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galaxy.schema package¶

class galaxy.schema.BootstrapAdminUser(*, email: str = None, preferences: Dict[str, str] = {}, id: int = 0, bootstrap_admin_user: bool = True)[source]¶

Bases: pydantic.main.BaseModel

email: Optional[str]¶

preferences: Dict[str, str]¶

all_roles() → list [source]¶

class galaxy.schema.FilterQueryParams(*, q: Optional[Union[str, List[str]]] = None, qv: Optional[Union[str, List[str]]] = None, offset: galaxy.schema.ConstrainedIntValue = 0, limit: galaxy.schema.ConstrainedIntValue = None, order: str = None)[source]¶

Bases: pydantic.main.BaseModel

q: Optional[Union[str, List[str]]]¶

qv: Optional[Union[str, List[str]]]¶

offset: Optional[int]¶

limit: Optional[int]¶

order: Optional[str]¶

Submodules¶

galaxy.schema.fields module¶

class galaxy.schema.fields.EncodedDatabaseIdField[source]¶

Bases: str

Encoded Database ID validation.

classmethod validate(v)[source]¶

galaxy.schema.fields.ModelClassField(class_name: str) → str [source]¶: Represents a database model class name annotated as a constant pydantic Field. :param class_name: The name of the database class. :return: A constant pydantic Field with default annotations for model classes.

galaxy.schema.fields.OrderParamField(default_order: str) → Optional[str][source]¶

galaxy.schema.fields.optional(*fields)[source]¶: Decorator function used to modify a pydantic model’s fields to all be optional. Alternatively, you can also pass the field names that should be made optional as arguments to the decorator. Taken from https://github.com/samuelcolvin/pydantic/issues/1223#issuecomment-775363074

galaxy.schema.schema module¶

This module contains general pydantic models and common schema field annotations for them.

class galaxy.schema.schema.Model[source]¶

Bases: pydantic.main.BaseModel

Base model definition with common configuration used by all derived models.

class Config[source]¶

Bases: object

use_enum_values = True¶

allow_population_by_field_name = True¶

class galaxy.schema.schema.UserModel(*, id: galaxy.schema.fields.EncodedDatabaseIdField, username: str, email: str, active: bool, deleted: bool, last_password_change: datetime.datetime, model_class: str = 'User')[source]¶

Bases: galaxy.schema.schema.Model

User in a transaction context.

id: galaxy.schema.fields.EncodedDatabaseIdField¶

username: str¶

email: str¶

active: bool¶

deleted: bool¶

last_password_change: datetime.datetime¶

model_class: str¶

class galaxy.schema.schema.GroupModel(*, model_class: str = 'Group', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str)[source]¶

Bases: pydantic.main.BaseModel

User group model

model_class: str¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

class galaxy.schema.schema.JobSourceType(value)[source]¶

Bases: str, enum.Enum

Available types of job sources (model classes) that produce dataset collections.

Job = 'Job'¶

ImplicitCollectionJobs = 'ImplicitCollectionJobs'¶

WorkflowInvocation = 'WorkflowInvocation'¶

class galaxy.schema.schema.HistoryContentType(value)[source]¶

Bases: str, enum.Enum

Available types of History contents.

dataset = 'dataset'¶

dataset_collection = 'dataset_collection'¶

class galaxy.schema.schema.HistoryImportArchiveSourceType(value)[source]¶

Bases: str, enum.Enum

Available types of History archive sources.

url = 'url'¶

file = 'file'¶

class galaxy.schema.schema.DCEType(value)[source]¶

Bases: str, enum.Enum

Available types of dataset collection elements.

hda = 'hda'¶

dataset_collection = 'dataset_collection'¶

class galaxy.schema.schema.DatasetSourceType(value)[source]¶

Bases: str, enum.Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

class galaxy.schema.schema.ColletionSourceType(value)[source]¶

Bases: str, enum.Enum

An enumeration.

hda = 'hda'¶

ldda = 'ldda'¶

hdca = 'hdca'¶

new_collection = 'new_collection'¶

class galaxy.schema.schema.HistoryContentSource(value)[source]¶

Bases: str, enum.Enum

An enumeration.

hda = 'hda'¶

hdca = 'hdca'¶

library = 'library'¶

library_folder = 'library_folder'¶

new_collection = 'new_collection'¶

class galaxy.schema.schema.TagCollection(*, __root__: List[str])[source]¶

Bases: galaxy.schema.schema.Model

Represents the collection of tags associated with an item.

class galaxy.schema.schema.MetadataFile(*, file_type: str, download_url: str)[source]¶

Bases: galaxy.schema.schema.Model

Metadata file associated with a dataset.

file_type: str¶

download_url: str¶

class galaxy.schema.schema.DatasetPermissions(*, manage: List[galaxy.schema.fields.EncodedDatabaseIdField] = [], access: List[galaxy.schema.fields.EncodedDatabaseIdField] = [])[source]¶

Bases: galaxy.schema.schema.Model

Role-based permissions for accessing and managing a dataset.

manage: List[galaxy.schema.fields.EncodedDatabaseIdField]¶

access: List[galaxy.schema.fields.EncodedDatabaseIdField]¶

class galaxy.schema.schema.Hyperlink(*, target: str, href: pydantic.networks.AnyUrl, text: str)[source]¶

Bases: galaxy.schema.schema.Model

Represents some text with an Hyperlink.

target: str¶

href: pydantic.networks.AnyUrl¶

text: str¶

class galaxy.schema.schema.DisplayApp(*, label: str, links: List[galaxy.schema.schema.Hyperlink])[source]¶

Bases: galaxy.schema.schema.Model

Basic linked information about an application that can display certain datatypes.

label: str¶

links: List[galaxy.schema.schema.Hyperlink]¶

class galaxy.schema.schema.Visualization(**extra_data: Any)[source]¶

Bases: galaxy.schema.schema.Model

class Config[source]¶

Bases: object

extra = 'allow'¶

class galaxy.schema.schema.HistoryItemBase(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool)[source]¶

Bases: galaxy.schema.schema.Model

Basic information provided by items contained in a History.

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

history_id: galaxy.schema.fields.EncodedDatabaseIdField¶

hid: int¶

history_content_type: galaxy.schema.schema.HistoryContentType¶

deleted: bool¶

visible: bool¶

class galaxy.schema.schema.HistoryItemCommon(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str, create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection)[source]¶

Bases: galaxy.schema.schema.HistoryItemBase

Common information provided by items contained in a History.

type_id: str¶

type: str¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

url: str¶

tags: galaxy.schema.schema.TagCollection¶

class galaxy.schema.schema.HDASummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str, create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, dataset_id: galaxy.schema.fields.EncodedDatabaseIdField, state: galaxy.model.Dataset.states, extension: str, purged: bool)[source]¶

Bases: galaxy.schema.schema.HistoryItemCommon

History Dataset Association summary information.

dataset_id: galaxy.schema.fields.EncodedDatabaseIdField¶

state: galaxy.model.Dataset.states¶

extension: str¶

purged: bool¶

class galaxy.schema.schema.HDAInaccessible(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, accessible: bool, state: galaxy.model.Dataset.states)[source]¶

Bases: galaxy.schema.schema.HistoryItemBase

History Dataset Association information when the user can not access it.

accessible: bool¶

state: galaxy.model.Dataset.states¶

class galaxy.schema.schema.HDADetailed(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'file', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, dataset_id: galaxy.schema.fields.EncodedDatabaseIdField, state: galaxy.model.Dataset.states, extension: str, purged: bool, model_class: str = 'HistoryDatasetAssociation', hda_ldda: galaxy.schema.schema.DatasetSourceType = <DatasetSourceType.hda: 'hda'>, accessible: bool, genome_build: str = '?', misc_info: str, misc_blurb: str, file_ext: str, file_size: int, resubmitted: bool, metadata: Any, meta_files: List[galaxy.schema.schema.MetadataFile] = [], data_type: str, peek: str, creating_job: str, rerunnable: bool, uuid: pydantic.types.UUID4, permissions: galaxy.schema.schema.DatasetPermissions, file_name: pydantic.types.FilePath, display_apps: List[galaxy.schema.schema.DisplayApp] = [], display_types: List[galaxy.schema.schema.DisplayApp] = [], visualizations: List[galaxy.schema.schema.Visualization] = [], validated_state: galaxy.model.DatasetInstance.validated_states, validated_state_message: str, annotation: str, download_url: str, api_type: str = 'file', created_from_basename: str = None)[source]¶

Bases: galaxy.schema.schema.HDASummary

History Dataset Association detailed information.

model_class: str¶

hda_ldda: galaxy.schema.schema.DatasetSourceType¶

accessible: bool¶

genome_build: Optional[str]¶

misc_info: str¶

misc_blurb: str¶

file_ext: str¶

file_size: int¶

resubmitted: bool¶

metadata: Any¶

meta_files: List[galaxy.schema.schema.MetadataFile]¶

data_type: str¶

peek: str¶

creating_job: str¶

rerunnable: bool¶

uuid: pydantic.types.UUID4¶

permissions: galaxy.schema.schema.DatasetPermissions¶

file_name: pydantic.types.FilePath¶

display_apps: List[galaxy.schema.schema.DisplayApp]¶

display_types: List[galaxy.schema.schema.DisplayApp]¶

visualizations: List[galaxy.schema.schema.Visualization]¶

validated_state: galaxy.model.DatasetInstance.validated_states¶

validated_state_message: Optional[str]¶

annotation: Optional[str]¶

download_url: str¶

type: str¶

api_type: str¶

created_from_basename: Optional[str]¶

class galaxy.schema.schema.HDAExtended(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'file', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, dataset_id: galaxy.schema.fields.EncodedDatabaseIdField, state: galaxy.model.Dataset.states, extension: str, purged: bool, model_class: str = 'HistoryDatasetAssociation', hda_ldda: galaxy.schema.schema.DatasetSourceType = <DatasetSourceType.hda: 'hda'>, accessible: bool, genome_build: str = '?', misc_info: str, misc_blurb: str, file_ext: str, file_size: int, resubmitted: bool, metadata: Any, meta_files: List[galaxy.schema.schema.MetadataFile] = [], data_type: str, peek: str, creating_job: str, rerunnable: bool, uuid: pydantic.types.UUID4, permissions: galaxy.schema.schema.DatasetPermissions, file_name: pydantic.types.FilePath, display_apps: List[galaxy.schema.schema.DisplayApp] = [], display_types: List[galaxy.schema.schema.DisplayApp] = [], visualizations: List[galaxy.schema.schema.Visualization] = [], validated_state: galaxy.model.DatasetInstance.validated_states, validated_state_message: str, annotation: str, download_url: str, api_type: str = 'file', created_from_basename: str = None, tool_version: str, parent_id: galaxy.schema.fields.EncodedDatabaseIdField = None, designation: str = None)[source]¶

Bases: galaxy.schema.schema.HDADetailed

History Dataset Association extended information.

tool_version: str¶

parent_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

designation: Optional[str]¶

class galaxy.schema.schema.HDABeta(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'file', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, dataset_id: galaxy.schema.fields.EncodedDatabaseIdField, state: galaxy.model.Dataset.states, extension: str, purged: bool, model_class: str = 'HistoryDatasetAssociation', hda_ldda: galaxy.schema.schema.DatasetSourceType = <DatasetSourceType.hda: 'hda'>, accessible: bool, genome_build: str = '?', misc_info: str, misc_blurb: str, file_ext: str, file_size: int, resubmitted: bool, metadata: Any, meta_files: List[galaxy.schema.schema.MetadataFile] = [], data_type: str, peek: str, creating_job: str, rerunnable: bool, uuid: pydantic.types.UUID4, permissions: galaxy.schema.schema.DatasetPermissions, file_name: pydantic.types.FilePath, display_apps: List[galaxy.schema.schema.DisplayApp] = [], display_types: List[galaxy.schema.schema.DisplayApp] = [], visualizations: List[galaxy.schema.schema.Visualization] = [], validated_state: galaxy.model.DatasetInstance.validated_states, validated_state_message: str, annotation: str, download_url: str, api_type: str = 'file', created_from_basename: str = None)[source]¶

Bases: galaxy.schema.schema.HDADetailed

History Dataset Association information used in the new Beta History.

model_class: str¶

hda_ldda: galaxy.schema.schema.DatasetSourceType¶

accessible: bool¶

genome_build: Optional[str]¶

misc_info: str¶

misc_blurb: str¶

file_ext: str¶

file_size: int¶

resubmitted: bool¶

metadata: Any¶

meta_files: List[galaxy.schema.schema.MetadataFile]¶

data_type: str¶

peek: str¶

creating_job: str¶

rerunnable: bool¶

uuid: pydantic.types.UUID4¶

permissions: galaxy.schema.schema.DatasetPermissions¶

file_name: pydantic.types.FilePath¶

display_apps: List[galaxy.schema.schema.DisplayApp]¶

display_types: List[galaxy.schema.schema.DisplayApp]¶

visualizations: List[galaxy.schema.schema.Visualization]¶

validated_state: galaxy.model.DatasetInstance.validated_states¶

validated_state_message: Optional[str]¶

annotation: Optional[str]¶

download_url: str¶

type: str¶

api_type: str¶

created_from_basename: Optional[str]¶

dataset_id: galaxy.schema.fields.EncodedDatabaseIdField¶

state: galaxy.model.Dataset.states¶

extension: str¶

purged: bool¶

type_id: str¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

url: str¶

tags: galaxy.schema.schema.TagCollection¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

history_id: galaxy.schema.fields.EncodedDatabaseIdField¶

hid: int¶

history_content_type: galaxy.schema.schema.HistoryContentType¶

deleted: bool¶

visible: bool¶

class galaxy.schema.schema.UpdateHDAPayload(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'file', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, dataset_id: galaxy.schema.fields.EncodedDatabaseIdField, state: galaxy.model.Dataset.states, extension: str, purged: bool, model_class: str = 'HistoryDatasetAssociation', hda_ldda: galaxy.schema.schema.DatasetSourceType = <DatasetSourceType.hda: 'hda'>, accessible: bool, genome_build: str = '?', misc_info: str, misc_blurb: str, file_ext: str, file_size: int, resubmitted: bool, metadata: Any, meta_files: List[galaxy.schema.schema.MetadataFile] = [], data_type: str, peek: str, creating_job: str, rerunnable: bool, uuid: pydantic.types.UUID4, permissions: galaxy.schema.schema.DatasetPermissions, file_name: pydantic.types.FilePath, display_apps: List[galaxy.schema.schema.DisplayApp] = [], display_types: List[galaxy.schema.schema.DisplayApp] = [], visualizations: List[galaxy.schema.schema.Visualization] = [], validated_state: galaxy.model.DatasetInstance.validated_states, validated_state_message: str, annotation: str, download_url: str, api_type: str = 'file', created_from_basename: str = None)[source]¶

Bases: galaxy.schema.schema.HDABeta

Used for updating a particular HDA. All fields are optional.

model_class: str¶

hda_ldda: galaxy.schema.schema.DatasetSourceType¶

accessible: bool¶

genome_build: Optional[str]¶

misc_info: str¶

misc_blurb: str¶

file_ext: str¶

file_size: int¶

resubmitted: bool¶

metadata: Any¶

meta_files: List[galaxy.schema.schema.MetadataFile]¶

data_type: str¶

peek: str¶

creating_job: str¶

rerunnable: bool¶

uuid: pydantic.types.UUID4¶

permissions: galaxy.schema.schema.DatasetPermissions¶

file_name: pydantic.types.FilePath¶

display_apps: List[galaxy.schema.schema.DisplayApp]¶

display_types: List[galaxy.schema.schema.DisplayApp]¶

visualizations: List[galaxy.schema.schema.Visualization]¶

validated_state: galaxy.model.DatasetInstance.validated_states¶

validated_state_message: Optional[str]¶

annotation: Optional[str]¶

download_url: str¶

type: str¶

api_type: str¶

created_from_basename: Optional[str]¶

dataset_id: galaxy.schema.fields.EncodedDatabaseIdField¶

state: galaxy.model.Dataset.states¶

extension: str¶

purged: bool¶

type_id: str¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

url: str¶

tags: galaxy.schema.schema.TagCollection¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

history_id: galaxy.schema.fields.EncodedDatabaseIdField¶

hid: int¶

history_content_type: galaxy.schema.schema.HistoryContentType¶

deleted: bool¶

visible: bool¶

class galaxy.schema.schema.DCSummary(*, model_class: str = 'DatasetCollection', id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, update_time: datetime.datetime, collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None)[source]¶

Bases: galaxy.schema.schema.Model

Dataset Collection summary information.

model_class: str¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

collection_type: str¶

populated_state: galaxy.model.DatasetCollection.populated_states¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

class galaxy.schema.schema.DCESummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'DatasetCollectionElement', element_index: int, element_identifier: str, element_type: galaxy.schema.schema.DCEType, object: Union[galaxy.schema.schema.HDASummary, galaxy.schema.schema.DCSummary])[source]¶

Bases: galaxy.schema.schema.Model

Dataset Collection Element summary information.

id: galaxy.schema.fields.EncodedDatabaseIdField¶

model_class: str¶

element_index: int¶

element_identifier: str¶

element_type: galaxy.schema.schema.DCEType¶

object: Union[galaxy.schema.schema.HDASummary, galaxy.schema.schema.DCSummary]¶

class galaxy.schema.schema.DCDetailed(*, model_class: str = 'DatasetCollection', id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, update_time: datetime.datetime, collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None, populated: bool, elements: List[galaxy.schema.schema.DCESummary] = [])[source]¶

Bases: galaxy.schema.schema.DCSummary

Dataset Collection detailed information.

populated: bool¶

elements: List[galaxy.schema.schema.DCESummary]¶

class galaxy.schema.schema.HDCASummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'collection', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, model_class: str = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None, job_source_id: galaxy.schema.fields.EncodedDatabaseIdField = None, job_source_type: galaxy.schema.schema.JobSourceType = None, contents_url: str)[source]¶

Bases: galaxy.schema.schema.HistoryItemCommon

History Dataset Collection Association summary information.

model_class: str¶

type: str¶

collection_type: str¶

populated_state: galaxy.model.DatasetCollection.populated_states¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

job_source_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

job_source_type: Optional[galaxy.schema.schema.JobSourceType]¶

contents_url: str¶

class galaxy.schema.schema.HDCADetailed(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'collection', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, model_class: str = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None, job_source_id: galaxy.schema.fields.EncodedDatabaseIdField = None, job_source_type: galaxy.schema.schema.JobSourceType = None, contents_url: str, populated: bool, elements: List[galaxy.schema.schema.DCESummary] = [])[source]¶

Bases: galaxy.schema.schema.HDCASummary

History Dataset Collection Association detailed information.

populated: bool¶

elements: List[galaxy.schema.schema.DCESummary]¶

class galaxy.schema.schema.UpdateHDCAPayload(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'collection', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, model_class: str = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None, job_source_id: galaxy.schema.fields.EncodedDatabaseIdField = None, job_source_type: galaxy.schema.schema.JobSourceType = None, contents_url: str, populated: bool, elements: List[galaxy.schema.schema.DCESummary] = [])[source]¶

Bases: galaxy.schema.schema.HDCADetailed

Used for updating a particular HDCA. All fields are optional.

populated: bool¶

elements: List[galaxy.schema.schema.DCESummary]¶

model_class: str¶

type: str¶

collection_type: str¶

populated_state: galaxy.model.DatasetCollection.populated_states¶

populated_state_message: Optional[str]¶

element_count: Optional[int]¶

job_source_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

job_source_type: Optional[galaxy.schema.schema.JobSourceType]¶

contents_url: str¶

type_id: str¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

url: str¶

tags: galaxy.schema.schema.TagCollection¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

history_id: galaxy.schema.fields.EncodedDatabaseIdField¶

hid: int¶

history_content_type: galaxy.schema.schema.HistoryContentType¶

deleted: bool¶

visible: bool¶

class galaxy.schema.schema.UpdateHistoryContentsBatchPayload(*, items: List[Union[galaxy.schema.schema.UpdateHDAPayload, galaxy.schema.schema.UpdateHDCAPayload]], deleted: bool = None, visible: bool = None, **extra_data: Any)[source]¶

Bases: pydantic.main.BaseModel

class Config[source]¶

Bases: object

use_enum_values = True¶

allow_population_by_field_name = True¶

extra = 'allow'¶

items: List[Union[galaxy.schema.schema.UpdateHDAPayload, galaxy.schema.schema.UpdateHDCAPayload]]¶

deleted: Optional[bool]¶

visible: Optional[bool]¶

class galaxy.schema.schema.HistoryBase(**extra_data: Any)[source]¶

Bases: pydantic.main.BaseModel

Provides basic configuration for all the History models.

class Config[source]¶

Bases: object

use_enum_values = True¶

extra = 'allow'¶

class galaxy.schema.schema.HistorySummary(*, model_class: str = 'History', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, deleted: bool, purged: bool, url: str, published: bool, annotation: str, tags: galaxy.schema.schema.TagCollection, **extra_data: Any)[source]¶

Bases: galaxy.schema.schema.HistoryBase

History summary information.

model_class: str¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

deleted: bool¶

purged: bool¶

url: str¶

published: bool¶

annotation: Optional[str]¶

tags: galaxy.schema.schema.TagCollection¶

class galaxy.schema.schema.HistoryActiveContentCounts(*, active: int, hidden: int, deleted: int)[source]¶

Bases: galaxy.schema.schema.Model

Contains the number of active, deleted or hidden items in a History.

active: int¶

hidden: int¶

deleted: int¶

class galaxy.schema.schema.HistoryDetailed(*, model_class: str = 'History', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, deleted: bool, purged: bool, url: str, published: bool, annotation: str, tags: galaxy.schema.schema.TagCollection, contents_url: str, size: int, user_id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, update_time: datetime.datetime, importable: bool, slug: str = None, username_and_slug: str = None, genome_build: str = '?', state: galaxy.model.Dataset.states, state_ids: Dict[galaxy.model.Dataset.states, List[galaxy.schema.fields.EncodedDatabaseIdField]], state_details: Dict[galaxy.model.Dataset.states, int], **extra_data: Any)[source]¶

Bases: galaxy.schema.schema.HistorySummary

History detailed information.

contents_url: str¶

size: int¶

user_id: galaxy.schema.fields.EncodedDatabaseIdField¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

importable: bool¶

slug: Optional[str]¶

username_and_slug: Optional[str]¶

genome_build: Optional[str]¶

state: galaxy.model.Dataset.states¶

state_ids: Dict[galaxy.model.Dataset.states, List[galaxy.schema.fields.EncodedDatabaseIdField]]¶

state_details: Dict[galaxy.model.Dataset.states, int]¶

class galaxy.schema.schema.HistoryBeta(*, model_class: str = 'History', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, deleted: bool, purged: bool, url: str, published: bool, annotation: str, tags: galaxy.schema.schema.TagCollection, contents_url: str, size: int, user_id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, update_time: datetime.datetime, importable: bool, slug: str = None, username_and_slug: str = None, genome_build: str = '?', state: galaxy.model.Dataset.states, state_ids: Dict[galaxy.model.Dataset.states, List[galaxy.schema.fields.EncodedDatabaseIdField]], state_details: Dict[galaxy.model.Dataset.states, int], empty: bool, nice_size: str, hid_counter: int, contents_active: galaxy.schema.schema.HistoryActiveContentCounts, **extra_data: Any)[source]¶

Bases: galaxy.schema.schema.HistoryDetailed

History detailed information used in the new Beta History.

annotation: Optional[str]¶

empty: bool¶

nice_size: str¶

purged: bool¶

tags: galaxy.schema.schema.TagCollection¶

hid_counter: int¶

contents_active: galaxy.schema.schema.HistoryActiveContentCounts¶

class galaxy.schema.schema.ExportHistoryArchivePayload(*, gzip: bool = True, include_hidden: bool = False, include_deleted: bool = False, file_name: str = None, directory_uri: str = None, force: bool = None)[source]¶

Bases: galaxy.schema.schema.Model

gzip: Optional[bool]¶

include_hidden: Optional[bool]¶

include_deleted: Optional[bool]¶

file_name: Optional[str]¶

directory_uri: Optional[str]¶

force: Optional[bool]¶

class galaxy.schema.schema.CreateHistoryPayload(*, name: str = None, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, all_datasets: bool = True, archive_source: str = None, archive_type: galaxy.schema.schema.HistoryImportArchiveSourceType = <HistoryImportArchiveSourceType.url: 'url'>, archive_file: Any = None)[source]¶

Bases: galaxy.schema.schema.Model

name: Optional[str]¶

history_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

all_datasets: Optional[bool]¶

archive_source: Optional[str]¶

archive_type: Optional[galaxy.schema.schema.HistoryImportArchiveSourceType]¶

archive_file: Optional[Any]¶

class galaxy.schema.schema.JobExportHistoryArchive(*, id: galaxy.schema.fields.EncodedDatabaseIdField, job_id: galaxy.schema.fields.EncodedDatabaseIdField, ready: bool, preparing: bool, up_to_date: bool, download_url: str, external_download_latest_url: pydantic.networks.AnyUrl, external_download_permanent_url: pydantic.networks.AnyUrl)[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

job_id: galaxy.schema.fields.EncodedDatabaseIdField¶

ready: bool¶

preparing: bool¶

up_to_date: bool¶

download_url: str¶

external_download_latest_url: pydantic.networks.AnyUrl¶

external_download_permanent_url: pydantic.networks.AnyUrl¶

class galaxy.schema.schema.LabelValuePair(*, label: str, value: str)[source]¶

Bases: pydantic.main.BaseModel

Generic Label/Value pair model.

label: str¶

value: str¶

class galaxy.schema.schema.CustomBuildsMetadataResponse(*, installed_builds: List[galaxy.schema.schema.LabelValuePair], fasta_hdas: List[galaxy.schema.schema.LabelValuePair])[source]¶

Bases: pydantic.main.BaseModel

installed_builds: List[galaxy.schema.schema.LabelValuePair]¶

fasta_hdas: List[galaxy.schema.schema.LabelValuePair]¶

class galaxy.schema.schema.JobIdResponse(*, job_id: galaxy.schema.fields.EncodedDatabaseIdField)[source]¶

Bases: pydantic.main.BaseModel

Contains the ID of the job associated with a particular request.

job_id: galaxy.schema.fields.EncodedDatabaseIdField¶

class galaxy.schema.schema.HDCJobStateSummary(*, all_jobs: int = 0, new: int = 0, waiting: int = 0, running: int = 0, error: int = 0, paused: int = 0, deleted_new: int = 0, resubmitted: int = 0, queued: int = 0, ok: int = 0, failed: int = 0, deleted: int = 0, upload: int = 0)[source]¶

Bases: galaxy.schema.schema.Model

Overview of the job states working inside a dataset collection.

all_jobs: int¶

new: int¶

waiting: int¶

running: int¶

error: int¶

paused: int¶

deleted_new: int¶

resubmitted: int¶

queued: int¶

ok: int¶

failed: int¶

deleted: int¶

upload: int¶

class galaxy.schema.schema.HDCABeta(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField, hid: int, history_content_type: galaxy.schema.schema.HistoryContentType, deleted: bool, visible: bool, type_id: str, type: str = 'collection', create_time: datetime.datetime, update_time: datetime.datetime, url: str, tags: galaxy.schema.schema.TagCollection, model_class: str = 'HistoryDatasetCollectionAssociation', collection_type: str, populated_state: galaxy.model.DatasetCollection.populated_states, populated_state_message: str = None, element_count: int = None, job_source_id: galaxy.schema.fields.EncodedDatabaseIdField = None, job_source_type: galaxy.schema.schema.JobSourceType = None, contents_url: str, populated: bool, elements: List[galaxy.schema.schema.DCESummary] = [], collection_id: galaxy.schema.fields.EncodedDatabaseIdField, job_state_summary: galaxy.schema.schema.HDCJobStateSummary = None)[source]¶

Bases: galaxy.schema.schema.HDCADetailed

History Dataset Collection Association information used in the new Beta History.

collection_id: galaxy.schema.fields.EncodedDatabaseIdField¶

job_state_summary: Optional[galaxy.schema.schema.HDCJobStateSummary]¶

class galaxy.schema.schema.JobBaseModel(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, state: galaxy.model.Job.states, exit_code: int = None, create_time: datetime.datetime, update_time: datetime.datetime, galaxy_version: str)[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

model_class: str¶

tool_id: str¶

history_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

state: galaxy.model.Job.states¶

exit_code: Optional[int]¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

galaxy_version: str¶

class galaxy.schema.schema.JobImportHistoryResponse(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, state: galaxy.model.Job.states, exit_code: int = None, create_time: datetime.datetime, update_time: datetime.datetime, galaxy_version: str, message: str)[source]¶

Bases: galaxy.schema.schema.JobBaseModel

message: str¶

class galaxy.schema.schema.JobStateSummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model: str = 'Job', populated_state: galaxy.model.DatasetCollection.populated_states, states: Dict[galaxy.model.Job.states, int] = {})[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

model: str¶

populated_state: galaxy.model.DatasetCollection.populated_states¶

states: Dict[galaxy.model.Job.states, int]¶

class galaxy.schema.schema.ImplicitCollectionJobsStateSummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model: str = 'ImplicitCollectionJobs', populated_state: galaxy.model.DatasetCollection.populated_states, states: Dict[galaxy.model.Job.states, int] = {})[source]¶

Bases: galaxy.schema.schema.JobStateSummary

model: str¶

class galaxy.schema.schema.WorkflowInvocationStateSummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model: str = 'WorkflowInvocation', populated_state: galaxy.model.DatasetCollection.populated_states, states: Dict[galaxy.model.Job.states, int] = {})[source]¶

Bases: galaxy.schema.schema.JobStateSummary

model: str¶

class galaxy.schema.schema.JobSummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, state: galaxy.model.Job.states, exit_code: int = None, create_time: datetime.datetime, update_time: datetime.datetime, galaxy_version: str, external_id: str = None, command_line: str = None, user_email: str = None)[source]¶

Bases: galaxy.schema.schema.JobBaseModel

Basic information about a job.

external_id: Optional[str]¶

command_line: Optional[str]¶

user_email: Optional[str]¶

class galaxy.schema.schema.DatasetJobInfo(*, id: galaxy.schema.fields.EncodedDatabaseIdField, src: galaxy.schema.schema.DatasetSourceType, uuid: pydantic.types.UUID4)[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

src: galaxy.schema.schema.DatasetSourceType¶

uuid: pydantic.types.UUID4¶

class galaxy.schema.schema.JobDetails(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, state: galaxy.model.Job.states, exit_code: int = None, create_time: datetime.datetime, update_time: datetime.datetime, galaxy_version: str, external_id: str = None, command_line: str = None, user_email: str = None, command_version: str, params: Any, inputs: Dict[str, galaxy.schema.schema.DatasetJobInfo] = {}, outputs: Dict[str, galaxy.schema.schema.DatasetJobInfo] = {})[source]¶

Bases: galaxy.schema.schema.JobSummary

command_version: str¶

params: Any¶

inputs: Dict[str, galaxy.schema.schema.DatasetJobInfo]¶

outputs: Dict[str, galaxy.schema.schema.DatasetJobInfo]¶

class galaxy.schema.schema.JobMetric(*, title: str, value: str, plugin: str, name: str, raw_value: str)[source]¶

Bases: galaxy.schema.schema.Model

title: str¶

value: str¶

plugin: str¶

name: str¶

raw_value: str¶

class Config[source]¶

Bases: object

schema_extra = {'example': {'name': 'start_epoch', 'plugin': 'core', 'raw_value': '1614261340.0000000', 'title': 'Job Start Time', 'value': '2021-02-25 14:55:40'}}¶

class galaxy.schema.schema.JobMetricCollection(*, __root__: List[galaxy.schema.schema.JobMetric] = [])[source]¶

Bases: galaxy.schema.schema.Model

Represents a collection of metrics associated with a Job.

class galaxy.schema.schema.JobFullDetails(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'Job', tool_id: str, history_id: galaxy.schema.fields.EncodedDatabaseIdField = None, state: galaxy.model.Job.states, exit_code: int = None, create_time: datetime.datetime, update_time: datetime.datetime, galaxy_version: str, external_id: str = None, command_line: str = None, user_email: str = None, command_version: str, params: Any, inputs: Dict[str, galaxy.schema.schema.DatasetJobInfo] = {}, outputs: Dict[str, galaxy.schema.schema.DatasetJobInfo] = {}, tool_stdout: str, tool_stderr: str, job_stdout: str, job_stderr: str, stdout: str, stderr: str, job_messages: List[str], job_metrics: galaxy.schema.schema.JobMetricCollection = None)[source]¶

Bases: galaxy.schema.schema.JobDetails

tool_stdout: str¶

tool_stderr: str¶

job_stdout: str¶

job_stderr: str¶

stdout: str¶

stderr: str¶

job_messages: List[str]¶

job_metrics: Optional[galaxy.schema.schema.JobMetricCollection]¶

class galaxy.schema.schema.StoredWorkflowSummary(*, id: galaxy.schema.fields.EncodedDatabaseIdField, model_class: str = 'StoredWorkflow', create_time: datetime.datetime, update_time: datetime.datetime, name: str, url: str, published: bool, annotations: List[str], tags: galaxy.schema.schema.TagCollection, deleted: bool, hidden: bool, owner: str, latest_workflow_uuid: pydantic.types.UUID4, number_of_steps: int, show_in_tool_panel: bool)[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

model_class: str¶

create_time: datetime.datetime¶

update_time: datetime.datetime¶

name: str¶

url: str¶

published: bool¶

annotations: List[str]¶

tags: galaxy.schema.schema.TagCollection¶

deleted: bool¶

hidden: bool¶

owner: str¶

latest_workflow_uuid: pydantic.types.UUID4¶

number_of_steps: int¶

show_in_tool_panel: bool¶

class galaxy.schema.schema.WorkflowInput(*, label: str, value: str, uuid: pydantic.types.UUID4)[source]¶

Bases: pydantic.main.BaseModel

label: str¶

value: str¶

uuid: pydantic.types.UUID4¶

class galaxy.schema.schema.WorkflowOutput(*, label: str = None, output_name: str, uuid: pydantic.types.UUID4)[source]¶

Bases: pydantic.main.BaseModel

label: Optional[str]¶

output_name: str¶

uuid: Optional[pydantic.types.UUID4]¶

class galaxy.schema.schema.InputStep(*, source_step: int, step_output: str)[source]¶

Bases: pydantic.main.BaseModel

source_step: int¶

step_output: str¶

class galaxy.schema.schema.WorkflowModuleType(value)[source]¶

Bases: str, enum.Enum

Available types of modules that represent a step in a Workflow.

data_input = 'data_input'¶

data_collection_input = 'data_collection_input'¶

parameter_input = 'parameter_input'¶

subworkflow = 'subworkflow'¶

tool = 'tool'¶

pause = 'pause'¶

class galaxy.schema.schema.WorkflowStepBase(*, id: int, type: galaxy.schema.schema.WorkflowModuleType, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep])[source]¶

Bases: pydantic.main.BaseModel

id: int¶

type: galaxy.schema.schema.WorkflowModuleType¶

annotation: Optional[str]¶

input_steps: Dict[str, galaxy.schema.schema.InputStep]¶

class galaxy.schema.schema.ToolBasedWorkflowStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], tool_id: str = None, tool_version: str = None, tool_inputs: Any)[source]¶

Bases: galaxy.schema.schema.WorkflowStepBase

tool_id: Optional[str]¶

tool_version: Optional[str]¶

tool_inputs: Any¶

class galaxy.schema.schema.InputDataStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.data_input: 'data_input'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], tool_id: str = None, tool_version: str = None, tool_inputs: Any)[source]¶

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

type: galaxy.schema.schema.WorkflowModuleType¶

class galaxy.schema.schema.InputDataCollectionStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.data_collection_input: 'data_collection_input'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], tool_id: str = None, tool_version: str = None, tool_inputs: Any)[source]¶

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

type: galaxy.schema.schema.WorkflowModuleType¶

class galaxy.schema.schema.InputParameterStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.parameter_input: 'parameter_input'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], tool_id: str = None, tool_version: str = None, tool_inputs: Any)[source]¶

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

type: galaxy.schema.schema.WorkflowModuleType¶

class galaxy.schema.schema.PauseStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.pause: 'pause'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep])[source]¶

Bases: galaxy.schema.schema.WorkflowStepBase

type: galaxy.schema.schema.WorkflowModuleType¶

class galaxy.schema.schema.ToolStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.tool: 'tool'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], tool_id: str = None, tool_version: str = None, tool_inputs: Any)[source]¶

Bases: galaxy.schema.schema.ToolBasedWorkflowStep

type: galaxy.schema.schema.WorkflowModuleType¶

class galaxy.schema.schema.SubworkflowStep(*, id: int, type: galaxy.schema.schema.WorkflowModuleType = <WorkflowModuleType.subworkflow: 'subworkflow'>, annotation: str, input_steps: Dict[str, galaxy.schema.schema.InputStep], workflow_id: galaxy.schema.fields.EncodedDatabaseIdField)[source]¶

Bases: galaxy.schema.schema.WorkflowStepBase

type: galaxy.schema.schema.WorkflowModuleType¶

workflow_id: galaxy.schema.fields.EncodedDatabaseIdField¶

class galaxy.schema.schema.Creator(*, class: str, name: str, address: str = None, alternateName: str = None, email: str = None, faxNumber: str = None, identifier: str = None, image: pydantic.networks.AnyHttpUrl = None, telephone: str = None, url: pydantic.networks.AnyHttpUrl = None)[source]¶

Bases: pydantic.main.BaseModel

class_: str¶

name: str¶

address: Optional[str]¶

alternate_name: Optional[str]¶

email: Optional[str]¶

fax_number: Optional[str]¶

identifier: Optional[str]¶

image: Optional[pydantic.networks.AnyHttpUrl]¶

telephone: Optional[str]¶

url: Optional[pydantic.networks.AnyHttpUrl]¶

class galaxy.schema.schema.Organization(*, class: str = 'Organization', name: str, address: str = None, alternateName: str = None, email: str = None, faxNumber: str = None, identifier: str = None, image: pydantic.networks.AnyHttpUrl = None, telephone: str = None, url: pydantic.networks.AnyHttpUrl = None)[source]¶

Bases: galaxy.schema.schema.Creator

class_: str¶

class galaxy.schema.schema.Person(*, class: str = 'Person', name: str, address: str = None, alternateName: str = None, email: str = None, faxNumber: str = None, identifier: str = None, image: pydantic.networks.AnyHttpUrl = None, telephone: str = None, url: pydantic.networks.AnyHttpUrl = None, familyName: str = None, givenName: str = None, honorificPrefix: str = None, honorificSuffix: str = None, jobTitle: str = None)[source]¶

Bases: galaxy.schema.schema.Creator

class_: str¶

family_name: Optional[str]¶

givenName: Optional[str]¶

honorific_prefix: Optional[str]¶

honorific_suffix: Optional[str]¶

job_title: Optional[str]¶

Bases: galaxy.schema.schema.StoredWorkflowSummary

annotation: Optional[str]¶

license: Optional[str]¶

version: int¶

inputs: Dict[int, galaxy.schema.schema.WorkflowInput]¶

creator: Optional[List[Union[galaxy.schema.schema.Person, galaxy.schema.schema.Organization]]]¶

steps: Dict[int, Union[galaxy.schema.schema.InputDataStep, galaxy.schema.schema.InputDataCollectionStep, galaxy.schema.schema.InputParameterStep, galaxy.schema.schema.PauseStep, galaxy.schema.schema.ToolStep, galaxy.schema.schema.SubworkflowStep]]¶

class galaxy.schema.schema.Input(*, name: str, description: str)[source]¶

Bases: pydantic.main.BaseModel

name: str¶

description: str¶

class galaxy.schema.schema.Output(*, name: str, type: str)[source]¶

Bases: pydantic.main.BaseModel

name: str¶

type: str¶

class galaxy.schema.schema.InputConnection(*, id: int, output_name: str, input_subworkflow_step_id: int = None)[source]¶

Bases: pydantic.main.BaseModel

id: int¶

output_name: str¶

input_subworkflow_step_id: Optional[int]¶

class galaxy.schema.schema.WorkflowStepLayoutPosition(*, bottom: int, top: int, left: int, right: int, x: int, y: int, height: int, width: int)[source]¶

Bases: pydantic.main.BaseModel

Position and dimensions of the workflow step represented by a box on the graph.

bottom: int¶

top: int¶

left: int¶

right: int¶

x: int¶

y: int¶

height: int¶

width: int¶

class galaxy.schema.schema.WorkflowStepToExportBase(*, id: int, type: str, name: str, annotation: str, tool_id: str = None, uuid: pydantic.types.UUID4, label: str = None, inputs: List[galaxy.schema.schema.Input], outputs: List[galaxy.schema.schema.Output], input_connections: Dict[str, galaxy.schema.schema.InputConnection] = {}, position: galaxy.schema.schema.WorkflowStepLayoutPosition, workflow_outputs: List[galaxy.schema.schema.WorkflowOutput] = [])[source]¶

Bases: pydantic.main.BaseModel

id: int¶

type: str¶

name: str¶

annotation: Optional[str]¶

tool_id: Optional[str]¶

uuid: pydantic.types.UUID4¶

label: Optional[str]¶

inputs: List[galaxy.schema.schema.Input]¶

outputs: List[galaxy.schema.schema.Output]¶

input_connections: Dict[str, galaxy.schema.schema.InputConnection]¶

position: galaxy.schema.schema.WorkflowStepLayoutPosition¶

workflow_outputs: List[galaxy.schema.schema.WorkflowOutput]¶

class galaxy.schema.schema.WorkflowStepToExport(*, id: int, type: str, name: str, annotation: str, tool_id: str = None, uuid: pydantic.types.UUID4, label: str = None, inputs: List[galaxy.schema.schema.Input], outputs: List[galaxy.schema.schema.Output], input_connections: Dict[str, galaxy.schema.schema.InputConnection] = {}, position: galaxy.schema.schema.WorkflowStepLayoutPosition, workflow_outputs: List[galaxy.schema.schema.WorkflowOutput] = [], content_id: str = None, tool_version: str = None, tool_state: pydantic.types.Json, errors: str = None)[source]¶

Bases: galaxy.schema.schema.WorkflowStepToExportBase

content_id: Optional[str]¶

tool_version: Optional[str]¶

tool_state: pydantic.types.Json¶

errors: Optional[str]¶

class galaxy.schema.schema.ToolShedRepositorySummary(*, name: str, owner: str, changeset_revision: str, tool_shed: str)[source]¶

Bases: pydantic.main.BaseModel

name: str¶

owner: str¶

changeset_revision: str¶

tool_shed: str¶

class galaxy.schema.schema.PostJobAction(*, action_type: str, output_name: str, action_arguments: Dict[str, Any])[source]¶

Bases: pydantic.main.BaseModel

action_type: str¶

output_name: str¶

action_arguments: Dict[str, Any]¶

class galaxy.schema.schema.WorkflowToolStepToExport(*, id: int, type: str, name: str, annotation: str, tool_id: str = None, uuid: pydantic.types.UUID4, label: str = None, inputs: List[galaxy.schema.schema.Input], outputs: List[galaxy.schema.schema.Output], input_connections: Dict[str, galaxy.schema.schema.InputConnection] = {}, position: galaxy.schema.schema.WorkflowStepLayoutPosition, workflow_outputs: List[galaxy.schema.schema.WorkflowOutput] = [], tool_shed_repository: galaxy.schema.schema.ToolShedRepositorySummary, post_job_actions: Dict[str, galaxy.schema.schema.PostJobAction])[source]¶

Bases: galaxy.schema.schema.WorkflowStepToExportBase

tool_shed_repository: galaxy.schema.schema.ToolShedRepositorySummary¶

post_job_actions: Dict[str, galaxy.schema.schema.PostJobAction]¶

class galaxy.schema.schema.SubworkflowStepToExport(*, id: int, type: str, name: str, annotation: str, tool_id: str = None, uuid: pydantic.types.UUID4, label: str = None, inputs: List[galaxy.schema.schema.Input], outputs: List[galaxy.schema.schema.Output], input_connections: Dict[str, galaxy.schema.schema.InputConnection] = {}, position: galaxy.schema.schema.WorkflowStepLayoutPosition, workflow_outputs: List[galaxy.schema.schema.WorkflowOutput] = [], subworkflow: WorkflowToExport)[source]¶

Bases: galaxy.schema.schema.WorkflowStepToExportBase

subworkflow: galaxy.schema.schema.WorkflowToExport¶

class galaxy.schema.schema.WorkflowToExport(*, a_galaxy_workflow: str = 'true', name: str, annotation: str, tags: galaxy.schema.schema.TagCollection, uuid: pydantic.types.UUID4 = None, creator: List[Union[galaxy.schema.schema.Person, galaxy.schema.schema.Organization]] = None, license: str = None, version: int, steps: Dict[int, Union[galaxy.schema.schema.SubworkflowStepToExport, galaxy.schema.schema.WorkflowToolStepToExport, galaxy.schema.schema.WorkflowStepToExport]] = {}, **extra_data: Any)[source]¶

Bases: pydantic.main.BaseModel

a_galaxy_workflow: str¶

format_version: str¶

name: str¶

annotation: Optional[str]¶

tags: galaxy.schema.schema.TagCollection¶

uuid: Optional[pydantic.types.UUID4]¶

creator: Optional[List[Union[galaxy.schema.schema.Person, galaxy.schema.schema.Organization]]]¶

license: Optional[str]¶

version: int¶

steps: Dict[int, Union[galaxy.schema.schema.SubworkflowStepToExport, galaxy.schema.schema.WorkflowToolStepToExport, galaxy.schema.schema.WorkflowStepToExport]]¶

class galaxy.schema.schema.BasicRoleModel(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, type: str)[source]¶

Bases: pydantic.main.BaseModel

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

type: str¶

class galaxy.schema.schema.RoleModel(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, type: str, description: str = None, url: str, model_class: str = 'Role')[source]¶

Bases: galaxy.schema.schema.BasicRoleModel

description: Optional[str]¶

url: str¶

model_class: str¶

class galaxy.schema.schema.RoleDefinitionModel(*, name: str, description: str, user_ids: List[galaxy.schema.fields.EncodedDatabaseIdField] = [], group_ids: List[galaxy.schema.fields.EncodedDatabaseIdField] = [])[source]¶

Bases: pydantic.main.BaseModel

name: str¶

description: str¶

user_ids: Optional[List[galaxy.schema.fields.EncodedDatabaseIdField]]¶

group_ids: Optional[List[galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.RoleListModel(*, __root__: List[galaxy.schema.schema.RoleModel])[source]¶: Bases: pydantic.main.BaseModel

class galaxy.schema.schema.GroupRoleModel(*, id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, url: str)[source]¶

Bases: pydantic.main.BaseModel

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

url: str¶

class galaxy.schema.schema.GroupRoleListModel(*, __root__: List[galaxy.schema.schema.GroupRoleModel])[source]¶: Bases: pydantic.main.BaseModel

class galaxy.schema.schema.LibraryPermissionScope(value)[source]¶

Bases: str, enum.Enum

An enumeration.

current = 'current'¶

available = 'available'¶

class galaxy.schema.schema.LibraryLegacySummary(*, model_class: str = 'Library', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, description: str = '', synopsis: str = None, root_folder_id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, deleted: bool)[source]¶

Bases: pydantic.main.BaseModel

model_class: str¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

root_folder_id: galaxy.schema.fields.EncodedDatabaseIdField¶

create_time: datetime.datetime¶

deleted: bool¶

class galaxy.schema.schema.LibrarySummary(*, model_class: str = 'Library', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, description: str = '', synopsis: str = None, root_folder_id: galaxy.schema.fields.EncodedDatabaseIdField, create_time: datetime.datetime, deleted: bool, create_time_pretty: str, public: bool, can_user_add: bool, can_user_modify: bool, can_user_manage: bool)[source]¶

Bases: galaxy.schema.schema.LibraryLegacySummary

create_time_pretty: str¶

public: bool¶

can_user_add: bool¶

can_user_modify: bool¶

can_user_manage: bool¶

class galaxy.schema.schema.LibrarySummaryList(*, __root__: List[galaxy.schema.schema.LibrarySummary] = [])[source]¶: Bases: pydantic.main.BaseModel

class galaxy.schema.schema.CreateLibraryPayload(*, name: str, description: str = '', synopsis: str = '')[source]¶

Bases: pydantic.main.BaseModel

name: str¶

description: Optional[str]¶

synopsis: Optional[str]¶

class galaxy.schema.schema.UpdateLibraryPayload(*, name: str = None, description: str = None, synopsis: str = None)[source]¶

Bases: pydantic.main.BaseModel

name: Optional[str]¶

description: Optional[str]¶

synopsis: Optional[str]¶

class galaxy.schema.schema.DeleteLibraryPayload(*, undelete: bool)[source]¶

Bases: pydantic.main.BaseModel

undelete: bool¶

class galaxy.schema.schema.LibraryCurrentPermissions(*, access_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]], modify_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]], manage_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]], add_library_item_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]])[source]¶

Bases: pydantic.main.BaseModel

access_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

modify_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

manage_library_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

add_library_item_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

Bases: pydantic.main.BaseModel

LIBRARY_ACCESS_in: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

LIBRARY_MODIFY_in: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

LIBRARY_ADD_in: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

LIBRARY_MANAGE_in: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.LibraryPermissionAction(value)[source]¶

Bases: str, enum.Enum

An enumeration.

set_permissions = 'set_permissions'¶

remove_restrictions = 'remove_restrictions'¶

class galaxy.schema.schema.DatasetPermissionAction(value)[source]¶

Bases: str, enum.Enum

An enumeration.

set_permissions = 'set_permissions'¶

make_private = 'make_private'¶

remove_restrictions = 'remove_restrictions'¶

class galaxy.schema.schema.LibraryPermissionsPayloadBase(*, add_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [])[source]¶

Bases: galaxy.schema.schema.Model

add_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

manage_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

modify_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

Bases: galaxy.schema.schema.LibraryPermissionsPayloadBase

action: Optional[galaxy.schema.schema.LibraryPermissionAction]¶

access_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.LibraryFolderPermissionAction(value)[source]¶

Bases: str, enum.Enum

An enumeration.

set_permissions = 'set_permissions'¶

class galaxy.schema.schema.LibraryFolderPermissionsPayload(*, add_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], action: galaxy.schema.schema.LibraryFolderPermissionAction = None)[source]¶

Bases: galaxy.schema.schema.LibraryPermissionsPayloadBase

action: Optional[galaxy.schema.schema.LibraryFolderPermissionAction]¶

class galaxy.schema.schema.LibraryFolderDetails(*, model_class: str = 'LibraryFolder', id: galaxy.schema.fields.EncodedDatabaseIdField, name: str, description: str = '', item_count: int, parent_library_id: galaxy.schema.fields.EncodedDatabaseIdField, parent_id: galaxy.schema.fields.EncodedDatabaseIdField = None, genome_build: str = '?', update_time: datetime.datetime, deleted: bool, library_path: List[str] = [])[source]¶

Bases: pydantic.main.BaseModel

model_class: str¶

id: galaxy.schema.fields.EncodedDatabaseIdField¶

name: str¶

description: Optional[str]¶

item_count: int¶

parent_library_id: galaxy.schema.fields.EncodedDatabaseIdField¶

parent_id: Optional[galaxy.schema.fields.EncodedDatabaseIdField]¶

genome_build: Optional[str]¶

update_time: datetime.datetime¶

deleted: bool¶

library_path: List[str]¶

class galaxy.schema.schema.CreateLibraryFolderPayload(*, name: str, description: str = '')[source]¶

Bases: pydantic.main.BaseModel

name: str¶

description: Optional[str]¶

class galaxy.schema.schema.UpdateLibraryFolderPayload(*, name: str = None, description: str = None)[source]¶

Bases: pydantic.main.BaseModel

name: Optional[str]¶

description: Optional[str]¶

class galaxy.schema.schema.LibraryAvailablePermissions(*, roles: List[galaxy.schema.schema.BasicRoleModel], page: int, page_limit: int, total: int)[source]¶

Bases: pydantic.main.BaseModel

roles: List[galaxy.schema.schema.BasicRoleModel]¶

page: int¶

page_limit: int¶

total: int¶

class galaxy.schema.schema.LibraryFolderCurrentPermissions(*, modify_folder_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]], manage_folder_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]], add_library_item_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]])[source]¶

Bases: pydantic.main.BaseModel

modify_folder_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

manage_folder_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

add_library_item_role_list: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.DatasetAssociationRoles(*, access_dataset_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]] = [], manage_dataset_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]] = [], modify_item_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]] = [])[source]¶

Bases: galaxy.schema.schema.Model

access_dataset_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

manage_dataset_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

modify_item_roles: List[Tuple[str, galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.UpdateDatasetPermissionsPayload(*, action: galaxy.schema.schema.DatasetPermissionAction, access_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], manage_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [], modify_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]] = [])[source]¶

Bases: galaxy.schema.schema.Model

action: Optional[galaxy.schema.schema.DatasetPermissionAction]¶

access_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

manage_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

modify_ids: Optional[Union[List[galaxy.schema.fields.EncodedDatabaseIdField], galaxy.schema.fields.EncodedDatabaseIdField]]¶

class galaxy.schema.schema.DeleteHDCAResult(*, id: galaxy.schema.fields.EncodedDatabaseIdField, deleted: bool)[source]¶

Bases: galaxy.schema.schema.Model

id: galaxy.schema.fields.EncodedDatabaseIdField¶

deleted: bool¶