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galaxy.datatypes.display_applications package

Contains functionality of the newer XML defined external display applications (not hardcoded into datatype classes).

Submodules

galaxy.datatypes.display_applications.application module

galaxy.datatypes.display_applications.application.quote_plus_string(value, **kwds)[source]

class galaxy.datatypes.display_applications.application.DisplayApplicationLink(display_application)[source]

Bases: object

classmethod from_elem(elem, display_application, other_values=None)[source]

__init__(display_application)[source]

get_display_url(data, trans)[source]

get_inital_values(data, trans)[source]

build_parameter_dict(data, dataset_hash, user_hash, trans, app_kwds)[source]

filter_by_dataset(data, trans)[source]

class galaxy.datatypes.display_applications.application.DynamicDisplayApplicationBuilder(elem, display_application, build_sites)[source]

Bases: object

__init__(elem, display_application, build_sites)[source]

class galaxy.datatypes.display_applications.application.PopulatedDisplayApplicationLink(display_application_link, data, dataset_hash, user_hash, trans, app_kwds)[source]

Bases: object

__init__(display_application_link, data, dataset_hash, user_hash, trans, app_kwds)[source]

display_ready()[source]

get_param_value(name)[source]

preparing_display()[source]

prepare_display()[source]

get_prepare_steps(datasets_only=True)[source]

display_url()[source]

get_param_name_by_url(url)[source]

property allow_cors

class galaxy.datatypes.display_applications.application.DisplayApplication(display_id, name, app, version=None, filename=None, elem=None)[source]

Bases: object

classmethod from_file(filename, app)[source]

classmethod from_elem(elem, app, filename=None)[source]

__init__(display_id, name, app, version=None, filename=None, elem=None)[source]

get_link(link_name, data, dataset_hash, user_hash, trans, app_kwds)[source]

filter_by_dataset(data, trans)[source]

reload()[source]

add_data_table_watch(table_name, version=None)[source]

galaxy.datatypes.display_applications.parameters module

class galaxy.datatypes.display_applications.parameters.DisplayApplicationParameter(elem, link)[source]

Bases: object

Abstract Class for Display Application Parameters

type: str | None = None

classmethod from_elem(elem, link)[source]

__init__(elem, link)[source]

get_value(other_values, dataset_hash, user_hash, trans)[source]

prepare(other_values, dataset_hash, user_hash, trans)[source]

ready(other_values)[source]

is_preparing(other_values)[source]

build_url(other_values)[source]

class galaxy.datatypes.display_applications.parameters.DatasetLikeObject(get_file_name: Callable, state: galaxy.schema.schema.DatasetState, extension: str, name: str, dbkey: str | NoneType, datatype: galaxy.datatypes.data.Data)[source]

Bases: object

get_file_name: Callable

state: DatasetState

extension: str

name: str

dbkey: str | None

datatype: Data

__init__(get_file_name: Callable, state: DatasetState, extension: str, name: str, dbkey: str | None, datatype: Data) → None

class galaxy.datatypes.display_applications.parameters.DisplayApplicationDataParameter(elem, link)[source]

Bases: DisplayApplicationParameter

Parameter that returns a file_name containing the requested content

type: str | None = 'data'

__init__(elem, link)[source]

property datatypes_registry: Registry

property formats

get_value(other_values, dataset_hash, user_hash, trans)[source]

prepare(other_values, dataset_hash, user_hash, trans)[source]

is_preparing(other_values)[source]

ready(other_values)[source]

class galaxy.datatypes.display_applications.parameters.DisplayApplicationTemplateParameter(elem, link)[source]

Bases: DisplayApplicationParameter

Parameter that returns a string containing the requested content

type: str | None = 'template'

__init__(elem, link)[source]

get_value(other_values, dataset_hash, user_hash, trans)[source]

class galaxy.datatypes.display_applications.parameters.DisplayParameterValueWrapper(value, parameter, other_values, dataset_hash, user_hash, trans)[source]

Bases: object

ACTION_NAME = 'param'

__init__(value, parameter, other_values, dataset_hash, user_hash, trans)[source]

mime_type(action_param_extra=None)[source]

property url

property action_name

property qp

class galaxy.datatypes.display_applications.parameters.DisplayDataValueWrapper(value, parameter, other_values, dataset_hash, user_hash, trans)[source]

Bases: DisplayParameterValueWrapper

ACTION_NAME = 'data'

mime_type(action_param_extra=None)[source]

property action_name

property qp

galaxy.datatypes.display_applications.util module

galaxy.datatypes.display_applications.util.encode_dataset_user(trans, dataset, user)[source]

galaxy.datatypes.display_applications.util.decode_dataset_user(trans, dataset_hash, user_hash)[source]