model.DefaultUserPermissions(user, action, role)[source]

Bases: Base, RepresentById

id: int
user_id
role_id
__init__(user, action, role)

A simple constructor that allows initialization from kwargs.

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

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

user
action
role
table = Table('default_user_permissions', MetaData(), Column('id', Integer(), table=<default_user_permissions>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<default_user_permissions>), Column('action', TEXT(), table=<default_user_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_user_permissions>), schema=None)
class galaxy.model.DefaultHistoryPermissions(history, action, role)[source]

Bases: Base, RepresentById

id: int
history_id
role_id
__init__(history, action, role)

A simple constructor that allows initialization from kwargs.

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

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

history
action
role
table = Table('default_history_permissions', MetaData(), Column('id', Integer(), table=<default_history_permissions>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<default_history_permissions>), Column('action', TEXT(), table=<default_history_permissions>), Column('role_id', Integer(), ForeignKey('role.id'), table=<default_history_permissions>), schema=None)
class galaxy.model.StorableObject[source]

Bases: object

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

Bases: Base, StorableObject, Serializable

job_id
create_time
update_time
object_store_id
created_from_basename
total_size
actions
job
active_history_associations
purged_history_associations
active_library_associations
history_associations
library_associations
states

alias of DatasetState

non_ready_states = (<DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)
ready_states = (<DatasetState.DISCARDED: 'discarded'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.OK: 'ok'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.ERROR: 'error'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>)
valid_input_states = (<DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.PAUSED: 'paused'>, <DatasetState.OK: 'ok'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.RUNNING: 'running'>, <DatasetState.NEW: 'new'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>)
no_data_states = (<DatasetState.PAUSED: 'paused'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.NEW: 'new'>, <DatasetState.UPLOAD: 'upload'>, <DatasetState.QUEUED: 'queued'>, <DatasetState.RUNNING: 'running'>, <DatasetState.SETTING_METADATA: 'setting_metadata'>)
terminal_states = (<DatasetState.OK: 'ok'>, <DatasetState.EMPTY: 'empty'>, <DatasetState.ERROR: 'error'>, <DatasetState.DEFERRED: 'deferred'>, <DatasetState.DISCARDED: 'discarded'>, <DatasetState.FAILED_METADATA: 'failed_metadata'>)
class conversion_messages(value)[source]

Bases: str, Enum

An enumeration.

PENDING = 'pending'
NO_DATA = 'no data'
NO_CHROMOSOME = 'no chromosome'
NO_CONVERTER = 'no converter'
NO_TOOL = 'no tool'
DATA = 'data'
ERROR = 'error'
OK = 'ok'
permitted_actions = <galaxy.util.bunch.Bunch object>
file_path = '/tmp/'
object_store: ObjectStore | None = None
engine = None
__init__(id=None, state=None, external_filename=None, extra_files_path=None, file_size=None, purgable=True, uuid=None)

A simple constructor that allows initialization from kwargs.

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

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

id: int
uuid
state
deleted
purged
purgable
external_filename
file_size
sources
hashes
property is_new
in_ready_state()[source]
property shareable

Return True if placed into an objectstore not labeled as private.

ensure_shareable()[source]
get_file_name(sync_cache=True)[source]
property quota_source_label
property quota_source_info
property device_source_label
property device_source_info
set_file_name(filename)[source]
get_extra_files_path()[source]
create_extra_files_path()[source]
set_extra_files_path(extra_files_path)[source]
property extra_files_path
extra_files_path_exists()[source]
property store_by
extra_files_path_name_from(object_store)[source]
property extra_files_path_name
get_size(nice_size: typing_extensions.Literal[False], calculate_size: bool = True) int[source]
get_size(nice_size: typing_extensions.Literal[True], calculate_size: bool = True) str

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]
property user_can_purge
full_delete()[source]

Remove the file and extra files, marks deleted and purged

get_access_roles(security_agent)[source]
get_manage_permissions_roles(security_agent)[source]
has_manage_permissions_roles(security_agent)[source]
table = Table('dataset', MetaData(), Column('id', Integer(), table=<dataset>, primary_key=True, nullable=False), Column('job_id', Integer(), ForeignKey('job.id'), table=<dataset>), Column('create_time', DateTime(), table=<dataset>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<dataset>), Column('deleted', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<dataset>, default=ColumnDefault(False)), Column('purgable', Boolean(), table=<dataset>, default=ColumnDefault(True)), Column('object_store_id', TrimmedString(length=255), table=<dataset>), Column('external_filename', TEXT(), table=<dataset>), Column('_extra_files_path', TEXT(), table=<dataset>), Column('created_from_basename', TEXT(), table=<dataset>), Column('file_size', Numeric(precision=15, scale=0), table=<dataset>), Column('total_size', Numeric(precision=15, scale=0), table=<dataset>), Column('uuid', UUIDType(), table=<dataset>), schema=None)
class galaxy.model.DatasetSource(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

id: int
dataset_id
source_uri
extra_files_path
transform
dataset
hashes
dict_collection_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']
dict_element_visible_keys = ['id', 'source_uri', 'extra_files_path', 'transform']
copy() DatasetSource[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('dataset_source', MetaData(), Column('id', Integer(), table=<dataset_source>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_source>), Column('source_uri', TEXT(), table=<dataset_source>), Column('extra_files_path', TEXT(), table=<dataset_source>), Column('transform', MutableJSONType(), table=<dataset_source>), schema=None)
class galaxy.model.DatasetSourceHash(**kwargs)[source]

Bases: Base, Serializable

id: int
dataset_source_id
hash_function
hash_value
source
copy() DatasetSourceHash[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('dataset_source_hash', MetaData(), Column('id', Integer(), table=<dataset_source_hash>, primary_key=True, nullable=False), Column('dataset_source_id', Integer(), ForeignKey('dataset_source.id'), table=<dataset_source_hash>), Column('hash_function', TEXT(), table=<dataset_source_hash>), Column('hash_value', TEXT(), table=<dataset_source_hash>), schema=None)
class galaxy.model.DatasetHash(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

id: int
dataset_id
hash_function
hash_value
extra_files_path
dataset
dict_collection_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
dict_element_visible_keys = ['id', 'hash_function', 'hash_value', 'extra_files_path']
copy() DatasetHash[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('dataset_hash', MetaData(), Column('id', Integer(), table=<dataset_hash>, primary_key=True, nullable=False), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<dataset_hash>), Column('hash_function', TEXT(), table=<dataset_hash>), Column('hash_value', TEXT(), table=<dataset_hash>), Column('extra_files_path', TEXT(), table=<dataset_hash>), schema=None)
galaxy.model.datatype_for_extension(extension, datatypes_registry=None) Data[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, validated_state=DatasetValidatedState.UNKNOWN, validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True, metadata_deferred=False, creating_job_id=None)[source]

Bases: RepresentById, UsesCreateAndUpdateTime, object

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

states

alias of DatasetState

class conversion_messages(value)

Bases: str, Enum

An enumeration.

PENDING = 'pending'
NO_DATA = 'no data'
NO_CHROMOSOME = 'no chromosome'
NO_CONVERTER = 'no converter'
NO_TOOL = 'no tool'
DATA = 'data'
ERROR = 'error'
OK = 'ok'
permitted_actions = <galaxy.util.bunch.Bunch object>
purged: bool
creating_job_associations: List[JobToOutputDatasetCollectionAssociation | JobToOutputDatasetAssociation]
validated_states

alias of DatasetValidatedState

__init__(id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, parent_id=None, validated_state=DatasetValidatedState.UNKNOWN, validated_state_message=None, visible=True, create_dataset=False, sa_session=None, extended_metadata=None, flush=True, metadata_deferred=False, creating_job_id=None)[source]
property peek
property ext
property has_deferred_data
property state
set_metadata_success_state()[source]
get_object_store_id()[source]
property object_store_id
get_quota_source_label()[source]
property quota_source_label
get_file_name(sync_cache=True) str[source]
set_file_name(filename: str)[source]
property extra_files_path
extra_files_path_exists()[source]
property datatype: Data
get_metadata()[source]
property set_metadata_requires_flush
set_metadata(bunch)[source]
property metadata
property has_metadata_files
property metadata_file_types
get_metadata_file_paths_and_extensions() List[Tuple[str, str]][source]
get_dbkey()[source]
set_dbkey(value)[source]
property dbkey
ok_to_edit_metadata()[source]

Prevent modifying metadata when dataset is queued or running as input/output: return False if there exists an associated job with a non-terminal state.

change_datatype(new_ext)[source]
get_size(nice_size=False, calculate_size=True)[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]
property created_from_basename
property sources
property hashes
get_mime()[source]

Returns the mime type of the data

set_peek(**kwd)[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.

attach_implicitly_converted_dataset(session, new_dataset, target_ext: str)[source]
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: List[str], **kwd) Tuple[bool, str | None, DatasetInstance | None][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]
property is_ok
property is_pending

Return true if the dataset is neither ready nor in error

property source_library_dataset
property source_dataset_chain
property creating_job: Job | None
get_display_applications(trans)[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.

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: DatasetInstance, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable

Resource class that creates a relation between a dataset and a user history.

__init__(hid=None, history=None, copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, sa_session=None, **kwd)

Create a a new HDA and associate it with the given history.

hid
history
copied_from_history_dataset_association
copied_from_library_dataset_dataset_association
property user
copy_from(other_hda, new_dataset=None, include_tags=True, include_metadata=False)[source]
copy(parent_id=None, copy_tags=None, 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, 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(security_agent)[source]

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

purge_usage_from_quota(user, quota_source_info)[source]

Remove this HDA’s quota_amount from user’s quota.

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.

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]
property history_content_type
content_type = 'dataset'
type_id
annotations
blurb
copied_from_history_dataset_association_id
copied_from_library_dataset_dataset_association_id
copied_to_history_dataset_associations
copied_to_library_dataset_dataset_associations
create_time
creating_job_associations: List[JobToOutputDatasetCollectionAssociation | JobToOutputDatasetAssociation]
dataset
dataset_id
deleted
dependent_jobs
designation
extended_metadata
extended_metadata_id
extension
hidden_beneath_collection_instance
hidden_beneath_collection_instance_id
history_id
id: int
implicitly_converted_datasets
implicitly_converted_parent_datasets
info
metadata_deferred
name
parent_id
purged: bool
ratings
table = Table('history_dataset_association', MetaData(), Column('id', Integer(), table=<history_dataset_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<history_dataset_association>), Column('create_time', DateTime(), table=<history_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<history_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<history_dataset_association>), Column('name', TrimmedString(length=255), table=<history_dataset_association>), Column('info', TrimmedString(length=255), table=<history_dataset_association>), Column('blurb', TrimmedString(length=255), table=<history_dataset_association>), Column('peek', TEXT(), table=<history_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<history_dataset_association>), Column('extension', TrimmedString(length=64), table=<history_dataset_association>), Column('metadata', MetadataType(), table=<history_dataset_association>, key='_metadata'), Column('metadata_deferred', Boolean(), table=<history_dataset_association>), Column('parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association>), Column('designation', TrimmedString(length=255), table=<history_dataset_association>), Column('deleted', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('visible', Boolean(), table=<history_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association>), Column('version', Integer(), table=<history_dataset_association>, default=ColumnDefault(1)), Column('hid', Integer(), table=<history_dataset_association>), Column('purged', Boolean(), table=<history_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<history_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<history_dataset_association>), Column('hidden_beneath_collection_instance_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_association>), schema=None)
tags: List[ItemTagAssociation]
tool_version
update_time: DateTime
validated_state
validated_state_message
version
visible
class galaxy.model.HistoryDatasetAssociationHistory(history_dataset_association_id, name, dbkey, update_time, version, extension, extended_metadata_id, metadata)[source]

Bases: Base, Serializable

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

A simple constructor that allows initialization from kwargs.

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

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

history_dataset_association_id
name
update_time
version
extension
extended_metadata_id
table = Table('history_dataset_association_history', MetaData(), Column('id', Integer(), table=<history_dataset_association_history>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_history>), Column('update_time', DateTime(), table=<history_dataset_association_history>, default=ColumnDefault(<function datetime.utcnow>)), Column('version', Integer(), table=<history_dataset_association_history>), Column('name', TrimmedString(length=255), table=<history_dataset_association_history>), Column('extension', TrimmedString(length=64), table=<history_dataset_association_history>), Column('metadata', MetadataType(), table=<history_dataset_association_history>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<history_dataset_association_history>), schema=None)
class galaxy.model.HistoryDatasetAssociationDisplayAtAuthorization(hda=None, user=None, site=None)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
history_dataset_association_id
user_id
__init__(hda=None, user=None, site=None)

A simple constructor that allows initialization from kwargs.

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

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

history_dataset_association
user
site
table = Table('history_dataset_association_display_at_authorization', MetaData(), Column('id', Integer(), table=<history_dataset_association_display_at_authorization>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<history_dataset_association_display_at_authorization>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_association_display_at_authorization>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_display_at_authorization>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_display_at_authorization>), Column('site', TrimmedString(length=255), table=<history_dataset_association_display_at_authorization>), schema=None)
class galaxy.model.HistoryDatasetAssociationSubset(hda, subset, location)[source]

Bases: Base, RepresentById

id: int
history_dataset_association_id
history_dataset_association_subset_id
__init__(hda, subset, location)

A simple constructor that allows initialization from kwargs.

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

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

hda
subset
location
table = Table('history_dataset_association_subset', MetaData(), Column('id', Integer(), table=<history_dataset_association_subset>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('history_dataset_association_subset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_subset>), Column('location', Unicode(length=255), table=<history_dataset_association_subset>), schema=None)
class galaxy.model.Library(name=None, description=None, synopsis=None, root_folder=None)[source]

Bases: Base, Dictifiable, HasName, Serializable

id: int
root_folder_id
create_time
update_time
deleted
purged
actions
permitted_actions = <galaxy.util.bunch.Bunch object>
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id', 'create_time']
__init__(name=None, description=None, synopsis=None, root_folder=None)

A simple constructor that allows initialization from kwargs.

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

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

name
description
synopsis
root_folder
to_dict(view='collection', value_mapper=None)[source]

We prepend an F to folders.

get_active_folders(folder, folders=None)[source]
get_access_roles(security_agent)[source]
table = Table('library', MetaData(), Column('id', Integer(), table=<library>, primary_key=True, nullable=False), Column('root_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library>), Column('create_time', DateTime(), table=<library>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', String(length=255), table=<library>), Column('deleted', Boolean(), table=<library>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library>, default=ColumnDefault(False)), Column('description', TEXT(), table=<library>), Column('synopsis', TEXT(), table=<library>), schema=None)
class galaxy.model.LibraryFolder(name=None, description=None, item_count=0, order_id=None, genome_build=None)[source]

Bases: Base, Dictifiable, HasName, Serializable

id: int
parent_id
create_time
update_time
deleted
purged
folders
parent
active_folders
datasets
active_datasets
library_root
actions
dict_element_visible_keys = ['id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time', 'deleted']
__init__(name=None, description=None, item_count=0, order_id=None, genome_build=None)

A simple constructor that allows initialization from kwargs.

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

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

name
description
item_count
order_id
genome_build
add_library_dataset(library_dataset, genome_build=None)[source]
add_folder(folder)[source]
property activatable_library_datasets
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

property library_path
property parent_library
table = Table('library_folder', MetaData(), Column('id', Integer(), table=<library_folder>, primary_key=True, nullable=False), Column('parent_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder>), Column('create_time', DateTime(), table=<library_folder>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_folder>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TEXT(), table=<library_folder>), Column('description', TEXT(), table=<library_folder>), Column('order_id', Integer(), table=<library_folder>), Column('item_count', Integer(), table=<library_folder>), Column('deleted', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_folder>, default=ColumnDefault(False)), Column('genome_build', TrimmedString(length=40), table=<library_folder>), schema=None)
class galaxy.model.LibraryDataset(**kwargs)[source]

Bases: Base, Serializable

id: int
library_dataset_dataset_association_id
folder_id
order_id
create_time
update_time
deleted
purged
folder
library_dataset_dataset_association
expired_datasets
actions
upload_options = [('upload_file', 'Upload files'), ('upload_directory', 'Upload directory of files'), ('upload_paths', 'Upload files from filesystem paths'), ('import_from_history', 'Import datasets from your current history')]
get_info()[source]
set_info(info)[source]
property info
get_name()[source]
set_name(name)[source]
property name
display_name()[source]
to_dict(view='collection')[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('library_dataset', MetaData(), Column('id', Integer(), table=<library_dataset>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset>), Column('order_id', Integer(), table=<library_dataset>), Column('create_time', DateTime(), table=<library_dataset>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('name', TrimmedString(length=255), table=<library_dataset>), Column('info', TrimmedString(length=255), table=<library_dataset>), Column('deleted', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<library_dataset>, default=ColumnDefault(False)), schema=None)
class galaxy.model.LibraryDatasetDatasetAssociation(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)[source]

Bases: DatasetInstance, HasName, Serializable

__init__(copied_from_history_dataset_association=None, copied_from_library_dataset_dataset_association=None, library_dataset=None, user=None, sa_session=None, **kwd)
copied_from_history_dataset_association_id
copied_from_library_dataset_dataset_association_id
library_dataset
user
to_history_dataset_association(target_history, parent_id=None, add_to_history=False, visible=None)[source]
copy(parent_id=None, target_folder=None, flush=True)[source]
clear_associated_files(metadata_safe=False, purge=False)[source]
get_access_roles(security_agent)[source]
get_manage_permissions_roles(security_agent)[source]
has_manage_permissions_roles(security_agent)[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: List[JobToOutputDatasetCollectionAssociation | JobToOutputDatasetAssociation]
dataset
dataset_id
deleted
dependent_jobs
designation
extended_metadata
extended_metadata_id
extension
id: int
implicitly_converted_datasets
implicitly_converted_parent_datasets
info
library_dataset_id
message
metadata_deferred
name
parent_id
table = Table('library_dataset_dataset_association', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_association>, primary_key=True, nullable=False), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<library_dataset_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<library_dataset_dataset_association>), Column('create_time', DateTime(), table=<library_dataset_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<library_dataset_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('state', TrimmedString(length=64), table=<library_dataset_dataset_association>, key='_state'), Column('copied_from_history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<library_dataset_dataset_association>), Column('copied_from_library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('name', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('info', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('blurb', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('peek', TEXT(), table=<library_dataset_dataset_association>, key='_peek'), Column('tool_version', TEXT(), table=<library_dataset_dataset_association>), Column('extension', TrimmedString(length=64), table=<library_dataset_dataset_association>), Column('metadata', MetadataType(), table=<library_dataset_dataset_association>, key='_metadata'), Column('metadata_deferred', Boolean(), table=<library_dataset_dataset_association>), Column('parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association>), Column('designation', TrimmedString(length=255), table=<library_dataset_dataset_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_association>, default=ColumnDefault(False)), Column('validated_state', TrimmedString(length=64), table=<library_dataset_dataset_association>, nullable=False, default=ColumnDefault('unvalidated')), Column('validated_state_message', TEXT(), table=<library_dataset_dataset_association>), Column('visible', Boolean(), table=<library_dataset_dataset_association>), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<library_dataset_dataset_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association>), Column('message', TrimmedString(length=255), table=<library_dataset_dataset_association>), schema=None)
tags
tool_version
update_time: DateTime
user_id
validated_state
validated_state_message
visible
purged: bool
class galaxy.model.ExtendedMetadata(data)[source]

Bases: Base, RepresentById

id: int
children
__init__(data)

A simple constructor that allows initialization from kwargs.

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

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

data
table = Table('extended_metadata', MetaData(), Column('id', Integer(), table=<extended_metadata>, primary_key=True, nullable=False), Column('data', MutableJSONType(), table=<extended_metadata>), schema=None)
class galaxy.model.ExtendedMetadataIndex(extended_metadata, path, value)[source]

Bases: Base, RepresentById

id: int
extended_metadata_id
__init__(extended_metadata, path, value)

A simple constructor that allows initialization from kwargs.

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

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

extended_metadata
path
value
table = Table('extended_metadata_index', MetaData(), Column('id', Integer(), table=<extended_metadata_index>, primary_key=True, nullable=False), Column('extended_metadata_id', Integer(), ForeignKey('extended_metadata.id'), table=<extended_metadata_index>), Column('path', String(length=255), table=<extended_metadata_index>), Column('value', TEXT(), table=<extended_metadata_index>), schema=None)
class galaxy.model.LibraryInfoAssociation(library, form_definition, info, inheritable=False)[source]

Bases: Base, RepresentById

id: int
library_id
form_definition_id
form_values_id
deleted
__init__(library, form_definition, info, inheritable=False)

A simple constructor that allows initialization from kwargs.

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

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

library
template
info
inheritable
table = Table('library_info_association', MetaData(), Column('id', Integer(), table=<library_info_association>, primary_key=True, nullable=False), Column('library_id', Integer(), ForeignKey('library.id'), table=<library_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_info_association>), Column('inheritable', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_info_association>, default=ColumnDefault(False)), schema=None)
class galaxy.model.LibraryFolderInfoAssociation(folder, form_definition, info, inheritable=False)[source]

Bases: Base, RepresentById

id: int
library_folder_id
form_definition_id
form_values_id
deleted
__init__(folder, form_definition, info, inheritable=False)

A simple constructor that allows initialization from kwargs.

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

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

folder
template
info
inheritable
table = Table('library_folder_info_association', MetaData(), Column('id', Integer(), table=<library_folder_info_association>, primary_key=True, nullable=False), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_folder_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_folder_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_folder_info_association>), Column('inheritable', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), Column('deleted', Boolean(), table=<library_folder_info_association>, default=ColumnDefault(False)), schema=None)
class galaxy.model.LibraryDatasetDatasetInfoAssociation(library_dataset_dataset_association, form_definition, info)[source]

Bases: Base, RepresentById

id: int
library_dataset_dataset_association_id
form_definition_id
form_values_id
deleted
__init__(library_dataset_dataset_association, form_definition, info)

A simple constructor that allows initialization from kwargs.

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

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

library_dataset_dataset_association
template
info
property inheritable
table = Table('library_dataset_dataset_info_association', MetaData(), Column('id', Integer(), table=<library_dataset_dataset_info_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_info_association>), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<library_dataset_dataset_info_association>), Column('form_values_id', Integer(), ForeignKey('form_values.id'), table=<library_dataset_dataset_info_association>), Column('deleted', Boolean(), table=<library_dataset_dataset_info_association>, default=ColumnDefault(False)), schema=None)
class galaxy.model.ImplicitlyConvertedDatasetAssociation(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True, for_import=False)[source]

Bases: Base, Serializable

create_time
update_time
hda_id
ldda_id
hda_parent_id
ldda_parent_id
__init__(id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True, for_import=False)

A simple constructor that allows initialization from kwargs.

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

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

id: int
dataset
dataset_ldda
parent_hda
parent_ldda
type
deleted
metadata_safe
clear(purge=False, delete_dataset=True)[source]
table = Table('implicitly_converted_dataset_association', MetaData(), Column('id', Integer(), table=<implicitly_converted_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<implicitly_converted_dataset_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('hda_parent_id', Integer(), ForeignKey('history_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('ldda_parent_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<implicitly_converted_dataset_association>), Column('deleted', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(False)), Column('metadata_safe', Boolean(), table=<implicitly_converted_dataset_association>, default=ColumnDefault(True)), Column('type', TrimmedString(length=255), table=<implicitly_converted_dataset_association>), schema=None)
class galaxy.model.InnerCollectionFilter(column, operator_function, expected_value)[source]

Bases: tuple

column: str

Alias for field number 0

operator_function: Callable

Alias for field number 1

expected_value: str | int | float | bool

Alias for field number 2

produce_filter(table)[source]
class galaxy.model.DatasetCollection(id=None, collection_type=None, populated=True, element_count=None)[source]

Bases: Base, Dictifiable, UsesAnnotations, Serializable

populated_state_message
create_time
update_time
elements
dict_collection_visible_keys = ['id', 'collection_type']
dict_element_visible_keys = ['id', 'collection_type']
populated_states

alias of DatasetCollectionPopulatedState

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

A simple constructor that allows initialization from kwargs.

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

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

id: int
collection_type
populated_state
element_count
property dataset_states_and_extensions_summary
property has_deferred_data
property populated_optimized
property populated
property dataset_action_tuples
property element_identifiers_extensions_paths_and_metadata_files: List[List[Any]]
property waiting_for_elements
mark_as_populated()[source]
handle_population_failed(message)[source]
finalize(collection_type_description)[source]
property dataset_instances
property dataset_elements
dataset_elements_and_identifiers(identifiers=None)[source]
property first_dataset_element
property state
validate()[source]
copy(destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)[source]
replace_failed_elements(replacements)[source]
set_from_dict(new_data)[source]
property has_subcollections
table = Table('dataset_collection', MetaData(), Column('id', Integer(), table=<dataset_collection>, primary_key=True, nullable=False), Column('collection_type', Unicode(length=255), table=<dataset_collection>, nullable=False), Column('populated_state', TrimmedString(length=64), table=<dataset_collection>, nullable=False, default=ColumnDefault('ok')), Column('populated_state_message', TEXT(), table=<dataset_collection>), Column('element_count', Integer(), table=<dataset_collection>), Column('create_time', DateTime(), table=<dataset_collection>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<dataset_collection>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.DatasetCollectionInstance[source]

Bases: HasName, UsesCreateAndUpdateTime

property state
property populated
property 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.

property has_deferred_data
update_time: DateTime
class galaxy.model.HistoryDatasetCollectionAssociation(deleted=False, visible=True, **kwd)[source]

Bases: Base, DatasetCollectionInstance, HasTags, Dictifiable, UsesAnnotations, Serializable

Associates a DatasetCollection with a History.

id: int
collection_id
history_id
name
hid
copied_from_history_dataset_collection_association_id
implicit_output_name
job_id
implicit_collection_jobs_id
create_time
update_time: DateTime
collection
history
copied_from_history_dataset_collection_association
copied_to_history_dataset_collection_association
implicit_collection_jobs
job
tags: List[ItemTagAssociation]
annotations
ratings
creating_job_associations
dict_dbkeysandextensions_visible_keys = ['dbkeys', 'extensions']
editable_keys = ('name', 'deleted', 'visible')
__init__(deleted=False, visible=True, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

deleted
visible
implicit_input_collections
property history_content_type
content_type = 'dataset_collection'
type_id
property job_source_type
property job_state_summary

Aggregate counts of jobs by state, stored in a JobStateSummary object.

property job_state_summary_dict
property dataset_dbkeys_and_extensions_summary
property job_source_id
touch()[source]
to_hda_representative(multiple=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, dataset_instance_attributes=None, flush=True, set_hid=True, minimize_copies=False)[source]

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

property waiting_for_elements
contains_collection(collection_id)[source]

Checks to see that the indicated collection is a member of the hdca by using a recursive CTE sql query to find the collection’s parents and checking to see if any of the parents are associated with this hdca

table = Table('history_dataset_collection_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<history_dataset_collection_association>), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<history_dataset_collection_association>), Column('hid', Integer(), table=<history_dataset_collection_association>), Column('visible', Boolean(), table=<history_dataset_collection_association>), Column('deleted', Boolean(), table=<history_dataset_collection_association>, default=ColumnDefault(False)), Column('copied_from_history_dataset_collection_association_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_association>), Column('implicit_output_name', Unicode(length=255), table=<history_dataset_collection_association>), Column('job_id', Integer(), ForeignKey('job.id'), table=<history_dataset_collection_association>), Column('implicit_collection_jobs_id', Integer(), ForeignKey('implicit_collection_jobs.id'), table=<history_dataset_collection_association>), Column('create_time', DateTime(), table=<history_dataset_collection_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<history_dataset_collection_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
class galaxy.model.LibraryDatasetCollectionAssociation(deleted=False, **kwd)[source]

Bases: Base, DatasetCollectionInstance, RepresentById

Associates a DatasetCollection with a library folder.

id: int
collection_id
folder_id
name
collection
folder
tags
annotations
ratings
editable_keys = ('name', 'deleted')
__init__(deleted=False, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

deleted
to_dict(view='collection')[source]
table = Table('library_dataset_collection_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_association>, primary_key=True, nullable=False), Column('collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<library_dataset_collection_association>), Column('folder_id', Integer(), ForeignKey('library_folder.id'), table=<library_dataset_collection_association>), Column('name', TrimmedString(length=255), table=<library_dataset_collection_association>), Column('deleted', Boolean(), table=<library_dataset_collection_association>, default=ColumnDefault(False)), schema=None)
class galaxy.model.DatasetCollectionElement(id=None, collection=None, element=None, element_index=None, element_identifier=None)[source]

Bases: Base, Dictifiable, Serializable

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

dataset_collection_id
hda_id
ldda_id
child_collection_id
dict_collection_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
dict_element_visible_keys = ['id', 'element_type', 'element_index', 'element_identifier']
UNINITIALIZED_ELEMENT = <object object>
__init__(id=None, collection=None, element=None, element_index=None, element_identifier=None)

A simple constructor that allows initialization from kwargs.

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

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

hda
ldda
child_collection
id: int
collection
element_index
element_identifier
property element_type
property is_collection
property element_object
property dataset_instance
property dataset
first_dataset_instance()[source]
property dataset_instances
property has_deferred_data
copy_to_collection(collection, destination=None, element_destination=None, dataset_instance_attributes=None, flush=True, minimize_copies=False)[source]
table = Table('dataset_collection_element', MetaData(), Column('id', Integer(), table=<dataset_collection_element>, primary_key=True, nullable=False), Column('dataset_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>, nullable=False), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<dataset_collection_element>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<dataset_collection_element>), Column('child_collection_id', Integer(), ForeignKey('dataset_collection.id'), table=<dataset_collection_element>), Column('element_index', Integer(), table=<dataset_collection_element>), Column('element_identifier', Unicode(length=255), table=<dataset_collection_element>), schema=None)
class galaxy.model.Event(**kwargs)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
history_id
user_id
message
session_id
tool_id
history
user
galaxy_session
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('event', MetaData(), Column('id', Integer(), table=<event>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<event>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<event>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<event>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<event>), Column('message', TrimmedString(length=1024), table=<event>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<event>), Column('tool_id', String(length=255), table=<event>), schema=None)
class galaxy.model.GalaxySession(is_valid=False, **kwd)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
user_id
remote_host
remote_addr
referer
current_history_id
session_key
prev_session_id
disk_usage
current_history
histories
user
__init__(is_valid=False, **kwd)

A simple constructor that allows initialization from kwargs.

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

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

is_valid
last_action
add_history(history, association=None)[source]
get_disk_usage()[source]
set_disk_usage(bytes)[source]
property total_disk_usage
table = Table('galaxy_session', MetaData(), Column('id', Integer(), table=<galaxy_session>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<galaxy_session>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<galaxy_session>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<galaxy_session>), Column('remote_host', String(length=255), table=<galaxy_session>), Column('remote_addr', String(length=255), table=<galaxy_session>), Column('referer', TEXT(), table=<galaxy_session>), Column('current_history_id', Integer(), ForeignKey('history.id'), table=<galaxy_session>), Column('session_key', TrimmedString(length=255), table=<galaxy_session>), Column('is_valid', Boolean(), table=<galaxy_session>, default=ColumnDefault(False)), Column('prev_session_id', Integer(), table=<galaxy_session>), Column('disk_usage', Numeric(precision=15, scale=0), table=<galaxy_session>), Column('last_action', DateTime(), table=<galaxy_session>), schema=None)
class galaxy.model.GalaxySessionToHistoryAssociation(galaxy_session, history)[source]

Bases: Base, RepresentById

id: int
create_time
session_id
history_id
__init__(galaxy_session, history)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: object

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

Bases: Base, HasTags, Dictifiable, RepresentById

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

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

id: int
user_id
latest_workflow_id
deleted
importable
from_path
tags: List[ItemTagAssociation]
owner_tags
annotations
ratings
users_shared_with
average_rating: column_property
users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))
dict_collection_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'importable', 'deleted', 'hidden']
dict_element_visible_keys = ['id', 'name', 'create_time', 'update_time', 'published', 'importable', 'deleted', 'hidden']
__init__(user=None, name=None, slug=None, create_time=None, update_time=None, published=False, latest_workflow_id=None, workflow=None, hidden=False)

A simple constructor that allows initialization from kwargs.

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

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

user
name
slug
create_time
update_time
published
latest_workflow
workflows
hidden
get_internal_version(version)[source]
version_of(workflow)[source]
show_in_tool_panel(user_id)[source]
copy_tags_from(target_user, source_workflow)[source]
invocation_counts() RootModel[Dict[str, int]][source]
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

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

Bases: Base, Dictifiable, RepresentById

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

See galaxy.model.WorkflowStep for more information

id: int
create_time
update_time
stored_workflow_id
parent_workflow_id
name
has_cycles
has_errors
reports_config
creator_metadata
license
source_metadata
steps: List[WorkflowStep]
comments: List[WorkflowComment]
parent_workflow_steps
stored_workflow
step_count: column_property
dict_collection_visible_keys = ['name', 'has_cycles', 'has_errors']
dict_element_visible_keys = ['name', 'has_cycles', 'has_errors']
input_step_types = ['data_input', 'data_collection_input', 'parameter_input']
__init__(uuid=None)

A simple constructor that allows initialization from kwargs.

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

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

uuid
has_outputs_defined()[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.

property steps_by_id
step_by_index(order_index: int)[source]
step_by_label(label)[source]
property input_steps
property workflow_outputs
workflow_output_for(output_label)[source]
property workflow_output_labels
property top_level_workflow

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

property top_level_stored_workflow

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

copy(user=None)[source]

Copy a workflow for a new StoredWorkflow object.

Pass user if user-specific information needed.

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

Bases: Base, RepresentById

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

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

id: int
create_time
update_time
workflow_id
subworkflow_id
dynamic_tool_id
type: str
tool_id
tool_version
tool_inputs
tool_errors
position
config
order_index: int
when_expression
label
temp_input_connections: Dict[str, Dict[str, Any] | List[Dict[str, Any]]] | None
parent_comment_id
parent_comment
subworkflow: Workflow | None
dynamic_tool
tags
annotations
post_job_actions
inputs
workflow_outputs
output_connections
workflow
module: WorkflowModule | None
state: DefaultToolState | None
upgrade_messages: Dict | None
STEP_TYPE_TO_INPUT_TYPE = {'data_collection_input': 'dataset_collection', 'data_input': 'dataset', 'parameter_input': 'parameter'}
DEFAULT_POSITION = {'left': 0, 'top': 0}
__init__()

A simple constructor that allows initialization from kwargs.

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

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

uuid
init_on_load()[source]
property tool_uuid
property input_type
property input_default_value
get_input_default_value(default_default)[source]
property input_optional
setup_inputs_by_name()[source]
property inputs_by_name
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]
property input_connections
property unique_workflow_outputs
property content_id
property 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, user=None)[source]
log_str()[source]
clear_module_extras()[source]
table = Table('workflow_step', MetaData(), Column('id', Integer(), table=<workflow_step>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_step>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_step>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>, nullable=False), Column('subworkflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_step>), Column('dynamic_tool_id', Integer(), ForeignKey('dynamic_tool.id'), table=<workflow_step>), Column('type', String(length=64), table=<workflow_step>), Column('tool_id', TEXT(), table=<workflow_step>), Column('tool_version', TEXT(), table=<workflow_step>), Column('tool_inputs', JSONType(), table=<workflow_step>), Column('tool_errors', JSONType(), table=<workflow_step>), Column('position', MutableJSONType(), table=<workflow_step>), Column('config', JSONType(), table=<workflow_step>), Column('order_index', Integer(), table=<workflow_step>), Column('when_expression', JSONType(), table=<workflow_step>), Column('uuid', UUIDType(), table=<workflow_step>), Column('label', Unicode(length=255), table=<workflow_step>), Column('parent_comment_id', Integer(), ForeignKey('workflow_comment.id'), table=<workflow_step>), schema=None)
class galaxy.model.WorkflowStepInput(workflow_step)[source]

Bases: Base, RepresentById

id: int
workflow_step_id
name
merge_type
scatter_type
value_from
value_from_type
default_value
runtime_value
connections
__init__(workflow_step)

A simple constructor that allows initialization from kwargs.

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

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

workflow_step
default_value_set
copy(copied_step)[source]
table = Table('workflow_step_input', MetaData(), Column('id', Integer(), table=<workflow_step_input>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_input>), Column('name', TEXT(), table=<workflow_step_input>), Column('merge_type', TEXT(), table=<workflow_step_input>), Column('scatter_type', TEXT(), table=<workflow_step_input>), Column('value_from', MutableJSONType(), table=<workflow_step_input>), Column('value_from_type', TEXT(), table=<workflow_step_input>), Column('default_value', MutableJSONType(), table=<workflow_step_input>), Column('default_value_set', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), Column('runtime_value', Boolean(), table=<workflow_step_input>, default=ColumnDefault(False)), schema=None)
class galaxy.model.WorkflowStepConnection(**kwargs)[source]

Bases: Base, RepresentById

id: int
output_step_id
input_step_input_id
output_name
input_subworkflow_step_id
input_step_input
input_subworkflow_step
output_step
NON_DATA_CONNECTION = '__NO_INPUT_OUTPUT_NAME__'
property non_data_connection
property input_name
property input_step: WorkflowStep | None
property input_step_id
copy()[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_step_connection', MetaData(), Column('id', Integer(), table=<workflow_step_connection>, primary_key=True, nullable=False), Column('output_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), Column('input_step_input_id', Integer(), ForeignKey('workflow_step_input.id'), table=<workflow_step_connection>), Column('output_name', TEXT(), table=<workflow_step_connection>), Column('input_subworkflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_connection>), schema=None)
class galaxy.model.WorkflowOutput(workflow_step, output_name=None, label=None, uuid=None)[source]

Bases: Base, Serializable

id: int
workflow_step_id
__init__(workflow_step, output_name=None, label=None, uuid=None)

A simple constructor that allows initialization from kwargs.

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

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

workflow_step
output_name
label
uuid
copy(copied_step)[source]
table = Table('workflow_output', MetaData(), Column('id', Integer(), table=<workflow_output>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_output>, nullable=False), Column('output_name', String(length=255), table=<workflow_output>), Column('label', Unicode(length=255), table=<workflow_output>), Column('uuid', UUIDType(), table=<workflow_output>), schema=None)
class galaxy.model.WorkflowComment(**kwargs)[source]

Bases: Base, RepresentById

WorkflowComment represents an in-editor comment which is no associated to any WorkflowStep. It is purely decorative, and should not influence how a workflow is ran.

id: int
order_index: int
workflow_id
position
size
type
color
data
parent_comment_id
workflow
child_steps: List[WorkflowStep]
parent_comment: WorkflowComment
child_comments: List[WorkflowComment]
to_dict()[source]
from_dict()[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_comment', MetaData(), Column('id', Integer(), table=<workflow_comment>, primary_key=True, nullable=False), Column('order_index', Integer(), table=<workflow_comment>), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_comment>, nullable=False), Column('position', MutableJSONType(), table=<workflow_comment>), Column('size', JSONType(), table=<workflow_comment>), Column('type', String(length=16), table=<workflow_comment>), Column('color', String(length=16), table=<workflow_comment>), Column('data', JSONType(), table=<workflow_comment>), Column('parent_comment_id', Integer(), ForeignKey('workflow_comment.id'), table=<workflow_comment>), schema=None)
class galaxy.model.StoredWorkflowUserShareAssociation(**kwargs)[source]

Bases: Base, UserShareAssociation

id: int
stored_workflow_id
user_id
user: User | None
stored_workflow
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('stored_workflow_user_share_connection', MetaData(), Column('id', Integer(), table=<stored_workflow_user_share_connection>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_user_share_connection>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_user_share_connection>), schema=None)
class galaxy.model.StoredWorkflowMenuEntry(**kwargs)[source]

Bases: Base, RepresentById

id: int
stored_workflow_id
user_id
order_index
stored_workflow
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('stored_workflow_menu_entry', MetaData(), Column('id', Integer(), table=<stored_workflow_menu_entry>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_menu_entry>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_menu_entry>), Column('order_index', Integer(), table=<stored_workflow_menu_entry>), schema=None)
class galaxy.model.WorkflowInvocation(**kwargs)[source]

Bases: Base, UsesCreateAndUpdateTime, Dictifiable, Serializable

id: int
create_time
update_time: DateTime
workflow_id
state
scheduler
handler
uuid
history_id
history
input_parameters
step_states
input_step_parameters
input_datasets
input_dataset_collections
subworkflow_invocations
steps
workflow: Workflow
output_dataset_collections
output_datasets
output_values
messages
dict_collection_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']
dict_element_visible_keys = ['id', 'update_time', 'create_time', 'workflow_id', 'history_id', 'uuid', 'state']
states

alias of InvocationState

non_terminal_states = [<InvocationState.NEW: 'new'>, <InvocationState.READY: 'ready'>]
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]
property active

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

set_state(state: InvocationState)[source]
cancel()[source]
cancel_invocation_steps()[source]
mark_cancelled()[source]
fail()[source]
step_states_by_step_id()[source]
step_invocations_by_step_id()[source]
step_invocation_for_step_id(step_id: int) WorkflowInvocationStep | None[source]
step_invocation_for_label(label)[source]
static poll_unhandled_workflow_ids(sa_session)[source]
static poll_active_workflow_ids(engine, scheduler=None, handler=None)[source]
add_output(workflow_output, step, output_object)[source]
get_output_object(label)[source]
get_input_object(label)[source]
property output_associations
property input_associations
to_dict(view='collection', value_mapper=None, step_details=False, legacy_job_state=False)[source]

Return item dictionary.

add_input(content, step_id=None, step=None)[source]
add_message(message: InvocationMessageUnion)[source]
property resource_parameters
has_input_for_step(step_id)[source]
set_handler(handler)[source]
log_str()[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation', MetaData(), Column('id', Integer(), table=<workflow_invocation>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<workflow_invocation>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<workflow_invocation>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('workflow_id', Integer(), ForeignKey('workflow.id'), table=<workflow_invocation>, nullable=False), Column('state', TrimmedString(length=64), table=<workflow_invocation>), Column('scheduler', TrimmedString(length=255), table=<workflow_invocation>), Column('handler', TrimmedString(length=255), table=<workflow_invocation>), Column('uuid', UUIDType(), table=<workflow_invocation>), Column('history_id', Integer(), ForeignKey('history.id'), table=<workflow_invocation>), schema=None)
class galaxy.model.WorkflowInvocationToSubworkflowInvocationAssociation(**kwargs)[source]

Bases: Base, Dictifiable, RepresentById

id: int
workflow_invocation_id
subworkflow_invocation_id
workflow_step_id
subworkflow_invocation
workflow_step
parent_workflow_invocation
dict_collection_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
dict_element_visible_keys = ['id', 'workflow_step_id', 'workflow_invocation_id', 'subworkflow_invocation_id']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_to_subworkflow_invocation_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_to_subworkflow_invocation_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('subworkflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_to_subworkflow_invocation_association>), schema=None)
class galaxy.model.WorkflowInvocationMessage(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

id: int
workflow_invocation_id
reason
details
output_name
workflow_step_id
dependent_workflow_step_id
job_id
hda_id
hdca_id
workflow_invocation
workflow_step
dependent_workflow_step
property workflow_step_index
property dependent_workflow_step_index
property history_id
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: TypedDict

An output for the sake or determining full workflow outputs.

A workflow output might not be an effective output if it is an output on a subworkflow or a parent workflow that doesn’t declare it an output.

This is currently only used for determining object store selections. We don’t want to capture subworkflow outputs that the user would like to ignore and discard as effective workflow outputs.

output_name: str
step_id: int
class galaxy.model.WorkflowInvocationStepObjectStores(preferred_object_store_id, preferred_outputs_object_store_id, preferred_intermediate_object_store_id, step_effective_outputs)[source]

Bases: tuple

preferred_object_store_id: str | None

Alias for field number 0

preferred_outputs_object_store_id: str | None

Alias for field number 1

preferred_intermediate_object_store_id: str | None

Alias for field number 2

step_effective_outputs: List[EffectiveOutput] | None

Alias for field number 3

is_output_name_an_effective_output(output_name: str) bool[source]
property is_split_configuration
class galaxy.model.WorkflowInvocationStep(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

id: int
create_time
update_time
workflow_invocation_id
workflow_step_id
state
job_id
implicit_collection_jobs_id
action
workflow_step
job
implicit_collection_jobs
output_dataset_collections
output_datasets
workflow_invocation
output_value
order_index
subworkflow_invocation_id: column_property
dict_collection_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']
dict_element_visible_keys = ['id', 'update_time', 'job_id', 'workflow_step_id', 'subworkflow_invocation_id', 'state', 'action']
states

alias of InvocationStepState

property is_new
add_output(output_name, output_object)[source]
property jobs
property preferred_object_stores: WorkflowInvocationStepObjectStores
to_dict(view='collection', value_mapper=None)[source]

Return item dictionary.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, Dictifiable, Serializable

Workflow-related parameters not tied to steps or inputs.

id: int
workflow_invocation_id
name
value
type
workflow_invocation
dict_collection_visible_keys = ['id', 'name', 'value', 'type']
class types(value)[source]

Bases: str, Enum

An enumeration.

REPLACEMENT_PARAMETERS = 'replacements'
STEP_PARAMETERS = 'step'
META_PARAMETERS = 'meta'
RESOURCE_PARAMETERS = 'resource'
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_request_input_parameters', MetaData(), Column('id', Integer(), table=<workflow_request_input_parameters>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_parameters>), Column('name', Unicode(length=255), table=<workflow_request_input_parameters>), Column('value', TEXT(), table=<workflow_request_input_parameters>), Column('type', Unicode(length=255), table=<workflow_request_input_parameters>), schema=None)
class galaxy.model.WorkflowRequestStepState(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Workflow step value parameters.

id: int
workflow_invocation_id
workflow_step_id
value
workflow_step
workflow_invocation
dict_collection_visible_keys = ['id', 'name', 'value', 'workflow_step_id']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_request_step_states', MetaData(), Column('id', Integer(), table=<workflow_request_step_states>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_step_states>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_step_states>), Column('value', MutableJSONType(), table=<workflow_request_step_states>), schema=None)
class galaxy.model.WorkflowRequestToInputDatasetAssociation(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Workflow step input dataset parameters.

id: int
name
workflow_invocation_id
workflow_step_id
dataset_id
workflow_step
dataset
workflow_invocation
history_content_type = 'dataset'
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_request_to_input_dataset', MetaData(), Column('id', Integer(), table=<workflow_request_to_input_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_dataset>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_request_to_input_dataset>), schema=None)
class galaxy.model.WorkflowRequestToInputDatasetCollectionAssociation(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Workflow step input dataset collection parameters.

id: int
name
workflow_invocation_id
workflow_step_id
dataset_collection_id
workflow_step
dataset_collection
workflow_invocation
history_content_type = 'dataset_collection'
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_request_to_input_collection_dataset', MetaData(), Column('id', Integer(), table=<workflow_request_to_input_collection_dataset>, primary_key=True, nullable=False), Column('name', String(length=255), table=<workflow_request_to_input_collection_dataset>), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_to_input_collection_dataset>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_to_input_collection_dataset>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_request_to_input_collection_dataset>), schema=None)
class galaxy.model.WorkflowRequestInputStepParameter(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Workflow step parameter inputs.

id: int
workflow_invocation_id
workflow_step_id
parameter_value
workflow_step
workflow_invocation
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'parameter_value']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_request_input_step_parameter', MetaData(), Column('id', Integer(), table=<workflow_request_input_step_parameter>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_request_input_step_parameter>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_request_input_step_parameter>), Column('parameter_value', MutableJSONType(), table=<workflow_request_input_step_parameter>), schema=None)
class galaxy.model.WorkflowInvocationOutputDatasetAssociation(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Represents links to output datasets for the workflow.

id: int
workflow_invocation_id
workflow_step_id
dataset_id
workflow_output_id
workflow_invocation
workflow_step
dataset
workflow_output
history_content_type = 'dataset'
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_id', 'name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_output_dataset_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_output_dataset_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_association>), schema=None)
class galaxy.model.WorkflowInvocationOutputDatasetCollectionAssociation(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Represents links to output dataset collections for the workflow.

id: int
workflow_invocation_id
workflow_step_id
dataset_collection_id
workflow_output_id
workflow_invocation
workflow_step
dataset_collection
workflow_output
history_content_type = 'dataset_collection'
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'dataset_collection_id', 'name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_output_dataset_collection_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_output_dataset_collection_association>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_dataset_collection_association>), schema=None)
class galaxy.model.WorkflowInvocationOutputValue(**kwargs)[source]

Bases: Base, Dictifiable, Serializable

Represents a link to a specified or computed workflow parameter.

id: int
workflow_invocation_id
workflow_step_id
workflow_output_id
value
workflow_invocation
workflow_invocation_step
workflow_step
workflow_output
dict_collection_visible_keys = ['id', 'workflow_invocation_id', 'workflow_step_id', 'value']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_output_value', MetaData(), Column('id', Integer(), table=<workflow_invocation_output_value>, primary_key=True, nullable=False), Column('workflow_invocation_id', Integer(), ForeignKey('workflow_invocation.id'), table=<workflow_invocation_output_value>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_output_value>), Column('workflow_output_id', Integer(), ForeignKey('workflow_output.id'), table=<workflow_invocation_output_value>), Column('value', MutableJSONType(), table=<workflow_invocation_output_value>), schema=None)
class galaxy.model.WorkflowInvocationStepOutputDatasetAssociation(**kwargs)[source]

Bases: Base, Dictifiable, RepresentById

Represents links to output datasets for the workflow.

id: int
workflow_invocation_step_id
dataset_id
output_name
workflow_invocation_step
dataset
dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_id', 'output_name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_step_output_dataset_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_association>), Column('dataset_id', Integer(), ForeignKey('history_dataset_association.id'), table=<workflow_invocation_step_output_dataset_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_association>), schema=None)
class galaxy.model.WorkflowInvocationStepOutputDatasetCollectionAssociation(**kwargs)[source]

Bases: Base, Dictifiable, RepresentById

Represents links to output dataset collections for the workflow.

id: int
workflow_invocation_step_id
workflow_step_id
dataset_collection_id
output_name
workflow_invocation_step
dataset_collection
dict_collection_visible_keys = ['id', 'workflow_invocation_step_id', 'dataset_collection_id', 'output_name']
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_invocation_step_output_dataset_collection_association', MetaData(), Column('id', Integer(), table=<workflow_invocation_step_output_dataset_collection_association>, primary_key=True, nullable=False), Column('workflow_invocation_step_id', Integer(), ForeignKey('workflow_invocation_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<workflow_invocation_step_output_dataset_collection_association>), Column('output_name', String(length=255), table=<workflow_invocation_step_output_dataset_collection_association>), schema=None)
class galaxy.model.MetadataFile(dataset=None, name=None, uuid=None)[source]

Bases: Base, StorableObject, Serializable

id: int
hda_id
lda_id
create_time
update_time
object_store_id
deleted
purged
__init__(dataset=None, name=None, uuid=None)

A simple constructor that allows initialization from kwargs.

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

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

uuid
history_dataset
library_dataset
name
property dataset: Dataset | None
update_from_file(file_name)[source]
get_file_name(sync_cache=True)[source]
table = Table('metadata_file', MetaData(), Column('id', Integer(), table=<metadata_file>, primary_key=True, nullable=False), Column('name', TEXT(), table=<metadata_file>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<metadata_file>), Column('lda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<metadata_file>), Column('create_time', DateTime(), table=<metadata_file>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<metadata_file>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('object_store_id', TrimmedString(length=255), table=<metadata_file>), Column('uuid', UUIDType(), table=<metadata_file>), Column('deleted', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<metadata_file>, default=ColumnDefault(False)), schema=None)
class galaxy.model.FormDefinition(**kwargs)[source]

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
name
desc
form_definition_current_id
fields
type
layout
form_definition_current
supported_field_types = [<class 'galaxy.util.form_builder.AddressField'>, <class 'galaxy.util.form_builder.CheckboxField'>, <class 'galaxy.util.form_builder.PasswordField'>, <class 'galaxy.util.form_builder.SelectField'>, <class 'galaxy.util.form_builder.TextArea'>, <class 'galaxy.util.form_builder.TextField'>, <class 'galaxy.util.form_builder.WorkflowField'>, <class 'galaxy.util.form_builder.WorkflowMappingField'>, <class 'galaxy.util.form_builder.HistoryField'>]
class types(value)[source]

Bases: str, Enum

An enumeration.

USER_INFO = 'User Information'
dict_collection_visible_keys = ['id', 'name']
dict_element_visible_keys = ['id', 'name', 'desc', 'form_definition_current_id', 'fields', 'layout']
populate(user=None, values=None, security=None)[source]
grid_fields(grid_index)[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, RepresentById

id: int
create_time
update_time
latest_form_id
deleted
forms
__init__(form_definition=None)

A simple constructor that allows initialization from kwargs.

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

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

latest_form
table = Table('form_definition_current', MetaData(), Column('id', Integer(), table=<form_definition_current>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_definition_current>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_definition_current>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('latest_form_id', Integer(), ForeignKey('form_definition.id'), table=<form_definition_current>), Column('deleted', Boolean(), table=<form_definition_current>, default=ColumnDefault(False)), schema=None)
class galaxy.model.FormValues(form_def=None, content=None)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
form_definition_id
__init__(form_def=None, content=None)

A simple constructor that allows initialization from kwargs.

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

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

form_definition
content
table = Table('form_values', MetaData(), Column('id', Integer(), table=<form_values>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<form_values>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<form_values>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('form_definition_id', Integer(), ForeignKey('form_definition.id'), table=<form_values>), Column('content', MutableJSONType(), table=<form_values>), schema=None)
class galaxy.model.UserAddress(**kwargs)[source]

Bases: Base, RepresentById

id: int
create_time
update_time
user_id
desc
name
institution
address
city
state
postal_code
country
phone
deleted
purged
user
to_dict(trans)[source]
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('user_address', MetaData(), Column('id', Integer(), table=<user_address>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_address>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<user_address>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_address>), Column('desc', TrimmedString(length=255), table=<user_address>), Column('name', TrimmedString(length=255), table=<user_address>, nullable=False), Column('institution', TrimmedString(length=255), table=<user_address>), Column('address', TrimmedString(length=255), table=<user_address>, nullable=False), Column('city', TrimmedString(length=255), table=<user_address>, nullable=False), Column('state', TrimmedString(length=255), table=<user_address>, nullable=False), Column('postal_code', TrimmedString(length=255), table=<user_address>, nullable=False), Column('country', TrimmedString(length=255), table=<user_address>, nullable=False), Column('phone', TrimmedString(length=255), table=<user_address>), Column('deleted', Boolean(), table=<user_address>, default=ColumnDefault(False)), Column('purged', Boolean(), table=<user_address>, default=ColumnDefault(False)), schema=None)
class galaxy.model.PSAAssociation(**kwargs)[source]

Bases: Base, AssociationMixin, RepresentById

id: int
server_url
handle
secret
issued
lifetime
assoc_type
sa_session = None
save()[source]
classmethod store(server_url, association)[source]

Create an Association instance (Required by social_core.storage.AssociationMixin interface)

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

Get an Association instance (Required by social_core.storage.AssociationMixin interface)

classmethod remove(ids_to_delete)[source]

Remove an Association instance (Required by social_core.storage.AssociationMixin interface)

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, CodeMixin, RepresentById

id: int
sa_session = None
__init__(email, code)

A simple constructor that allows initialization from kwargs.

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

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

email
code
save()[source]
classmethod get_code(code)[source]

(Required by social_core.storage.CodeMixin interface)

table = Table('psa_code', MetaData(), Column('id', Integer(), table=<psa_code>, primary_key=True, nullable=False), Column('email', VARCHAR(length=200), table=<psa_code>), Column('code', VARCHAR(length=32), table=<psa_code>), schema=None)
class galaxy.model.PSANonce(server_url, timestamp, salt)[source]

Bases: Base, NonceMixin, RepresentById

id: int
sa_session = None
__init__(server_url, timestamp, salt)

A simple constructor that allows initialization from kwargs.

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

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

server_url
timestamp
salt
save()[source]
classmethod use(server_url, timestamp, salt)[source]

Create a Nonce instance (Required by social_core.storage.NonceMixin interface)

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

Bases: Base, PartialMixin, RepresentById

id: int
sa_session = None
__init__(token, data, next_step, backend)

A simple constructor that allows initialization from kwargs.

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

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

token
data
next_step
backend
save()[source]
classmethod load(token)[source]

(Required by social_core.storage.PartialMixin interface)

classmethod destroy(token)[source]

(Required by social_core.storage.PartialMixin interface)

table = Table('psa_partial', MetaData(), Column('id', Integer(), table=<psa_partial>, primary_key=True, nullable=False), Column('token', VARCHAR(length=32), table=<psa_partial>), Column('data', TEXT(), table=<psa_partial>), Column('next_step', Integer(), table=<psa_partial>), Column('backend', VARCHAR(length=32), table=<psa_partial>), schema=None)
class galaxy.model.UserAuthnzToken(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)[source]

Bases: Base, UserMixin, RepresentById

id: int
user
sa_session = None
__init__(provider, uid, extra_data=None, lifetime=None, assoc_type=None, user=None)

A simple constructor that allows initialization from kwargs.

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

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

provider
uid
user_id
extra_data
lifetime
assoc_type
get_id_token(strategy)[source]
set_extra_data(extra_data=None)[source]
save()[source]
classmethod changed(user)[source]

The given user instance is ready to be saved (Required by social_core.storage.UserMixin interface)

classmethod get_username(user)[source]

Return the username for given user (Required by social_core.storage.UserMixin interface)

classmethod user_model()[source]

Return the user model (Required by social_core.storage.UserMixin interface)

classmethod username_max_length()[source]

Return the max length for username (Required by social_core.storage.UserMixin interface)

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. (Required by social_core.storage.UserMixin interface)

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

This is used by PSA authnz, do not use directly. Prefer using the user manager. (Required by social_core.storage.UserMixin interface)

classmethod get_user(pk)[source]

Return user instance for given id (Required by social_core.storage.UserMixin interface)

classmethod get_users_by_email(email)[source]

Return users instances for given email address (Required by social_core.storage.UserMixin interface)

classmethod get_social_auth(provider, uid)[source]

Return UserSocialAuth for given provider and uid (Required by social_core.storage.UserMixin interface)

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

Return all the UserSocialAuth instances for given user (Required by social_core.storage.UserMixin interface)

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

Create a UserSocialAuth instance for given user (Required by social_core.storage.UserMixin interface)

table = Table('oidc_user_authnz_tokens', MetaData(), Column('id', Integer(), table=<oidc_user_authnz_tokens>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<oidc_user_authnz_tokens>), Column('uid', VARCHAR(length=255), table=<oidc_user_authnz_tokens>), Column('provider', VARCHAR(length=32), table=<oidc_user_authnz_tokens>), Column('extra_data', MutableJSONType(), table=<oidc_user_authnz_tokens>), Column('lifetime', Integer(), table=<oidc_user_authnz_tokens>), Column('assoc_type', VARCHAR(length=64), table=<oidc_user_authnz_tokens>), schema=None)
class galaxy.model.CustosAuthnzToken(**kwargs)[source]

Bases: Base, RepresentById

id: int
user_id
external_user_id
provider
access_token
id_token
refresh_token
expiration_time
refresh_expiration_time
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('custos_authnz_token', MetaData(), Column('id', Integer(), table=<custos_authnz_token>, primary_key=True, nullable=False), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<custos_authnz_token>), Column('external_user_id', String(length=255), table=<custos_authnz_token>), Column('provider', String(length=255), table=<custos_authnz_token>), Column('access_token', Text(), table=<custos_authnz_token>), Column('id_token', Text(), table=<custos_authnz_token>), Column('refresh_token', Text(), table=<custos_authnz_token>), Column('expiration_time', DateTime(), table=<custos_authnz_token>), Column('refresh_expiration_time', DateTime(), table=<custos_authnz_token>), schema=None)
class galaxy.model.CloudAuthz(user_id, provider, config, authn_id, description=None)[source]

Bases: Base

id
tokens
create_time
user
authn
__init__(user_id, provider, config, authn_id, description=None)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, HasTags, Dictifiable, RepresentById

id: int
create_time
update_time
user_id
latest_revision_id
title
deleted
importable
slug
published
user
revisions
latest_revision
tags: List[ItemTagAssociation]
annotations
ratings
users_shared_with
average_rating: column_property
users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))
dict_element_visible_keys = ['id', 'title', 'latest_revision_id', 'slug', 'published', 'importable', 'deleted', 'username', 'email_hash', 'create_time', 'update_time']
to_dict(view='element')[source]

Return item dictionary.

property username
property email_hash
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, Dictifiable, RepresentById

id: int
create_time
update_time
page_id
title
content
page
DEFAULT_CONTENT_FORMAT = 'html'
dict_element_visible_keys = ['id', 'page_id', 'title', 'content', 'content_format']
__init__()

A simple constructor that allows initialization from kwargs.

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

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

content_format
to_dict(view='element')[source]

Return item dictionary.

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

Bases: Base, UserShareAssociation

id: int
page_id
user_id
user: User | None
page
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('page_user_share_association', MetaData(), Column('id', Integer(), table=<page_user_share_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_user_share_association>), schema=None)
class galaxy.model.Visualization(**kwd)[source]

Bases: Base, HasTags, Dictifiable, RepresentById

id: int
create_time
update_time
user_id
latest_revision_id
title
type
dbkey
deleted
importable
slug
published
user
revisions
latest_revision
tags: List[ItemTagAssociation]
annotations
ratings
users_shared_with
average_rating: column_property
users_shared_with_dot_users = ObjectAssociationProxyInstance(AssociationProxy('users_shared_with', 'user'))
dict_element_visible_keys = ['id', 'annotation', 'create_time', 'db_key', 'deleted', 'importable', 'published', 'tags', 'title', 'type', 'update_time', 'username']
__init__(**kwd)

A simple constructor that allows initialization from kwargs.

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

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

property annotation
copy(user=None, title=None)[source]

Provide copy of visualization with only its latest revision.

to_dict(view='element')[source]

Return item dictionary.

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

Bases: Base, RepresentById

id: int
create_time
update_time
visualization_id
title
dbkey
config
visualization
copy(visualization=None)[source]

Returns a copy of this object.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, UserShareAssociation

id: int
visualization_id
user_id
user: User | None
visualization
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('visualization_user_share_association', MetaData(), Column('id', Integer(), table=<visualization_user_share_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_user_share_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_user_share_association>), schema=None)
class galaxy.model.Tag(**kwargs)[source]

Bases: Base, RepresentById

id: int
type
parent_id
name
children
parent
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('tag', MetaData(), Column('id', Integer(), table=<tag>, primary_key=True, nullable=False), Column('type', Integer(), table=<tag>), Column('parent_id', Integer(), ForeignKey('tag.id'), table=<tag>), Column('name', TrimmedString(length=255), table=<tag>), schema=None)
class galaxy.model.ItemTagAssociation[source]

Bases: Dictifiable

dict_collection_visible_keys = ['id', 'user_tname', 'user_value']
dict_element_visible_keys = ['id', 'user_tname', 'user_value']
user_tname: Column
user_value = Column(None, TrimmedString(length=255), table=None)
copy(cls=None)[source]
class galaxy.model.HistoryTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
history_id
tag_id
user_id
user_tname: Column
value
history
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_tag_association>), Column('id', Integer(), table=<history_tag_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_tag_association>), Column('value', TrimmedString(length=255), table=<history_tag_association>), schema=None)
user_value
class galaxy.model.HistoryDatasetAssociationTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
history_dataset_association_id
tag_id
user_id
user_tname: Column
value
history_dataset_association
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_association_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('id', Integer(), table=<history_dataset_association_tag_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_association_tag_association>), schema=None)
user_value
class galaxy.model.LibraryDatasetDatasetAssociationTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
library_dataset_dataset_association_id
tag_id
user_id
user_tname: Column
value
library_dataset_dataset_association
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('library_dataset_dataset_association_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('id', Integer(), table=<library_dataset_dataset_association_tag_association>, primary_key=True, nullable=False), Column('library_dataset_dataset_association_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<library_dataset_dataset_association_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_dataset_association_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_dataset_association_tag_association>), schema=None)
user_value
class galaxy.model.PageTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
page_id
tag_id
user_id
user_tname: Column
value
page
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('page_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<page_tag_association>), Column('id', Integer(), table=<page_tag_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<page_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_tag_association>), Column('user_tname', TrimmedString(length=255), table=<page_tag_association>), Column('value', TrimmedString(length=255), table=<page_tag_association>), schema=None)
user_value
class galaxy.model.WorkflowStepTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
workflow_step_id
tag_id
user_id
user_tname: Column
value
workflow_step
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_step_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<workflow_step_tag_association>), Column('id', Integer(), table=<workflow_step_tag_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<workflow_step_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_tag_association>), Column('user_tname', TrimmedString(length=255), table=<workflow_step_tag_association>), Column('value', TrimmedString(length=255), table=<workflow_step_tag_association>), schema=None)
user_value
class galaxy.model.StoredWorkflowTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
stored_workflow_id
tag_id
user_id
user_tname: Column
value
stored_workflow
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('stored_workflow_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<stored_workflow_tag_association>), Column('id', Integer(), table=<stored_workflow_tag_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<stored_workflow_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_tag_association>), Column('user_tname', TrimmedString(length=255), table=<stored_workflow_tag_association>), Column('value', TrimmedString(length=255), table=<stored_workflow_tag_association>), schema=None)
user_value
class galaxy.model.VisualizationTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
visualization_id
tag_id
user_id
user_tname: Column
value
visualization
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('visualization_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<visualization_tag_association>), Column('id', Integer(), table=<visualization_tag_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<visualization_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_tag_association>), Column('user_tname', TrimmedString(length=255), table=<visualization_tag_association>), Column('value', TrimmedString(length=255), table=<visualization_tag_association>), schema=None)
user_value
class galaxy.model.HistoryDatasetCollectionTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
history_dataset_collection_id
tag_id
user_id
user_tname: Column
value
dataset_collection
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_collection_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('id', Integer(), table=<history_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<history_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<history_dataset_collection_tag_association>), schema=None)
user_value
class galaxy.model.LibraryDatasetCollectionTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
library_dataset_collection_id
tag_id
user_id
user_tname: Column
value
dataset_collection
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('library_dataset_collection_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('id', Integer(), table=<library_dataset_collection_tag_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<library_dataset_collection_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_tag_association>), Column('user_tname', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), Column('value', TrimmedString(length=255), table=<library_dataset_collection_tag_association>), schema=None)
user_value
class galaxy.model.ToolTagAssociation(**kwargs)[source]

Bases: Base, ItemTagAssociation, RepresentById

id: int
tool_id
tag_id
user_id
user_tname: Column
value
tag
user
__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('tool_tag_association', MetaData(), Column('user_value', TrimmedString(length=255), table=<tool_tag_association>), Column('id', Integer(), table=<tool_tag_association>, primary_key=True, nullable=False), Column('tool_id', TrimmedString(length=255), table=<tool_tag_association>), Column('tag_id', Integer(), ForeignKey('tag.id'), table=<tool_tag_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<tool_tag_association>), Column('user_tname', TrimmedString(length=255), table=<tool_tag_association>), Column('value', TrimmedString(length=255), table=<tool_tag_association>), schema=None)
user_value
class galaxy.model.HistoryAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

id: int
table = Table('history_annotation_association', MetaData(), Column('id', Integer(), table=<history_annotation_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_annotation_association>), Column('annotation', TEXT(), table=<history_annotation_association>), schema=None)
history_id
user_id
annotation
history
user
class galaxy.model.HistoryDatasetAssociationAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_association_annotation_association', MetaData(), Column('id', Integer(), table=<history_dataset_association_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_association_annotation_association>), schema=None)
id: int
history_dataset_association_id
user_id
annotation
hda
user
class galaxy.model.StoredWorkflowAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('stored_workflow_annotation_association', MetaData(), Column('id', Integer(), table=<stored_workflow_annotation_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_annotation_association>), Column('annotation', TEXT(), table=<stored_workflow_annotation_association>), schema=None)
id: int
stored_workflow_id
user_id
annotation
stored_workflow
user
class galaxy.model.WorkflowStepAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('workflow_step_annotation_association', MetaData(), Column('id', Integer(), table=<workflow_step_annotation_association>, primary_key=True, nullable=False), Column('workflow_step_id', Integer(), ForeignKey('workflow_step.id'), table=<workflow_step_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<workflow_step_annotation_association>), Column('annotation', TEXT(), table=<workflow_step_annotation_association>), schema=None)
id: int
workflow_step_id
user_id
annotation
workflow_step
user
class galaxy.model.PageAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('page_annotation_association', MetaData(), Column('id', Integer(), table=<page_annotation_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_annotation_association>), Column('annotation', TEXT(), table=<page_annotation_association>), schema=None)
id: int
page_id
user_id
annotation
page
user
class galaxy.model.VisualizationAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('visualization_annotation_association', MetaData(), Column('id', Integer(), table=<visualization_annotation_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_annotation_association>), Column('annotation', TEXT(), table=<visualization_annotation_association>), schema=None)
id: int
visualization_id
user_id
annotation
visualization
user
class galaxy.model.HistoryDatasetCollectionAssociationAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_collection_annotation_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<history_dataset_collection_annotation_association>), schema=None)
id: int
history_dataset_collection_id
user_id
annotation
history_dataset_collection
user
class galaxy.model.LibraryDatasetCollectionAnnotationAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('library_dataset_collection_annotation_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_annotation_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_annotation_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_annotation_association>), Column('annotation', TEXT(), table=<library_dataset_collection_annotation_association>), schema=None)
id: int
library_dataset_collection_id
user_id
annotation
dataset_collection
user
class galaxy.model.Vault(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('vault', MetaData(), Column('key', Text(), table=<vault>, primary_key=True, nullable=False), Column('parent_key', Text(), ForeignKey('vault.key'), table=<vault>), Column('value', Text(), table=<vault>), Column('create_time', DateTime(), table=<vault>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<vault>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), schema=None)
key
parent_key
children
parent
value
create_time
update_time
class galaxy.model.ItemRatingAssociation(user, item, rating=0)[source]

Bases: Base

__init__(user, item, rating=0)[source]

A simple constructor that allows initialization from kwargs.

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

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

class galaxy.model.HistoryRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_rating_association', MetaData(), Column('id', Integer(), table=<history_rating_association>, primary_key=True, nullable=False), Column('history_id', Integer(), ForeignKey('history.id'), table=<history_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_rating_association>), Column('rating', Integer(), table=<history_rating_association>), schema=None)
id: int
history_id
user_id
rating
history
user
class galaxy.model.HistoryDatasetAssociationRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_association_rating_association', MetaData(), Column('id', Integer(), table=<history_dataset_association_rating_association>, primary_key=True, nullable=False), Column('history_dataset_association_id', Integer(), ForeignKey('history_dataset_association.id'), table=<history_dataset_association_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_association_rating_association>), Column('rating', Integer(), table=<history_dataset_association_rating_association>), schema=None)
id: int
history_dataset_association_id
user_id
rating
history_dataset_association
user
class galaxy.model.StoredWorkflowRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('stored_workflow_rating_association', MetaData(), Column('id', Integer(), table=<stored_workflow_rating_association>, primary_key=True, nullable=False), Column('stored_workflow_id', Integer(), ForeignKey('stored_workflow.id'), table=<stored_workflow_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<stored_workflow_rating_association>), Column('rating', Integer(), table=<stored_workflow_rating_association>), schema=None)
id: int
stored_workflow_id
user_id
rating
stored_workflow
user
class galaxy.model.PageRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('page_rating_association', MetaData(), Column('id', Integer(), table=<page_rating_association>, primary_key=True, nullable=False), Column('page_id', Integer(), ForeignKey('page.id'), table=<page_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<page_rating_association>), Column('rating', Integer(), table=<page_rating_association>), schema=None)
id: int
page_id
user_id
rating
page
user
class galaxy.model.VisualizationRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('visualization_rating_association', MetaData(), Column('id', Integer(), table=<visualization_rating_association>, primary_key=True, nullable=False), Column('visualization_id', Integer(), ForeignKey('visualization.id'), table=<visualization_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<visualization_rating_association>), Column('rating', Integer(), table=<visualization_rating_association>), schema=None)
id: int
visualization_id
user_id
rating
visualization
user
class galaxy.model.HistoryDatasetCollectionRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('history_dataset_collection_rating_association', MetaData(), Column('id', Integer(), table=<history_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('history_dataset_collection_id', Integer(), ForeignKey('history_dataset_collection_association.id'), table=<history_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<history_dataset_collection_rating_association>), Column('rating', Integer(), table=<history_dataset_collection_rating_association>), schema=None)
id: int
history_dataset_collection_id
user_id
rating
dataset_collection
user
class galaxy.model.LibraryDatasetCollectionRatingAssociation(user, item, rating=0)[source]

Bases: ItemRatingAssociation, RepresentById

__init__(user, item, rating=0)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('library_dataset_collection_rating_association', MetaData(), Column('id', Integer(), table=<library_dataset_collection_rating_association>, primary_key=True, nullable=False), Column('library_dataset_collection_id', Integer(), ForeignKey('library_dataset_collection_association.id'), table=<library_dataset_collection_rating_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<library_dataset_collection_rating_association>), Column('rating', Integer(), table=<library_dataset_collection_rating_association>), schema=None)
id: int
library_dataset_collection_id
user_id
rating
dataset_collection
user
class galaxy.model.DataManagerHistoryAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('data_manager_history_association', MetaData(), Column('id', Integer(), table=<data_manager_history_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<data_manager_history_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('update_time', DateTime(), table=<data_manager_history_association>, onupdate=ColumnDefault(<function datetime.utcnow>), default=ColumnDefault(<function datetime.utcnow>)), Column('history_id', Integer(), ForeignKey('history.id'), table=<data_manager_history_association>), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<data_manager_history_association>), schema=None)
id: int
create_time
update_time
history_id
user_id
history
user
class galaxy.model.DataManagerJobAssociation(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

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

Bases: Base, RepresentById

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

A simple constructor that allows initialization from kwargs.

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

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

name
value
class galaxy.model.UserAction(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('user_action', MetaData(), Column('id', Integer(), table=<user_action>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<user_action>, default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<user_action>), Column('session_id', Integer(), ForeignKey('galaxy_session.id'), table=<user_action>), Column('action', Unicode(length=255), table=<user_action>), Column('context', Unicode(length=512), table=<user_action>), Column('params', Unicode(length=1024), table=<user_action>), schema=None)
id: int
create_time
user_id
session_id
action
context
params
user
class galaxy.model.APIKeys(**kwargs)[source]

Bases: Base, RepresentById

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('api_keys', MetaData(), Column('id', Integer(), table=<api_keys>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<api_keys>, default=ColumnDefault(<function datetime.utcnow>)), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<api_keys>), Column('key', TrimmedString(length=32), table=<api_keys>), Column('deleted', Boolean(), table=<api_keys>, nullable=False, server_default=DefaultClause(<sqlalchemy.sql.elements.False_ object>, for_update=False)), schema=None)
id: int
create_time
user_id
key
user
deleted
galaxy.model.copy_list(lst, *args, **kwds)[source]
class galaxy.model.CleanupEvent(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event', MetaData(), Column('id', Integer(), table=<cleanup_event>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event>, default=ColumnDefault(<function datetime.utcnow>)), Column('message', TrimmedString(length=1024), table=<cleanup_event>), schema=None)
id
create_time
message
class galaxy.model.CleanupEventDatasetAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_dataset_association', MetaData(), Column('id', Integer(), table=<cleanup_event_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_dataset_association>), Column('dataset_id', Integer(), ForeignKey('dataset.id'), table=<cleanup_event_dataset_association>), schema=None)
id
create_time
cleanup_event_id
dataset_id
class galaxy.model.CleanupEventMetadataFileAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_metadata_file_association', MetaData(), Column('id', Integer(), table=<cleanup_event_metadata_file_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_metadata_file_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_metadata_file_association>), Column('metadata_file_id', Integer(), ForeignKey('metadata_file.id'), table=<cleanup_event_metadata_file_association>), schema=None)
id
create_time
cleanup_event_id
metadata_file_id
class galaxy.model.CleanupEventHistoryAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_history_association', MetaData(), Column('id', Integer(), table=<cleanup_event_history_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_history_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_history_association>), Column('history_id', Integer(), ForeignKey('history.id'), table=<cleanup_event_history_association>), schema=None)
id
create_time
cleanup_event_id
history_id
class galaxy.model.CleanupEventHistoryDatasetAssociationAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_hda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_hda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_hda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_hda_association>), Column('hda_id', Integer(), ForeignKey('history_dataset_association.id'), table=<cleanup_event_hda_association>), schema=None)
id
create_time
cleanup_event_id
hda_id
class galaxy.model.CleanupEventLibraryAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_library_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_association>), Column('library_id', Integer(), ForeignKey('library.id'), table=<cleanup_event_library_association>), schema=None)
id
create_time
cleanup_event_id
library_id
class galaxy.model.CleanupEventLibraryFolderAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_library_folder_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_folder_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_folder_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_folder_association>), Column('library_folder_id', Integer(), ForeignKey('library_folder.id'), table=<cleanup_event_library_folder_association>), schema=None)
id
create_time
cleanup_event_id
library_folder_id
class galaxy.model.CleanupEventLibraryDatasetAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_library_dataset_association', MetaData(), Column('id', Integer(), table=<cleanup_event_library_dataset_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_library_dataset_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_library_dataset_association>), Column('library_dataset_id', Integer(), ForeignKey('library_dataset.id'), table=<cleanup_event_library_dataset_association>), schema=None)
id
create_time
cleanup_event_id
library_dataset_id
class galaxy.model.CleanupEventLibraryDatasetDatasetAssociationAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_ldda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_ldda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_ldda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_ldda_association>), Column('ldda_id', Integer(), ForeignKey('library_dataset_dataset_association.id'), table=<cleanup_event_ldda_association>), schema=None)
id
create_time
cleanup_event_id
ldda_id
class galaxy.model.CleanupEventImplicitlyConvertedDatasetAssociationAssociation(**kwargs)[source]

Bases: Base

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('cleanup_event_icda_association', MetaData(), Column('id', Integer(), table=<cleanup_event_icda_association>, primary_key=True, nullable=False), Column('create_time', DateTime(), table=<cleanup_event_icda_association>, default=ColumnDefault(<function datetime.utcnow>)), Column('cleanup_event_id', Integer(), ForeignKey('cleanup_event.id'), table=<cleanup_event_icda_association>), Column('icda_id', Integer(), ForeignKey('implicitly_converted_dataset_association.id'), table=<cleanup_event_icda_association>), schema=None)
id
create_time
cleanup_event_id
icda_id
class galaxy.model.CeleryUserRateLimit(**kwargs)[source]

Bases: Base

For each user stores the last time a task was scheduled for execution. Used to limit the number of tasks allowed per user per second.

__init__(**kwargs)

A simple constructor that allows initialization from kwargs.

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

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

table = Table('celery_user_rate_limit', MetaData(), Column('user_id', Integer(), ForeignKey('galaxy_user.id'), table=<celery_user_rate_limit>, primary_key=True, nullable=False), Column('last_scheduled_time', DateTime(), table=<celery_user_rate_limit>, nullable=False), schema=None)
user_id
last_scheduled_time
galaxy.model.receive_init(target, args, kwargs)[source]

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

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

class galaxy.model.JobStateSummary(new, resubmitted, upload, waiting, queued, running, ok, error, failed, paused, deleting, deleted, stop, stopped, skipped, all_jobs)

Bases: tuple

all_jobs: int

Alias for field number 15

deleted: int

Alias for field number 11

deleting: int

Alias for field number 10

error: int

Alias for field number 7

failed: int

Alias for field number 8

new: int

Alias for field number 0

ok: int

Alias for field number 6

paused: int

Alias for field number 9

queued: int

Alias for field number 4

resubmitted: int

Alias for field number 1

running: int

Alias for field number 5

skipped: int

Alias for field number 14

stop: int

Alias for field number 12

stopped: int

Alias for field number 13

upload: int

Alias for field number 2

waiting: int

Alias for field number 3

Subpackages

Submodules

galaxy.model.base module

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

galaxy.model.base.transaction(session: scoped_session | Session | SessionlessContext)[source]

Start a new transaction only if one is not present.

galaxy.model.base.check_database_connection(session)[source]

In the event of a database disconnect, if there exists an active database transaction, that transaction becomes invalidated. Accessing the database will raise sqlalchemy.exc.PendingRollbackError. This handles this situation by rolling back the invalidated transaction. Ref: https://docs.sqlalchemy.org/en/14/errors.html#can-t-reconnect-until-invalid-transaction-is-rolled-back

class galaxy.model.base.ModelMapping(model_modules, engine)[source]

Bases: Bunch

__init__(model_modules, engine)[source]
new_session()[source]

Return a new non-scoped Session object.

Use this when we need to operate on ORM entities, so a Connection object would be insufficient; yet the operation must be independent of the main session (self.session).

request_scopefunc()[source]

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

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

static set_request_id(request_id)[source]
unset_request_id(request_id)[source]
property context: scoped_session
property Session

For backward compat., deprecated.

class galaxy.model.base.SharedModelMapping(model_modules, engine)[source]

Bases: ModelMapping

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

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

User: Type
GalaxySession: Type
APIKeys: Type
PasswordResetToken: Type
galaxy.model.base.versioned_objects_strict(iter)[source]
galaxy.model.base.versioned_objects(iter)[source]
galaxy.model.base.versioned_session(session)[source]
galaxy.model.base.ensure_object_added_to_session(object_to_add, *, object_in_session=None, session=None) bool[source]

This function is intended as a safeguard to mimic pre-SQLAlchemy 2.0 behavior. object_to_add was implicitly merged into a Session prior to SQLAlchemy 2.0, which was indicated by RemovedIn20Warning warnings logged while running Galaxy’s tests. (See https://github.com/galaxyproject/galaxy/issues/12541) As part of the upgrade to 2.0, the cascade_backrefs=False argument was added to the relevant relationships that turned off this behavior. This function is called from the code that triggered these warnings, thus emulating the cascading behavior. The intention is to remove all such calls, as well as this function definition, after the move to SQLAlchemy 2.0. # Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0

galaxy.model.custom_types module

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

Bases: 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: LargeBinary

result_processor(dialect, coltype)[source]

Return a conversion function for processing result row values.

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

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

Note

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

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

See also

types_typedecorator

Parameters:
  • dialect – Dialect instance in use.

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

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

Bases: TypeDecorator

Represents an immutable structure as a json-encoded string.

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

impl

alias of GalaxyLargeBinary

cache_ok = True

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

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

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

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

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

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

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

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

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

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

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

    '''

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

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

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

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

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

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

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

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

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

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

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

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

    '''

    cache_ok = True

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

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

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

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

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

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

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

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

See also

sql_caching

process_bind_param(value, dialect)[source]

Receive a bound parameter value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

load_dialect_impl(dialect)[source]

Return a TypeEngine object corresponding to a dialect.

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

By default returns self.impl.

copy_value(value)[source]
compare_values(x, y)[source]

Given two values, compare them for equality.

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

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

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

Bases: JSONType

cache_ok = True

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

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

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

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

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

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

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

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

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

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

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

    '''

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

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

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

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

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

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

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

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

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

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

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

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

    '''

    cache_ok = True

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

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

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

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

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

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

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

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

See also

sql_caching

process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

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

Bases: JSONType

Associated with MutationObj

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

Bases: Mutable

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

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

And other minor changes to make it work for us.

classmethod coerce(key, value)[source]

Given a value, coerce it into the target type.

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

By default, raises ValueError.

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

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

  • value – the incoming value.

Returns:

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

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

Bases: MutationObj, dict

classmethod coerce(key, value)[source]

Convert plain dictionary to MutationDict

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

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

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

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

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

Bases: MutationObj, list

classmethod coerce(key, value)[source]

Convert plain list to MutationList

append(value)[source]

Append object to the end of the list.

insert(idx, value)[source]

Insert object before index.

extend(values)[source]

Extend list by appending elements from the iterable.

pop(*args, **kw)[source]

Remove and return item at index (default last).

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

remove(value)[source]

Remove first occurrence of value.

Raises ValueError if the value is not present.

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

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

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

handlers = {SomeContainerClass: iter,

OtherContainerClass: OtherContainerClass.get_elements}

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

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

Bases: JSONType

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

cache_ok = True

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

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

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

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

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

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

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

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

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

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

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

    '''

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

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

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

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

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

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

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

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

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

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

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

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

    '''

    cache_ok = True

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

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

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

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

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

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

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

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

See also

sql_caching

process_bind_param(value, dialect)[source]

Receive a bound parameter value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

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

Bases: TypeDecorator

Platform-independent UUID type.

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

CHAR(32), storing as stringified hex values.

impl

alias of CHAR

cache_ok = True

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

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

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

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

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

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

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

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

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

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

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

    '''

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

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

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

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

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

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

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

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

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

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

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

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

    '''

    cache_ok = True

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

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

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

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

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

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

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

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

See also

sql_caching

load_dialect_impl(dialect)[source]

Return a TypeEngine object corresponding to a dialect.

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

By default returns self.impl.

process_bind_param(value, dialect)[source]

Receive a bound parameter value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_result_value()

process_result_value(value, dialect)[source]

Receive a result-row column value to be converted.

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

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

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

  • dialect – the Dialect in use.

See also

types_typedecorator

_types.TypeDecorator.process_bind_param()

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

Bases: TypeDecorator

impl

alias of String

cache_ok = True

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

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

class MyType(TypeDecorator):
    impl = String

    cache_ok = True

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

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

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

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

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

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

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

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

    '''

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

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

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

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

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

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

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

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

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

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

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

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

    '''

    cache_ok = True

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

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

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

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

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

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

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

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

See also

sql_caching

process_bind_param(value, dialect)[source]

Automatically truncate string values

galaxy.model.database_heartbeat module

galaxy.model.database_heartbeat.now()

Return a new datetime representing UTC day and time.

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

Bases: object

__init__(application_stack, heartbeat_interval=60)[source]
property sa_session
property server_name
start()[source]
shutdown()[source]
get_active_processes(last_seen_seconds=None)[source]

Return all processes seen in last_seen_seconds seconds.

add_change_callback(callback)[source]
property is_config_watcher
update_watcher_designation()[source]
send_database_heartbeat()[source]

galaxy.model.database_utils module

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

Check if database exists; connect with db_url.

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

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

Create database; connect with db_url.

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

galaxy.model.database_utils.sqlalchemy_engine(url)[source]
class galaxy.model.database_utils.DatabaseManager(db_url, database)[source]

Bases: object

static make_manager(db_url, database)[source]
__init__(db_url, database)[source]
class galaxy.model.database_utils.PosgresDatabaseManager(db_url, database)[source]

Bases: DatabaseManager

exists()[source]
create(encoding, template)[source]
class galaxy.model.database_utils.SqliteDatabaseManager(db_url, database)[source]

Bases: DatabaseManager

exists()[source]
create(*args)[source]
class galaxy.model.database_utils.MySQLDatabaseManager(db_url, database)[source]

Bases: DatabaseManager

exists()[source]
create(encoding, *arg)[source]
galaxy.model.database_utils.is_one_database(db1_url: str, db2_url: str | None)[source]

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

galaxy.model.database_utils.supports_returning(engine: Engine) bool[source]

Return True if the database bound to engine supports the RETURNING SQL clause.

galaxy.model.database_utils.supports_skip_locked(engine: Engine) bool[source]

Return True if the database bound to engine supports the SKIP_LOCKED parameter.

galaxy.model.database_utils.is_postgres(url: DbUrl) bool[source]
galaxy.model.database_utils.ensure_object_added_to_session(object_to_add, *, object_in_session=None, session=None) bool[source]

This function is intended as a safeguard to mimic pre-SQLAlchemy 2.0 behavior. object_to_add was implicitly merged into a Session prior to SQLAlchemy 2.0, which was indicated by RemovedIn20Warning warnings logged while running Galaxy’s tests. (See https://github.com/galaxyproject/galaxy/issues/12541) As part of the upgrade to 2.0, the cascade_backrefs=False argument was added to the relevant relationships that turned off this behavior. This function is called from the code that triggered these warnings, thus emulating the cascading behavior. The intention is to remove all such calls, as well as this function definition, after the move to SQLAlchemy 2.0. # Ref: https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0

galaxy.model.deferred module

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

Bases: tuple

external_filename: str

Alias for field number 0

external_extra_files_path: str

Alias for field number 1

metadata_files_dir: str

Alias for field number 2

class galaxy.model.deferred.TransientPathMapper[source]

Bases: object

abstract transient_paths_for(old_dataset: Dataset) TransientDatasetPaths[source]

Map dataset to transient paths for detached HDAs.

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

class galaxy.model.deferred.SimpleTransientPathMapper(staging_directory: str)[source]

Bases: TransientPathMapper

__init__(staging_directory: str)[source]
transient_paths_for(old_dataset: Dataset) TransientDatasetPaths[source]

Map dataset to transient paths for detached HDAs.

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

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

Bases: object

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

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

Constructor for DatasetInstanceMaterializer.

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

ensure_materialized(dataset_instance: HistoryDatasetAssociation | LibraryDatasetDatasetAssociation, target_history: History | None = None) HistoryDatasetAssociation[source]

Create a new detached dataset instance from the supplied instance.

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

galaxy.model.deferred.materialize_collection_input(collection_input: HistoryDatasetCollectionAssociation | DatasetCollectionElement, materializer: DatasetInstanceMaterializer) HistoryDatasetCollectionAssociation | DatasetCollectionElement[source]
galaxy.model.deferred.materialize_collection_instance(hdca: HistoryDatasetCollectionAssociation, materializer: DatasetInstanceMaterializer) HistoryDatasetCollectionAssociation[source]
galaxy.model.deferred.materializer_factory(attached: bool, object_store: ObjectStore | None = None, object_store_populator: ObjectStorePopulator | None = None, transient_path_mapper: TransientPathMapper | None = None, transient_directory: str | None = None, file_sources: ConfiguredFileSources | None = None, sa_session: scoped_session | None = None) DatasetInstanceMaterializer[source]

galaxy.model.index_filter_util module

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

galaxy.model.index_filter_util.text_column_filter(column, term: FilteredTerm)[source]
galaxy.model.index_filter_util.raw_text_column_filter(columns: List[BinaryExpression | InstrumentedAttribute], term: RawTextTerm)[source]
galaxy.model.index_filter_util.tag_filter(assocation_model_class, term_text, quoted: bool = False)[source]
galaxy.model.index_filter_util.append_user_filter(query, model_class, term: FilteredTerm)[source]

galaxy.model.item_attrs module

galaxy.model.item_attrs.get_foreign_key(source_class, target_class)[source]

Returns foreign key in source class that references target class.

class galaxy.model.item_attrs.UsesAnnotations[source]

Bases: object

Mixin for getting and setting item annotations.

get_item_annotation_str(db_session, user, item)[source]
get_item_annotation_obj(db_session, user, item)[source]
add_item_annotation(db_session, user, item, annotation)[source]
delete_item_annotation(db_session, user, item)[source]
copy_item_annotation(db_session, source_user, source_item, target_user, target_item)[source]

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

class galaxy.model.item_attrs.UsesItemRatings[source]

Bases: object

Mixin for getting and setting item ratings.

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

get_ave_item_rating_data(db_session, item, webapp_model=None)[source]

Returns the average rating for an item.

rate_item(db_session, user, item, rating, webapp_model=None)[source]

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

get_user_item_rating(db_session, user, item, webapp_model=None)[source]

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

galaxy.model.mapping module

class galaxy.model.mapping.GalaxyModelMapping(model_modules, engine)[source]

Bases: SharedModelMapping

security_agent: GalaxyRBACAgent
thread_local_log: _local | None
User: Type
GalaxySession: Type
galaxy.model.mapping.init(file_path, url, engine_options=None, create_tables=False, map_install_models=False, database_query_profiling_proxy=False, object_store=None, trace_logger=None, use_pbkdf2=True, slow_query_log_threshold=0, thread_local_log: _local | None = None, log_query_counts=False) GalaxyModelMapping[source]
galaxy.model.mapping.create_additional_database_objects(engine)[source]
galaxy.model.mapping.configure_model_mapping(file_path: str, object_store, use_pbkdf2, engine, map_install_models, thread_local_log) GalaxyModelMapping[source]
galaxy.model.mapping.init_models_from_config(config: GalaxyAppConfiguration, map_install_models=False, object_store=None, trace_logger=None)[source]

galaxy.model.metadata module

Galaxy Metadata

class galaxy.model.metadata.Statement(target)[source]

Bases: object

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

__init__(target)[source]
classmethod process(element)[source]
galaxy.model.metadata.MetadataElement = <galaxy.model.metadata.Statement object>

MetadataParameter sub-classes.

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

Bases: Mapping

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

__init__(parent: DatasetInstance | NoneDataset, session: galaxy_scoped_session | SessionlessContext | None = None) None[source]
get_parent()[source]
set_parent(parent)[source]
property parent
property spec
remove_key(name)[source]
element_is_set(name) bool[source]

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

  • if the such a metadata actually exists and

  • if its value differs from no_value

Parameters:

name – the name of the metadata element

Returns:

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

get_metadata_parameter(name, **kwd)[source]
make_dict_copy(to_copy)[source]

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

property requires_dataset_id
from_JSON_dict(filename=None, path_rewriter=None, json_dict=None)[source]
to_JSON_dict(filename=None)[source]
class galaxy.model.metadata.MetadataSpecCollection(*args, **kwds)[source]

Bases: OrderedDict

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

__init__(*args, **kwds)[source]
append(item)[source]
class galaxy.model.metadata.MetadataParameter(spec)[source]

Bases: object

__init__(spec)[source]
get_field(value=None, context=None, other_values=None, **kwd)[source]
to_string(value)[source]
to_safe_string(value)[source]
make_copy(value, target_context: MetadataCollection, source_context)[source]
classmethod marshal(value)[source]

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

validate(value)[source]

Throw an exception if the value is invalid.

unwrap(form_value)[source]

Turns a value into its storable form.

wrap(value, session)[source]

Turns a value into its usable form.

from_external_value(value, parent)[source]

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

to_external_value(value)[source]

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

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

Bases: object

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

__init__(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, optional=False, **kwargs)[source]
get(name, default=None)[source]
wrap(value, session)[source]

Turns a stored value into its usable form.

unwrap(value)[source]

Turns an incoming value into its storable form.

class galaxy.model.metadata.SelectParameter(spec)[source]

Bases: MetadataParameter

__init__(spec)[source]
to_string(value)[source]
get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
wrap(value, session)[source]

Turns a value into its usable form.

classmethod marshal(value)[source]

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

class galaxy.model.metadata.DBKeyParameter(spec)[source]

Bases: SelectParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
make_copy(value, target_context: MetadataCollection, source_context)[source]
class galaxy.model.metadata.RangeParameter(spec)[source]

Bases: SelectParameter

__init__(spec)[source]
get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
classmethod marshal(value)[source]

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

class galaxy.model.metadata.ColumnParameter(spec)[source]

Bases: RangeParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)[source]
class galaxy.model.metadata.ColumnTypesParameter(spec)[source]

Bases: MetadataParameter

to_string(value)[source]
class galaxy.model.metadata.ListParameter(spec)[source]

Bases: MetadataParameter

to_string(value)[source]
class galaxy.model.metadata.DictParameter(spec)[source]

Bases: MetadataParameter

to_string(value)[source]
to_safe_string(value)[source]
class galaxy.model.metadata.PythonObjectParameter(spec)[source]

Bases: MetadataParameter

to_string(value)[source]
get_field(value=None, context=None, other_values=None, **kwd)[source]
classmethod marshal(value)[source]

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

class galaxy.model.metadata.FileParameter(spec)[source]

Bases: MetadataParameter

to_string(value)[source]
to_safe_string(value)[source]
get_field(value=None, context=None, other_values=None, **kwd)[source]
wrap(value, session)[source]

Turns a value into its usable form.

make_copy(value, target_context: MetadataCollection, source_context)[source]
classmethod marshal(value)[source]

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

from_external_value(value, parent, path_rewriter=None)[source]

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

to_external_value(value)[source]

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

new_file(dataset=None, metadata_tmp_files_dir=None, **kwds)[source]
class galaxy.model.metadata.MetadataTempFile(metadata_tmp_files_dir=None, **kwds)[source]

Bases: object

__init__(metadata_tmp_files_dir=None, **kwds)[source]
tmp_dir = 'database/tmp'
get_file_name()[source]
to_JSON()[source]
classmethod from_JSON(json_dict)[source]
classmethod is_JSONified_value(value)[source]
classmethod cleanup_from_JSON_dict_filename(filename)[source]

galaxy.model.none_like module

Objects with No values

class galaxy.model.none_like.RecursiveNone[source]

Bases: object

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

Bases: RecursiveNone

__init__(datatypes_registry=None, ext='data', dbkey='?')[source]
missing_meta()[source]
get_file_name(sync_cache=True)[source]

galaxy.model.scoped_session module

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

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

Bases: scoped_session

scoped_session used for galaxy model.

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

Bases: scoped_session

scoped_session used for tool_shed_install model.

galaxy.model.search module

galaxy.model.security module

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

Bases: RBACAgent

__init__(model, permitted_actions=None)[source]
property sa_session

Returns a SQLAlchemy session

sort_by_attr(seq, attr)[source]

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

get_all_roles(trans, cntrller)[source]
get_roles_for_action(item, action)[source]

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

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

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

get_legitimate_roles(trans, item, cntrller)[source]

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

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

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

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

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

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

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

ok_to_display(user, role)[source]

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

allow_action(roles, action, item)[source]

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

get_actions_for_items(trans, action, permission_items)[source]
allow_action_on_libitems(trans, user_roles, action, items)[source]

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

dataset_access_mapping(trans, user_roles, datasets)[source]

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

dataset_permission_map_for_access(trans, user_roles, libitems)[source]

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

item_permission_map_for_modify(trans, user_roles, libitems)[source]
item_permission_map_for_manage(trans, user_roles, libitems)[source]
item_permission_map_for_add(trans, user_roles, libitems)[source]
can_access_dataset(user_roles, dataset: Dataset)[source]
can_access_datasets(user_roles, action_tuples)[source]
can_access_collection(user_roles: List[Role], collection: DatasetCollection)[source]
can_manage_dataset(roles, dataset)[source]
can_access_library(roles, library)[source]
get_accessible_libraries(trans, user)[source]

Return all data libraries that the received user can access

has_accessible_folders(trans, folder, user, roles, search_downward=True)[source]
has_accessible_library_datasets(trans, folder, user, roles, search_downward=True)[source]
can_access_library_item(roles, item, user)[source]
can_add_library_item(roles, item)[source]
can_modify_library_item(roles, item)[source]
can_manage_library_item(roles, item)[source]
can_change_object_store_id(user, dataset)[source]
get_item_actions(action, item)[source]
guess_derived_permissions_for_datasets(datasets=None)[source]

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

guess_derived_permissions(all_input_permissions)[source]

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

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

associate_components(**kwd)[source]
associate_user_group(user, group)[source]
associate_user_role(user, role)[source]
associate_group_role(group, role)[source]
associate_action_dataset_role(action, dataset, role)[source]
create_user_role(user, app)[source]
create_private_user_role(user)[source]
get_private_user_role(user, auto_create=False)[source]
get_role(name, type=None)[source]
create_role(name, description, in_users, in_groups, create_group_for_role=False, type=None)[source]
get_sharing_roles(user)[source]
user_set_default_permissions(user, permissions=None, history=False, dataset=False, bypass_manage_permission=False, default_access_private=False)[source]
user_get_default_permissions(user)[source]
history_set_default_permissions(history, permissions=None, dataset=False, bypass_manage_permission=False)[source]
history_get_default_permissions(history)[source]
set_all_dataset_permissions(dataset, permissions=None, new=False, flush=True)[source]

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

set_dataset_permission(dataset, permission=None)[source]

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

get_permissions(item)[source]

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

copy_dataset_permissions(src, dst, flush=True)[source]
privately_share_dataset(dataset, users=None)[source]
set_all_library_permissions(trans, library_item, permissions=None)[source]
set_library_item_permission(library_item, permission=None)[source]

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

library_is_public(library, contents=False)[source]
library_is_unrestricted(library)[source]
make_library_public(library, contents=False)[source]
folder_is_public(folder)[source]
folder_is_unrestricted(folder)[source]
make_folder_public(folder)[source]
dataset_is_public(dataset: Dataset)[source]

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

dataset_is_unrestricted(trans, dataset)[source]

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

dataset_is_private_to_user(trans, dataset)[source]

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

dataset_is_private_to_a_user(dataset)[source]

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

datasets_are_public(trans, datasets)[source]

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

make_dataset_public(dataset)[source]
derive_roles_from_access(trans, item_id, cntrller, library=False, **kwd)[source]
copy_library_permissions(trans, source_library_item, target_library_item, user=None)[source]
get_permitted_libraries(trans, user, actions)[source]

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

libraries = trans.app.security_agent.get_permitted_libraries( trans, user,
    [ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
show_library_item(user, roles, library_item, actions_to_check, hidden_folder_ids='')[source]

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

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

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

set_entity_user_associations(users=None, roles=None, groups=None, delete_existing_assocs=True)[source]
set_entity_group_associations(groups=None, users=None, roles=None, delete_existing_assocs=True)[source]
set_entity_role_associations(roles=None, users=None, groups=None, delete_existing_assocs=True)[source]
get_component_associations(**kwd)[source]
check_folder_contents(user, roles, folder, hidden_folder_ids='')[source]

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

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

Bases: RBACAgent

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

sites = <galaxy.util.bunch.Bunch object>
__init__(model, permitted_actions=None)[source]
property sa_session

Returns a SQLAlchemy session

allow_action(addr, action, **kwd)[source]
set_dataset_permissions(hda, user, site)[source]

galaxy.model.tags module

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

Bases: object

__init__(item_class, tag_assoc_class, item_id_col)[source]
class galaxy.model.tags.TagHandler(sa_session: galaxy_scoped_session, galaxy_session=None)[source]

Bases: object

Manages CRUD operations related to tagging objects.

__init__(sa_session: galaxy_scoped_session, galaxy_session=None) None[source]
create_tag_handler_session(galaxy_session: GalaxySession | None)[source]
add_tags_from_list(user, item, new_tags_list, flush=True)[source]
remove_tags_from_list(user, item, tag_to_remove_list, flush=True)[source]
set_tags_from_list(user, item, new_tags_list, flush=True)[source]
get_tag_assoc_class(item_class)[source]

Returns tag association class for item class.

get_id_col_in_item_tag_assoc_table(item_class)[source]

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

get_community_tags(item=None, limit=None)[source]

Returns community tags for an item.

get_tool_tags()[source]
remove_item_tag(user: User, item, tag_name: str)[source]

Remove a tag from an item.

delete_item_tags(user: User | None, item)[source]

Delete tags from an item.

item_has_tag(user, item, tag)[source]

Returns true if item is has a given tag.

apply_item_tag(user: User | None, item, name, value=None, flush=True)[source]
apply_item_tags(user: User | None, item, tags_str: str | None, flush=True)[source]

Apply tags to an item.

get_tags_list(tags) List[str][source]

Build a list of tags from an item’s tags.

get_tags_str(tags)[source]

Build a string from an item’s tags.

get_tag_by_id(tag_id)[source]

Get a Tag object from a tag id.

get_tag_by_name(tag_name)[source]

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

parse_tags(tag_str)[source]

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

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

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

>>> th = TagHandler("bridge_of_death")
>>> tags = th.parse_tags_list(["name:Lancelot of Camelot", "#Holy Grail", "blue"])
>>> assert tags == [('name', 'LancelotofCamelot'), ('name', 'HolyGrail'), ('blue', None)]
class galaxy.model.tags.GalaxyTagHandler(sa_session: galaxy_scoped_session, galaxy_session=None)[source]

Bases: TagHandler

__init__(sa_session: galaxy_scoped_session, galaxy_session=None)[source]
classmethod init_tag_associations()[source]
class galaxy.model.tags.GalaxyTagHandlerSession(sa_session, galaxy_session: GalaxySession | None)[source]

Bases: GalaxyTagHandler

Like GalaxyTagHandler, but avoids one flush per created tag.

__init__(sa_session, galaxy_session: GalaxySession | None)[source]
class galaxy.model.tags.GalaxySessionlessTagHandler(sa_session, galaxy_session: GalaxySession | None)[source]

Bases: GalaxyTagHandlerSession

get_tag_by_name(tag_name)[source]

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

class galaxy.model.tags.CommunityTagHandler(sa_session)[source]

Bases: TagHandler

__init__(sa_session)[source]